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Bork Group

Deciphering function and evolution of biological systems

Publications

Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.

Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P

PloS one 2021

doi:10.1371/journal.pone.0254429.

eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale.

Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J

Molecular biology and evolution 2021

doi:10.1093/molbev/msab293.

Correction to 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets'.

Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2021

doi:10.1093/nar/gkab835.

Protein intake, metabolic status and the gut microbiota in different ethnicities: results from two independent cohorts.

Bel Lassen P, Attaye I, Adriouch S, Nicolaou M, Aron-Wisnewsky J, Nielsen T, Chakaroun R, Le Chatelier E, Forslund S, Belda E, Bork P, Bäckhed F, Stumvoll M, Pedersen O, Herrema H, Groen AK, Pinto-Sietsma SJ, Zwinderman AH, Nieuwdorp M, Clement K, On Behalf Of Metacardis Consortium

Nutrients 2021

doi:10.3390/nu13093159.

Bioaccumulation of therapeutic drugs by human gut bacteria.

Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature 2021

doi:10.1038/s41586-021-03891-8.

Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a Lynch syndrome mouse model.

Gebert J, Gelincik O, Oezcan-Wahlbrink M, Marshall JD, Hernandez-Sanchez A, Urban K, Long M, Cortes E, Tosti E, Katzenmaier EM, Song Y, Elsaadi A, Deng N, Vilar E, Fuchs V, Nelius N, Yuan, Ahadova A, Sei S, Shoemaker RH, Umar A, Wei L, Liu S, Bork P, Edelmann W, von Knebel Doeberitz M, Lipkin SM, Kloor M

Gastroenterology 2021

doi:10.1053/j.gastro.2021.06.073.

GUNC: detection of chimerism and contamination in prokaryotic genomes.

Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, Schmidt TSB, Bork P

Genome biology 2021

doi:10.1186/s13059-021-02393-0.

Dispersal strategies shape persistence and evolution of human gut bacteria.

Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P

Cell host & microbe 2021

doi:10.1016/j.chom.2021.05.008.

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.

Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM

Communications biology 2021

doi:10.1038/s42003-021-02112-2.

Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.

Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Olanipekun M, Hoyles L, Djouadi F, Neves AL, Rodriguez-Martinez A, Mouawad GI, Pons N, Forslund S, Le-Chatelier E, Le Lay A, Nicholson J, Hansen T, Hyötyläinen T, Clément K, Oresic M, Bork P, Ehrlich SD, Raes J, Pedersen OB, Gauguier D, Dumas ME

Gut 2021

doi:10.1136/gutjnl-2020-323314.

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.

Letunic I, Bork P

Nucleic acids research 2021

doi:10.1093/nar/gkab301.

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.

Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G

Genome biology 2021

doi:10.1186/s13059-021-02306-1.

A 12-genus bacterial signature identifies a group of severe autistic children with differential sensory behavior and brain structures.

Shi K, Zhang L, Yu J, Chen Z, Lai S, Zhao X, Li WG, Luo Q, Lin W, Feng J, Bork P, Zhao XM, Li F

Clinical and translational medicine 2021

doi:10.1002/ctm2.314.

The InterPro protein families and domains database: 20 years on.

Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD

Nucleic acids research 2020

doi:10.1093/nar/gkaa977.

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.

Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH

Nucleic acids research 2020

doi:10.1093/nar/gkaa884.

SMART: recent updates, new developments and status in 2020.

Letunic I, Khedkar S, Bork P

Nucleic acids research 2020

doi:10.1093/nar/gkaa937.

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.

Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2020

doi:10.1093/nar/gkaa1074.

Polarization of microbial communities between competitive and cooperative metabolism.

Machado D, Maistrenko OM, Andrejev S, Kim Y, Bork P, Patil KR, Patil KR

Nature ecology & evolution 2021

doi:10.1038/s41559-020-01353-4.

Author correction: imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.

Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F

Nature communications 2020

doi:10.1038/s41467-020-20412-9.

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.

Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisneswky J, Clément K, Bäckhed F

Nature communications 2020

doi:10.1038/s41467-020-19589-w.

Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure.

Trebicka J, Bork P, Krag A, Arumugam M

Nature reviews. Gastroenterology & hepatology 2020

doi:10.1038/s41575-020-00376-3.

Metagenomic assessment of the global distribution of bacteria and fungi.

Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F

Environmental microbiology 2020

doi:10.1111/1462-2920.15314.

(Phospho)proteomic profiling of microsatellite unstable CRC cells reveals alterations in nuclear signaling and cholesterol metabolism caused by frameshift mutation of NMD regulator UPF3A.

Michalak M, Katzenmaier EM, Roeckel N, Woerner SM, Fuchs V, Warnken U, Yuan YP, Bork P, Neu-Yilik G, Kulozik A, von Knebel Doeberitz M, Kloor M, Kopitz J, Gebert J

International journal of molecular sciences 2020

doi:10.3390/ijms21155234.

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.

Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, Bastard JP, Andreelli F, Galleron N, Coelho LP, Hulot JS, Hansen TH, Pedersen HK, Lewinter C, Rouault C, Quinquis B, Salem JE, Roume H, Touch S, Søndertoft NB, Dumas ME, Touch S, Gøtze JP, Hansen T, Ehrlich SD, Galan P, Letunic I, Nielsen J, Holst JJ, Køber L, Vestergaard H, Zucker JD, Oppert JM, Stumvoll M, Bäckhed F, Clément K, Bork P, Pedersen O, Raes J

Nature 2020

doi:10.1038/s41586-020-2269-x.

Diversity within species: interpreting strains in microbiomes.

Van Rossum T, Ferretti P, Maistrenko OM, Bork P

Nature reviews. Microbiology 2020

doi:10.1038/s41579-020-0368-1.

Tara Oceans: towards global ocean ecosystems biology.

Sunagawa S, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C

Nature reviews. Microbiology 2020

doi:10.1038/s41579-020-0364-5.

Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.

Bahram M, Netherway T, Hildebrand F, Pritsch K, Drenkhan R, Loit K, Anslan S, Bork P, Tedersoo L

The New phytologist 2020

doi:10.1111/nph.16598.

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.

Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P

The ISME journal 2020

doi:10.1038/s41396-020-0600-z.

Dissecting the collateral damage of antibiotics on gut microbes.

Maier L, Goemans CV, Pruteanu M, Wirbel J, Kuhn M, Cacace E, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KP, Zeller G, Bork P, Typas A

2020

doi:10.1101/2020.01.09.893560.

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.

Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P

Nucleic acids research 2019

doi:10.1093/nar/gkz1002.

Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells.

Poisa-Beiro L, Thoma J, Landry J, Sauer S, Yamamoto A, Eckstein V, Romanov N, Raffel S, Hoffmann GF, Bork P, Benes V, Gavin AC, Tanaka M, Ho AD

2020

doi:10.1038/s41598-020-68396-2.

Efficacy of Bifidobacterium longum, B. infantis and Lactobacillus acidophilus probiotics to prevent gut dysbiosis in preterm infants of 28+0–32+6 weeks of gestation: a randomised, placebo-controlled, double-blind, multicentre trial: the PRIMAL Clinical Study protocol.

Marißen J, Haiß A, Meyer C, Van Rossum T, Bünte LM, Frommhold D, Gille C, Goedicke-Fritz S, Göpel W, Hudalla H, Pagel J, Pirr S, Siller B, Viemann D, Vens M, Herting E, König I, Gehring S, Zemlin M, Henneke P, Bork P, Härtel C, Härtel C

BMJ open 2019

doi:10.1136/bmjopen-2019-032617.

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.

Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Sánchez P, Roux S, Zayed AA, Uehara H, Carmichael M, Zeller G, Ferland J, Dimier C, Picheral M, Kandels S, Poulain J, Pisarev S, Acinas SG, Poulain J, Bork P, Babin M, Guidi L, Hingamp P, Bowler C, de Vargas C, Karsenti E, Ogata H, Iudicone D, Karp-Boss L, Sullivan MB, Wincker P, Pesant S, Speich S, Sunagawa S

Cell 2019

doi:10.1016/j.cell.2019.10.014.

Quantitative proteome landscape of the NCI-60 cancer cell lines.

Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Iskar M, Ori A, Bi R, Gillet L, Zhang H, Zhang J, Zhong Q, Yu C, Schmitt U, Varma S, Zhang Q, Qiu P, Wild PJ, Zhu Y, Bork P, Garnett MJ, Saez-Rodriguez J, Elloumi F, Beck M, Liu K, Pommier Y, Aebersold R, Reinhold WC, Sander C

iScience 2019

doi:10.1016/j.isci.2019.10.059.

Author correction: metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, , Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N

Nature medicine 2019

doi:10.1038/s41591-019-0663-4.

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.

Li Y, Kuhn M, Gavin AC, Bork P

Bioinformatics (Oxford, England) 2019

doi:10.1093/bioinformatics/btz736.

Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome.

Hickl O, Heintz-Buschart A, Trautwein-Schult A, Hercog R, Bork P, Wilmes P, Becher D

Microorganisms 2019

doi:10.3390/microorganisms7090367.

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology.

Hildebrand F, Pallen MJ, Bork P

Gut 2019

doi:10.1136/gutjnl-2019-319045.

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P

Microbiome 2019

doi:10.1186/s40168-019-0684-8.

Ice-age climate adaptations trap the alpine marmot in a state of low genetic diversity.

Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Griffin JL, Zelezniak A, Allaine D, Bork P, Welch JJ, Cohas A, Ralser M, Timmermann B

Current biology : CB 2019

doi:10.1016/j.cub.2019.04.020.

Consent insufficient for data release–Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Munoz AR, Roberts RJ, Rossello-Mora R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I, Xenarios I, Whitman WB

SCIENCE 2019

doi:10.1126/science.aax7509.

Disentangling genetic and environmental effects on the proteotypes of individuals.

Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P

Cell 2019

doi:10.1016/j.cell.2019.03.015.

Marine DNA viral macro- and microdiversity from pole to pole.

Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Pesant S, Marec C, Pisarev S, Picheral M, Tremblay JÉ, Poulain J, Vik D, Vik D, Bowler C, Babin M, de Vargas C, Culley AI, Iudicone D, Dutilh BE, Roux S, Karp-Boss L, Sullivan MB, Sunagawa S, Wincker P

Cell 2019

doi:10.1016/j.cell.2019.03.040.

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.

Letunic I, Bork P

Nucleic acids research 2019

doi:10.1093/nar/gkz239.

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, , Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N

Nature medicine 2019

doi:10.1038/s41591-019-0405-7.

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.

Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G

Nature medicine 2019

doi:10.1038/s41591-019-0406-6.

Microbial abundance, activity and population genomic profiling with mOTUs2.

Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S

Nature communications 2019

doi:10.1038/s41467-019-08844-4.

Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Caputi L, Carradec Q, Eveillard D, Kirilovsky A, Pelletier E, Karlusich JJP, Vieira FRJ, Villar E, Chaffron S, Malviya S, Scalco E, Acinas SG, Alberti A, Aury JM, Benoiston AS, Bertrand A, Biard T, Bittner L, Boccara M, Brum JR, Brunet C, Busseni G, Carratala A, Claustre H, Coelho LP, Colin S, D'Aniello S, Da Silva C, Del Core M, Dore H, Gasparini S, Kokoszka F, Jamet JL, Lejeusne C, Lepoivre C, Lescot M, Lima-Mendez G, Lombard F, Lukes J, Maillet N, Madoui MA, Martinez E, Mazzocchi MG, Neou MB, Paz-Yepes J, Poulain J, Ramondenc S, Romagnan JB, Roux S, Manta DS, Sanges R, Speich S, Sprovieri M, Sunagawa S, Taillandier V, Tanaka A, Tirichine L, Trottier C, Uitz J, Veluchamy A, Vesela J, Vincent F, Yau S, Kandels-Lewis S, Searson S, Dimier C, Picheral M, Bork P, Boss E, De Vargas C, Follows MJ, Grimsley N, Guidi L, Hingamp P, Karsenti E, Sordino P, Stemmann L, Sullivan MB, Tagliabue A, Zingone A, Garczarek L, d'Ortenzio F, Testor P, Not F, d'Alcala MR, Wincker P, Bowler C, Iudicone D, Gorsky G, Jaillon O, Karp-Boss L, Krzic U, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Velayoudon D, Weissenbach J, Weissenbach J, Sieracki M, Velayoudon D

Global Biogeochemical Cycles 2019

doi:10.1029/2018GB006022.

Extensive transmission of microbes along the gastrointestinal tract.

Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P

eLife 2019

doi:10.7554/eLife.42693.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Munoz AR, Roberts RJ, Rossello-Mora R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I, Xenarios I, Whitman WB

Science (New York, N.Y.) 2019

doi:10.1126/science.aaw1280.

Antibiotics-induced monodominance of a novel gut bacterial order.

Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Huerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Belzer C, Aalvink S, Sunagawa S, Forslund SK, Merten C, Hentschel U, Benes V, Patil KR, Bork P

Gut 2019

doi:10.1136/gutjnl-2018-317715.

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2018

doi:10.1093/nar/gky1085.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Madeira F, Luciani A, Mi H, Marchler-Bauer A, Necci M, Natale DA, Orengo C, Nuka G, Paysan-Lafosse T, Pandurangan AP, Potter SC, Pesseat S, Rawlings ND, Qureshi MA, Richardson LJ, Redaschi N, Sangrador-Vegas A, Sigrist CJA, Rivoire C, Salazar GA, Thanki N, Thomas PD, Sillitoe I, Sutton GG, Tosatto SCE, Yong SY, Finn RD

Nucleic acids research 2018

doi:10.1093/nar/gky1100.

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2018

doi:10.1093/nar/gky1131.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Daly RA, Cochrane GR, Duhaime MB, Desnues C, Enault F, Emerson JB, Hingamp P, Fuhrman JA, Hurwitz BL, Hugenholtz P, Labonté JM, Ivanova NN, Malmstrom RR, Lee KB, Mizrachi IK, Martinez-Garcia M, Petit MA, Putonti C, Ogata H, Páez-Espino D, Rodriguez-Valera F, Rosario K, Rattei T, Reyes A, Steward GF, Sullivan MB, Schriml L, Schulz F, Temperton B, Tringe SG, Sunagawa S, Suttle CA, Wilhelm SW, Whiteson KL, Webster NS, Thurber RV, Yilmaz P, Wrighton KC, Woyke T, Wommack KE, Allen LZ, Yutin N, Young MJ, Yoshida T, Eloe-Fadrosh EA, Kyrpides NC

Nature biotechnology 2018

doi:10.1038/nbt.4306.

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes.

Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, Moebus S, Bork P, Fischer S, Herms S, Aretz S, Hoffmann P, Steinke-Lange V

International journal of cancer 2018

doi:10.1002/ijc.31725.

Recovery of gut microbiota of healthy adults following antibiotic exposure.

Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen HB, Nielsen MF, Wang J, Bork P, Hansen T, Vilsbøll T, Arumugam M, Knop FK, Pedersen O

Nature microbiology 2018

doi:10.1038/s41564-018-0257-9.

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.

Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB

Nature protocols 2018

doi:10.1038/s41596-018-0064-z.

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.

Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Aloy P, Bork P, Gavin AC, Ho AD

Nature communications 2018

doi:10.1038/s41467-018-06353-4.

Das Darmmikrobiom bei der Parkinson-Krankheit.

Bedarf JR, Hildebrand F, Goeser F, Bork P, Wüllner U

Der Nervenarzt 2018

doi:10.1007/s00115-018-0601-6.

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.

Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J

Gut 2018

doi:10.1136/gutjnl-2018-316106.

Structure and function of the global topsoil microbiome.

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Põlme S, Pent M, Ryberg M, Sunagawa S, Tedersoo L, Bork P

Nature 2018

doi:10.1038/s41586-018-0386-6.

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.

Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L

Environmental microbiology reports 2018

doi:10.1111/1758-2229.12684.

Metagenomic analysis of gut microbial communities from a Central Asian population.

Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P

BMJ open 2018

doi:10.1136/bmjopen-2018-021682.

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Cologna M, Clementi R, Cusumano G, Crifò T, Innamorati C, Gottardi S, Postai D, Masè C, Duranti S, Savoi D, Mancabelli L, Lugli GA, Ferrario C, Turroni F, Mangifesta M, Milani C, Yassour M, Vlamakis H, Anzalone R, Viappiani A, Koren O, Tateo S, Xavier R, Collado CM, Ventura M, Huttenhower C, Soffiati M, Pedrotti A, Bork P, Segata N

Cell host & microbe 2018

doi:10.1016/j.chom.2018.06.005.

Species-specific activity of antibacterial drug combinations.

Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Bork P, Savitski MM, Göttig S, Typas A

Nature 2018

doi:10.1038/s41586-018-0278-9.

iPath3.0: interactive pathways explorer v3.

Darzi Y, Letunic I, Bork P, Yamada T

Nucleic acids research 2018

doi:10.1093/nar/gky299.

Quantifying compartment-associated variations of protein abundance in proteomics data.

Parca L, Beck M, Bork P, Ori A

Molecular systems biology 2018

doi:10.15252/msb.20178131.

Pervasive protein thermal stability variation during the cell cycle.

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM

Cell 2018

doi:10.1016/j.cell.2018.03.053.

The gut microbiome is associated with behavioural task in honey bees.

Jones JC, Fruciano C, Marchant J, Hildebrand F, Forslund S, Bork P, Engel P, Hughes WOH

Insectes sociaux 2018

doi:10.1007/s00040-018-0624-9.

Selective maternal seeding and environment shape the human gut microbiome.

Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P

Genome research 2018

doi:10.1101/gr.233940.117.

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR

Nature microbiology 2018

doi:10.1038/s41564-018-0123-9.

Similarity of the dog and human gut microbiomes in gene content and response to diet.

Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P

Microbiome 2018

doi:10.1186/s40168-018-0450-3.

Extensive impact of non-antibiotic drugs on human gut bacteria.

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A

Nature 2018

doi:10.1038/nature25979.

Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.

Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O

Cell 2018

doi:10.1016/j.cell.2018.02.032.

The Human Gut Microbiome: From Association to Modulation.

Schmidt TSB, Raes J, Bork P

Cell 2018

doi:10.1016/j.cell.2018.02.044.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Birren B, Malmstrom RR, Bork P, Podar M, Garrity GM, Weinstock GM, Yooseph S, Dodsworth JA, Glöckner FO, Sutton G, Nelson WC, Gilbert JA, Jungbluth SP, Hallam SJ, Tighe S, Ettema TJG, Baker BJ, Rattei T, Konstantinidis KT, Liu WT, McMahon KD, Fierer N, Eisen JA, Hedlund B, Cochrane G, Karsch-Mizrachi I, Knight R, Finn R, Rinke C, Lapidus A, Tyson GW, Rinke C, Eren AM, Parks DH, Yilmaz P, Meyer F, Woyke T, Hugenholtz P, Banfield JF, Schriml L

Nature biotechnology 2018

doi:10.1038/nbt0218-196a.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P

Nature microbiology 2018

doi:10.1038/s41564-018-0114-x.

Gut microbiota composition is associated with environmental landscape in honey bees.

Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO

Ecology and evolution 2017

doi:10.1002/ece3.3597.

A global ocean atlas of eukaryotic genes.

Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Searson S, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P

Nature communications 2018

doi:10.1038/s41467-017-02342-1.

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.

Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Searson S, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P

Nature communications 2018

doi:10.1038/s41467-017-02235-3.

MVP: a microbe-phage interaction database.

Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH

Nucleic acids research 2017

doi:10.1093/nar/gkx1124.

20 years of the SMART protein domain annotation resource.

Letunic I, Bork P

Nucleic acids research 2017

doi:10.1093/nar/gkx922.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P

Nature microbiology 2017

doi:10.1038/s41564-017-0072-8.

Subspecies in the global human gut microbiome.

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P

Molecular systems biology 2017

doi:10.15252/msb.20177589.

Salt-responsive gut commensal modulates TH17 axis and disease.

Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN

Nature 2017

doi:10.1038/nature24628.

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.

Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC

Scientific reports 2017

doi:10.1038/s41598-017-16353-x.

Towards standards for human fecal sample processing in metagenomic studies.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P

Nature biotechnology 2017

doi:10.1038/nbt.3960.

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.

Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C

eLife 2017

doi:10.7554/eLife.26066.

RTK: efficient rarefaction analysis of large datasets.

Saary P, Forslund K, Bork P, Hildebrand F

Bioinformatics (Oxford, England) 2017

doi:10.1093/bioinformatics/btx206.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T

Nature biotechnology 2017

doi:10.1038/nbt.3893.

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.

Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P

Molecular biology and evolution 2017

doi:10.1093/molbev/msx148.

metaSNV: A tool for metagenomic strain level analysis.

Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P

PloS one 2017

doi:10.1371/journal.pone.0182392.

Capturing protein communities by structural proteomics in a thermophilic eukaryote.

Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC

Molecular systems biology 2017

doi:10.15252/msb.20167412.

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U

Genome medicine 2017

doi:10.1186/s13073-017-0451-z.

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U

Genome medicine 2017

doi:10.1186/s13073-017-0428-y.

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis.

Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S

American journal of physiology. Gastrointestinal and liver physiology 2016

doi:10.1152/ajpgi.00293.2016.

Systematic identification of phosphorylation-mediated protein interaction switches.

Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB

PLoS computational biology 2017

doi:10.1371/journal.pcbi.1005462.

GEAR: A database of Genomic Elements Associated with drug Resistance.

Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM

Scientific reports 2017

doi:10.1038/srep44085.

Metabolic anchor reactions for robust biorefining.

Jouhten P, Huerta-Cepas J, Bork P, Patil KR

Metabolic engineering 2017

doi:10.1016/j.ymben.2017.02.010.

Bioinformatics Analysis of Functional Associations of PTMs.

Minguez P, Bork P

Methods in molecular biology (Clifton, N.J.) 2017

doi:10.1007/978-1-4939-6783-4_14.

[Microbial Biomarkers for Early Cancer Detection].

Voigt AY, Zeller G, Bork P

Deutsche medizinische Wochenschrift (1946) 2017

doi:10.1055/s-0042-110193.

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.

Chen WH, Lu G, Chen X, Zhao XM, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw1013.

InterPro in 2017-beyond protein family and domain annotations.

Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Yong SY, Mitchell AL

Nucleic acids research 2016

doi:10.1093/nar/gkw1107.

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw989.

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2016

doi:10.1093/nar/gkw937.

Global genetic capacity for mixotrophy in marine picocyanobacteria.

Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW

The ISME journal 2016

doi:10.1038/ismej.2016.64.

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.

Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R

The Journal of cell biology 2016

doi:10.1083/jcb.201601090.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Bork P, Acinas SG, Wincker P, Sullivan MB

NATURE 2016

doi:10.1038/nature19366.

CART - a chemical annotation retrieval toolkit.

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P

Bioinformatics (Oxford, England) 2016

doi:10.1093/bioinformatics/btw233.

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Dore J, Machado AMD, de Evgrafov MCR, Hansen T, Jorgensen T, Bork P, Guarner F, Pedersen O, Sommer MOA, Ehrlich SD, Sicheritz-Ponten T, Brunak S, Nielsen HB

Nature microbiology 2016

doi:10.1038/nmicrobiol.2016.152.

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P

Bioinformatics (Oxford, England) 2016

doi:10.1093/bioinformatics/btw183.

Human gut microbes impact host serum metabolome and insulin sensitivity.

Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K, Consortium M, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O

Nature 2016

doi:10.1038/nature18646.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Letunic I, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw290.

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.

Huerta-Cepas J, Serra F, Bork P

Molecular biology and evolution 2016

doi:10.1093/molbev/msw046.

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC

Nature protocols 2016

doi:10.1038/nprot.2016.059.

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R

PloS one 2016

doi:10.1371/journal.pone.0155362.

Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C

Nature methods 2016

doi:10.1038/nmeth.3830.

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P

Science (New York, N.Y.) 2016

doi:10.1126/science.aad8852.

Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Chen WH, Lu G, Bork P, Hu S, Lercher MJ

Nature communications 2016

doi:10.1038/ncomms11334.

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG

NATURE COMMUNICATIONS 2016

doi:10.1038/ncomms11071.

Spatiotemporal variation of mammalian protein complex stoichiometries.

Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M

Genome biology 2016

doi:10.1186/s13059-016-0912-5.

Gut Microbiota Linked to Sexual Preference and HIV Infection.

Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R

EBioMedicine 2016

doi:10.1016/j.ebiom.2016.01.032.

Bacterial antisense RNAs are mainly the product of transcriptional noise.

Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M

Science Advances 2016

doi:10.1126/sciadv.1501363.

Plankton networks driving carbon export in the oligotrophic ocean.

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans Consortium Coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G

Nature 2016

doi:10.1038/nature16942.

The exploration of network motifs as potential drug targets from post-translational regulatory networks.

Zhang XD, Song J, Bork P, Zhao XM

Scientific reports 2016

doi:10.1038/srep20558.

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM

Nature communications 2016

doi:10.1038/ncomms10410.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw004.

The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex.

Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW

PloS one 2016

doi:10.1371/journal.pone.0146457.

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2015

doi:10.1093/nar/gkv1248.

The SIDER database of drugs and side effects.

Kuhn M, Letunic I, Jensen LJ, Bork P

Nucleic acids research 2015

doi:10.1093/nar/gkv1075.

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M

Nucleic acids research 2015

doi:10.1093/nar/gkv1277.

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Igor Costea P, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O

Nature 2015

doi:10.1038/nature15766.

Operon structure and cotranslational subunit association direct protein assembly in bacteria.

Shieh YW, Minguez P, Bork P, Auburger JJ, Guilbride DL, Kramer G, Bukau B

Science (New York, N.Y.) 2015

doi:10.1126/science.aac8171.

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.

Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M

2015

doi:10.1016/j.cels.2015.08.012.

In situ structural analysis of the human nuclear pore complex.

von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M

Nature 2015

doi:10.1038/nature15381.

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC

Cell reports 2015

doi:10.1016/j.celrep.2015.07.054.

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.

Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L

EBioMedicine 2015

doi:10.1016/j.ebiom.2015.07.007.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldon T

GENOME BIOLOGY AND EVOLUTION 2015

doi:10.1093/gbe/evv121.

Tara Oceans. Tara Oceans studies plankton at planetary scale. Introduction.

Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P

Science (New York, N.Y.) 2015

doi:10.1126/science.aac5605.

Computational eco-systems biology in Tara Oceans: translating data into knowledge.

Sunagawa S, Karsenti E, Bowler C, Bork P

Molecular systems biology 2015

doi:10.15252/msb.20156272.

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi.

Tedersoo L, Anslan S, Bahram M, Polme S, Riit T, Liiv I, Koljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K

MycoKeys 2015

doi:10.3897/mycokeys.10.4852.

Metabolic dependencies drive species co-occurrence in diverse microbial communities.

Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR

Proceedings of the National Academy of Sciences of the United States of America 2015

doi:10.1073/pnas.1421834112.

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Tara Oceans Coordinators, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB

Science (New York, N.Y.) 2015

doi:10.1126/science.1261498.

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E

Science (New York, N.Y.) 2015

doi:10.1126/science.1261605.

Ocean plankton. Determinants of community structure in the global plankton interactome.

Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J

Science (New York, N.Y.) 2015

doi:10.1126/science.1262073.

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).

Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M

Molecular & cellular proteomics : MCP 2015

doi:10.1074/mcp.m114.042499.

Ocean plankton. Structure and function of the global ocean microbiome.

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P

Science (New York, N.Y.) 2015

doi:10.1126/science.1261359.

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D

Science (New York, N.Y.) 2015

doi:10.1126/science.1261447.

Inter-individual differences in the gene content of human gut bacterial species.

Zhu A, Sunagawa S, Mende DR, Bork P

Genome biology 2015

doi:10.1186/s13059-015-0646-9.

Temporal and technical variability of human gut metagenomes.

Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P

Genome biology 2015

doi:10.1186/s13059-015-0639-8.

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

Betts MJ, Lu Q, Jiang Y, Drusko A, Wichmann O, Utz M, Valtierra-Gutiérrez IA, Schlesner M, Jaeger N, Jones DT, Pfister S, Lichter P, Eils R, Siebert R, Bork P, Apic G, Gavin AC, Russell RB

Nucleic acids research 2014

doi:10.1093/nar/gku1094.

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L

Molecular systems biology 2015

doi:10.15252/msb.20145558.

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P

Nucleic acids research 2014

doi:10.1093/nar/gku1081.

The InterPro protein families database: the classification resource after 15 years.

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD

Nucleic acids research 2014

doi:10.1093/nar/gku1243.

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2014

doi:10.1093/nar/gku1003.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P

Nucleic acids research 2014

doi:10.1093/nar/gku1147.

Potential of fecal microbiota for early-stage detection of colorectal cancer.

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P

Molecular systems biology 2014

doi:10.15252/msb.20145645.

Luminal signalling links cell communication to tissue architecture during organogenesis.

Durdu S, Iskar M, Revenu C, Schieber N, Kunze A, Bork P, Schwab Y, Gilmour D

Nature 2014

doi:10.1038/nature13852.

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P

PloS one 2014

doi:10.1371/journal.pone.0111122.

Correction: LotuS: an efficient and user-friendly OTU processing pipeline.

Hildebrand F, Tito RY, Voigt AY, Bork P, Raes J

Microbiome 2014

doi:10.1186/2049-2618-2-37.

LotuS: an efficient and user-friendly OTU processing pipeline.

Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J

Microbiome 2014

doi:10.1186/2049-2618-2-30.

Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors

Woerner SM, Tosti E, Yuan YP, Kloor M, Bork P, Edelmann W, Gebert J

Molecular carcinogenesis 2014

doi:10.1002/mc.22213.

An integrated catalog of reference genes in the human gut microbiome

Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD, Bork P, Wang J

Nature biotechnology 2014

doi:10.1038/nbt.2942.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD

Nature biotechnology 2014

doi:10.1038/nbt.2939.

Comments on "human dominant disease genes are enriched in paralogs originating from whole genome duplication"

Chen WH, Zhao XM, van Noort V, Bork P

PLoS computational biology 2014

doi:10.1371/journal.pcbi.1003758.

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene expression profiling

van Noort VV, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P

Cancer research 2014

doi:10.1158/0008-5472.CAN-13-3540.

Classification and quantification of bacteriophage taxa in human gut metagenomes

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P

The ISME journal 2014

doi:10.1038/ismej.2014.30.

Classification and quantification of bacteriophage taxa in human gut metagenomes.

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P

The ISME journal 2014

doi:10.1038/ismej.2014.66.

A fair comparison

Costea PI, Zeller G, Sunagawa S, Bork P

Nature methods 2014

doi:10.1038/nmeth.2897.

Metagenomic insights into the human gut resistome and the forces that shape it

Forslund K, Sunagawa S, Coelho LP, Bork P

BioEssays : news and reviews in molecular, cellular and developmental biology 2014

doi:10.1002/bies.201300143.

Enterotypes of the human gut microbiome (vol 473, pg 174, 2011)

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin JJ, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Weissenbach J, Ehrlich SD, Bork P

NATURE 2014

doi:10.1038/nature13075.

Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs

Gallina AM, Bork P, Bordo D

Journal of molecular recognition : JMR 2014

doi:10.1002/jmr.2332.

STITCH 4: integration of protein-chemical interactions with user data

Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P

Nucleic acids research 2013

doi:10.1093/nar/gkt1207.

eggNOG v4.0: nested orthology inference across 3686 organisms

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2013

doi:10.1093/nar/gkt1253.

A quantitative liposome microarray to systematically characterize protein-lipid interactions

Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin AC

Nature methods 2013

doi:10.1038/nmeth.2734.

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P

Nature methods 2013

doi:10.1038/nmeth.2693.

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H

The ISME journal 2013

doi:10.1038/ismej.2013.59.

Accurate and universal delineation of prokaryotic species

Mende DR, Sunagawa S, Zeller G, Bork P

Nature methods 2013

doi:10.1038/nmeth.2575.

Richness of human gut microbiome correlates with metabolic markers

Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O

Nature 2013

doi:10.1038/nature12506.

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG

Environmental microbiology 2013

doi:10.1111/1462-2920.12250.

Experimental characterization of the human non-sequence-specific nucleic acid interactome

Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J

Genome biology 2013

doi:10.1186/gb-2013-14-7-r81.

Country-specific antibiotic use practices impact the human gut resistome

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P

Genome research 2013

doi:10.1101/gr.155465.113.

The microbiome explored: recent insights and future challenges

Blaser M, Bork P, Fraser C, Knight R, Wang J

Nature reviews. Microbiology 2013

doi:10.1038/nrmicro2973.

Orthologous gene clusters and taxon signature genes for viruses of prokaryotes

Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV

Journal of bacteriology 2013

doi:10.1128/jb.01801-12.

Evolution and functional cross-talk of protein post-translational modifications

Beltrao P, Bork P, Krogan NJ, van Noort V

Molecular systems biology 2013

doi:10.1002/msb.201304521.

Human monogenic disease genes have frequently functionally redundant paralogs

Chen WH, Zhao XM, van Noort V, Bork P

PLoS computational biology 2013

doi:10.1371/journal.pcbi.1003073.

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ

Nucleic acids research 2013

doi:10.1093/nar/gks1094.

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P

Molecular systems biology 2013

doi:10.1038/msb.2013.20.

Systematic identification of proteins that elicit drug side effects

Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P

Molecular systems biology 2013

doi:10.1038/msb.2013.10.

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Minguez P, Letunic I, Parca L, Bork P

Nucleic acids research 2013

doi:10.1093/nar/gks1230.

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.

Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M

Molecular systems biology 2013

doi:10.1038/msb.2013.4.

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data

Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J

Bioinformatics (Oxford, England) 2013

doi:10.1093/bioinformatics/bts656.

Genomic variation landscape of the human gut microbiome

Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P

Nature 2013

doi:10.1038/nature11711.

Consistent mutational paths predict eukaryotic thermostability

van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P

BMC evolutionary biology 2013

doi:10.1186/1471-2148-13-7.

Role for urea in nitrification by polar marine Archaea

Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay JÉ, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedrós-Alió C, Bertilsson S

Proceedings of the National Academy of Sciences of the United States of America 2012

doi:10.1073/pnas.1201914109.

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

Iskar M, Zeller G, Zhao XM, van Noort V, Bork P

Current opinion in biotechnology 2012

doi:10.1016/j.copbio.2011.11.010.

Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age

Chen WH, Trachana K, Lercher MJ, Bork P

Molecular biology and evolution 2012

doi:10.1093/molbev/mss014.

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M

The ISME journal 2012

doi:10.1038/ismej.2011.212.

A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL

Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JW, Jauch A, Bartram CR, Reinhardt D, Koch KA, Bandapalli OR, Kulozik AE

British journal of haematology 2012

doi:10.1111/j.1365-2141.2012.09028.x.

OGEE: an online gene essentiality database

Chen WH, Minguez P, Lercher MJ, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr986.

The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). Introduction

Chen YP, Bork P

BMC genomics 2012

doi:10.1186/1471-2164-13-s1-i1.

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins

Doerks T, van Noort V, Minguez P, Bork P

PloS one 2012

doi:10.1371/journal.pone.0034302.

InterPro in 2011: new developments in the family and domain prediction database

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY

Nucleic acids research 2012

doi:10.1093/nar/gkr948.

STITCH 3: zooming in on protein-chemical interactions

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr1011.

MOCAT: a metagenomics assembly and gene prediction toolkit

Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P

PloS one 2012

doi:10.1371/journal.pone.0047656.

SMART 7: recent updates to the protein domain annotation resource

Letunic I, Doerks T, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr931.

Assessment of metagenomic assembly using simulated next generation sequencing data

Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P

PloS one 2012

doi:10.1371/journal.pone.0031386.

Deciphering a global network of functionally associated post-translational modifications

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P

Molecular systems biology 2012

doi:10.1038/msb.2012.31.

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr1060.

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium

van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC

Molecular systems biology 2012

doi:10.1038/msb.2012.4.

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P

Molecular systems biology 2012

doi:10.1038/msb.2012.13.

Transcription start site associated RNAs in bacteria

Yus E, Güell M, Vivancos AP, Chen WH, Lluch-Senar M, Delgado J, Gavin AC, Bork P, Serrano L

Molecular systems biology 2012

doi:10.1038/msb.2012.16.

Identifying single copy orthologs in Metazoa

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P

PLoS computational biology 2011

doi:10.1371/journal.pcbi.1002269.

Prediction of drug combinations by integrating molecular and pharmacological data

Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P

PLoS computational biology 2011

doi:10.1371/journal.pcbi.1002323.

A holistic approach to marine eco-systems biology

Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P, Tara Oceans Consortium

PLoS biology 2011

doi:10.1371/journal.pbio.1001177.

Orthology prediction methods: a quality assessment using curated protein families

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P

BioEssays : news and reviews in molecular, cellular and developmental biology 2011

doi:10.1002/bies.201100062.

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile

Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E

Cell 2011

doi:10.1016/j.cell.2011.06.039.

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Letunic I, Bork P

Nucleic acids research 2011

doi:10.1093/nar/gkr201.

iPath2.0: interactive pathway explorer

Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P

Nucleic acids research 2011

doi:10.1093/nar/gkr313.

Enterotypes of the human gut microbiome

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P

Nature 2011

doi:10.1038/nature09944.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO

Nature biotechnology 2011

doi:10.1038/nbt.1823.

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

Raes J, Letunic I, Yamada T, Jensen LJ, Bork P

Molecular systems biology 2011

doi:10.1038/msb.2011.6.

The ecoresponsive genome of Daphnia pulex

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL

Science (New York, N.Y.) 2011

doi:10.1126/science.1197761.

Network neighbors of drug targets contribute to drug side-effect similarity

Brouwers L, Iskar M, Zeller G, van Noort V, Bork P

PloS one 2011

doi:10.1371/journal.pone.0022187.

Universally distributed single-copy genes indicate a constant rate of horizontal transfer

Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P

PloS one 2011

doi:10.1371/journal.pone.0022099.

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2011

doi:10.1093/nar/gkq973.

SmashCommunity: a metagenomic annotation and analysis tool

Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P

Bioinformatics (Oxford, England) 2010

doi:10.1093/bioinformatics/btq536.

SmashCell: a software framework for the analysis of single-cell amplified genome sequences

Harrington ED, Arumugam M, Raes J, Bork P, Relman DA

Bioinformatics (Oxford, England) 2010

doi:10.1093/bioinformatics/btq564.

A network of conserved co-occurring motifs for the regulation of alternative splicing

Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkq705.

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae

Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC

Molecular systems biology 2010

doi:10.1038/msb.2010.87.

[Metagenomics of the intestinal microbiota: potential applications]

Dusko Ehrlich S, MetaHIT consortium

Gastroenterologie clinique et biologique 2010

doi:10.1016/s0399-8320(10)70017-8.

Ontologies in quantitative biology: a basis for comparison, integration, and discovery

Jensen LJ, Bork P

PLoS biology 2010

doi:10.1371/journal.pbio.1000374.

A method and server for predicting damaging missense mutations

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR

Nature methods 2010

doi:10.1038/nmeth0410-248.

A human gut microbial gene catalogue established by metagenomic sequencing

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J

Nature 2010

doi:10.1038/nature08821.

Evolution and regulation of cellular periodic processes: a role for paralogues

Trachana K, Jensen LJ, Bork P

EMBO reports 2010

doi:10.1038/embor.2010.9.

Ancient animal microRNAs and the evolution of tissue identity

Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D

Nature 2010

doi:10.1038/nature08744.

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM

Genome biology 2010

doi:10.1186/gb-2010-11-3-r24.

Drug-induced regulation of target expression

Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P

PLoS computational biology 2010

doi:10.1371/journal.pcbi.1000925.

A side effect resource to capture phenotypic effects of drugs

Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P

Molecular systems biology 2010

doi:10.1038/msb.2009.98.

STITCH 2: an interaction network database for small molecules and proteins

Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkp937.

AQUA: automated quality improvement for multiple sequence alignments

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P

Bioinformatics (Oxford, England) 2010

doi:10.1093/bioinformatics/btp651.

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkp951.

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA

Science (New York, N.Y.) 2010

doi:10.1126/science.1178028.

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology

Woerner SM, Yuan YP, Benner A, Korff S, von Knebel Doeberitz M, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkp839.

Transcriptome complexity in a genome-reduced bacterium

Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L

Science (New York, N.Y.) 2009

doi:10.1126/science.1176951.

Proteome organization in a genome-reduced bacterium

Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC

Science (New York, N.Y.) 2009

doi:10.1126/science.1176343.

Evolution of biomolecular networks: lessons from metabolic and protein interactions

Yamada T, Bork P

Nature reviews. Molecular cell biology 2009

doi:10.1038/nrm2787.

Impact of genome reduction on bacterial metabolism and its regulation

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L

Science (New York, N.Y.) 2009

doi:10.1126/science.1177263.

ASTD: The Alternative Splicing and Transcript Diversity database

Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D

Genomics 2009

doi:10.1016/j.ygeno.2008.11.003.

Quantifying environmental adaptation of metabolic pathways in metagenomics

Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB

Proceedings of the National Academy of Sciences of the United States of America 2009

doi:10.1073/pnas.0808022106.

InterPro: the integrative protein signature database

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C

Nucleic acids research 2009

doi:10.1093/nar/gkn785.

STRING 8--a global view on proteins and their functional interactions in 630 organisms

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C

Nucleic acids research 2009

doi:10.1093/nar/gkn760.

Sequence-based feature prediction and annotation of proteins

Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S

Genome biology 2009

doi:10.1186/gb-2009-10-2-206.

SMART 6: recent updates and new developments

Letunic I, Doerks T, Bork P

Nucleic acids research 2009

doi:10.1093/nar/gkn808.

Discovering functional novelty in metagenomes: examples from light-mediated processes

Singh AH, Doerks T, Letunic I, Raes J, Bork P

Journal of bacteriology 2009

doi:10.1128/jb.01084-08.

Biochemistry. Not comparable, but complementary

Jensen LJ, Bork P

Science (New York, N.Y.) 2008

doi:10.1126/science.1164801.

Sircah: a tool for the detection and visualization of alternative transcripts

Harrington ED, Bork P

Bioinformatics (Oxford, England) 2008

doi:10.1093/bioinformatics/btn361.

Molecular eco-systems biology: towards an understanding of community function

Raes J, Bork P

Nature reviews. Microbiology 2008

doi:10.1038/nrmicro1935.

Drug target identification using side-effect similarity

Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P

Science (New York, N.Y.) 2008

doi:10.1126/science.1158140.

KEGG Atlas mapping for global analysis of metabolic pathways

Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M

Nucleic acids research 2008

doi:10.1093/nar/gkn282.

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

Pincus D, Letunic I, Bork P, Lim WA

Proceedings of the National Academy of Sciences of the United States of America 2008

doi:10.1073/pnas.0803161105.

Predicting biological networks from genomic data

Harrington ED, Jensen LJ, Bork P

FEBS letters 2008

doi:10.1016/j.febslet.2008.02.033.

Large-scale prediction of drug-target relationships

Kuhn M, Campillos M, González P, Jensen LJ, Bork P

FEBS letters 2008

doi:10.1016/j.febslet.2008.02.024.

The genome of the model beetle and pest Tribolium castaneum

Tribolium Genome Sequencing Consortium, Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G

Nature 2008

doi:10.1038/nature06784.

Sequence and Structure of Proteins

Eisenhaber F, Bork P

1998

doi:DOI: 10.1002/9783527620869.

iPath: interactive exploration of biochemical pathways and networks

Letunic I, Yamada T, Kanehisa M, Bork P

Trends in biochemical sciences 2008

doi:10.1016/j.tibs.2008.01.001.

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D

Nature 2008

doi:10.1038/nature06617.

A computational screen for type I polyketide synthases in metagenomics shotgun data

Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P

PloS one 2008

doi:10.1371/journal.pone.0003515.

A nitrile hydratase in the eukaryote Monosiga brevicollis

Foerstner KU, Doerks T, Muller J, Raes J, Bork P

PloS one 2008

doi:10.1371/journal.pone.0003976.

SuperTarget and Matador: resources for exploring drug-target relationships

Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R

Nucleic acids research 2008

doi:10.1093/nar/gkm862.

4DXpress: a database for cross-species expression pattern comparisons

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T

Nucleic acids research 2008

doi:10.1093/nar/gkm797.

A molecular study of microbe transfer between distant environments

Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P

PloS one 2008

doi:10.1371/journal.pone.0002607.

Circular reasoning rather than cyclic expression

Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P

Genome biology 2008

doi:10.1186/gb-2008-9-6-403.

eggNOG: automated construction and annotation of orthologous groups of genes

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P

Nucleic acids research 2008

doi:10.1093/nar/gkm796.

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability

Korff S, Woerner SM, Yuan YP, Bork P, von Knebel Doeberitz M, Gebert J

BMC cancer 2008

doi:10.1186/1471-2407-8-329.

STITCH: interaction networks of chemicals and proteins

Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P

Nucleic acids research 2008

doi:10.1093/nar/gkm795.

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P

Molecular systems biology 2008

doi:10.1038/msb.2008.35.

NetworKIN: a resource for exploring cellular phosphorylation networks

Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T

Nucleic acids research 2008

doi:10.1093/nar/gkm902.

Linear motif atlas for phosphorylation-dependent signaling

Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R

Science signaling 2008

doi:10.1126/scisignal.1159433.

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

Pallejà A, Harrington ED, Bork P

BMC genomics 2008

doi:10.1186/1471-2164-9-335.

Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation

Perotti C, Liu R, Parusel CT, Böcher N, Schultz J, Bork P, Pfitzner E, Groner B, Shemanko CS

Breast cancer research : BCR 2008

doi:10.1186/bcr2193.

Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution

Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M

Genome biology 2008

doi:10.1186/gb-2008-9-12-r176.

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families

Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R

Gene 2008

doi:10.1016/j.gene.2007.10.012.

Non-random retention of protein-coding overlapping genes in Metazoa

Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD

BMC genomics 2008

doi:10.1186/1471-2164-9-174.

MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects

Wiemann S, Mehrle A, Hahne F, Hermjakob H, Apweiler R, Arlt D, Bechtel S, Bielke W, Birmingham A, Smith Q, Bork P, Buchholz F, Cai X, Camon E, Carninci P, Chanda SK, Chen Z, Cusick M, Echeverri C, Eils J, Eils R, Frank R, Fraser A, Girod A, Haedrich B, Hannus M, Harris M, Hayashizaki Y, Hide W, Hofmann O, Huber P, Hyman A, Jensen L, Kallioniemi O, Khvorova A, Koski L, Kraybill B, LaBaer J, Landegren U, Lawerenz C, Lehrach H, Liu F-F, Majety M, Mathey-Prevot B, Medico E, Mills GB, Nomura N, The OBI Consortium, Perrimon N, Pizarro A, Poustka A, Quackenbush J, Rosenfelder H, Sahin O, Salehi-Ashtiani K, Sasse F, Sauermann M, Schimmer AD, Schmidt C, Selfors L, Shamu C, Sönnichsen B, Taylor C, Temple G, Vidal M, Weidlich M, Wrobel DJ, Zhang J

2008

doi:.

Genome-wide experimental determination of barriers to horizontal gene transfer

Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM

Science (New York, N.Y.) 2007

doi:10.1126/science.1147112.

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing

Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E

Genes & development 2007

doi:10.1101/gad.443107.

Get the most out of your metagenome: computational analysis of environmental sequence data

Raes J, Foerstner KU, Bork P

Current opinion in microbiology 2007

doi:10.1016/j.mib.2007.09.001.

Evolution of cell cycle control: same molecular machines, different regulation

de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ

Cell cycle (Georgetown, Tex.) 2007

doi:10.4161/cc.6.15.4537.

Quantitative assessment of protein function prediction from metagenomics shotgun sequences

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P

Proceedings of the National Academy of Sciences of the United States of America 2007

doi:10.1073/pnas.0702636104.

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism

Pachkov M, Dandekar T, Korbel J, Bork P, Schuster S

Gene 2007

doi:10.1016/j.gene.2007.02.033.

Update of the G2D tool for prioritization of gene candidates to inherited diseases

Perez-Iratxeta C, Bork P, Andrade-Navarro MA

Nucleic acids research 2007

doi:10.1093/nar/gkm223.

Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals

Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE

The EMBO journal 2007

doi:10.1038/sj.emboj.7601699.

Systematic discovery of in vivo phosphorylation networks

Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T

Cell 2007

doi:10.1016/j.cell.2007.05.052.

Protein function space: viewing the limits or limited by our view?

Raes J, Harrington ED, Singh AH, Bork P

Current opinion in structural biology 2007

doi:10.1016/j.sbi.2007.05.010.

Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes

Boettner M, Steffens C, von Mering C, Bork P, Stahl U, Lang C

Journal of biotechnology 2007

doi:10.1016/j.jbiotec.2007.02.019.

Quantitative phylogenetic assessment of microbial communities in diverse environments

von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P

Science (New York, N.Y.) 2007

doi:10.1126/science.1133420.

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P

Molecular systems biology 2007

doi:10.1038/msb4100112.

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Letunic I, Bork P

Bioinformatics (Oxford, England) 2007

doi:10.1093/bioinformatics/btl529.

New developments in the InterPro database

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C

Nucleic acids research 2007

doi:10.1093/nar/gkl841.

Prediction of effective genome size in metagenomic samples

Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P

Genome biology 2007

doi:10.1186/gb-2007-8-1-r10.

STRING 7--recent developments in the integration and prediction of protein interactions

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P

Nucleic acids research 2007

doi:10.1093/nar/gkl825.

Quantification of insect genome divergence

Zdobnov EM, Bork P

Trends in genetics : TIG 2007

doi:10.1016/j.tig.2006.10.004.

Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome

Raible F, Tessmar-Raible K, Arboleda E, Kaller T, Bork P, Arendt D, Arnone MI

Developmental biology 2006

doi:10.1016/j.ydbio.2006.08.070.

Computational characterization of multiple Gag-like human proteins

Campillos M, Doerks T, Shah PK, Bork P

Trends in genetics : TIG 2006

doi:10.1016/j.tig.2006.09.006.

Insights into social insects from the genome of the honeybee Apis mellifera

Honeybee Genome Sequencing Consortium

Nature 2006

doi:10.1038/nature05260.

Co-evolution of transcriptional and post-translational cell-cycle regulation

Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P

Nature 2006

doi:10.1038/nature05186.

Assessing systems properties of yeast mitochondria through an interaction map of the organelle

Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM

PLoS genetics 2006

doi:10.1371/journal.pgen.0020170.

mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes

Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E

Genes & development 2006

doi:10.1101/gad.1424106.

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Suyama M, Torrents D, Bork P

Nucleic acids research 2006

doi:10.1093/nar/gkl315.

A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development

Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE

Developmental cell 2006

doi:10.1016/j.devcel.2006.04.009.

Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes

Suyama M, Harrington E, Bork P, Torrents D

PLoS computational biology 2006

doi:10.1371/journal.pcbi.0020076.

LSAT: learning about alternative transcripts in MEDLINE

Shah PK, Bork P

Bioinformatics (Oxford, England) 2006

doi:10.1093/bioinformatics/btk044.

Identification and analysis of evolutionarily cohesive functional modules in protein networks

Campillos M, von Mering C, Jensen LJ, Bork P

Genome research 2006

doi:10.1101/gr.4336406.

Toward automatic reconstruction of a highly resolved tree of life

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P

Science (New York, N.Y.) 2006

doi:10.1126/science.1123061.

Comparative analysis of environmental sequences: potential and challenges

Foerstner KU, von Mering C, Bork P

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006

doi:10.1098/rstb.2005.1809.

Proteome survey reveals modularity of the yeast cell machinery

Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G

Nature 2006

doi:10.1038/nature04532.

Extraction of regulatory gene/protein networks from Medline

Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P

Bioinformatics (Oxford, England) 2006

doi:10.1093/bioinformatics/bti597.

Similar gene expression profiles do not imply similar tissue functions

Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ

Trends in genetics : TIG 2006

doi:10.1016/j.tig.2006.01.006.

Literature mining for the biologist: from information retrieval to biological discovery

Jensen LJ, Saric J, Bork P

Nature reviews. Genetics 2006

doi:10.1038/nrg1768.

SMART 5: domains in the context of genomes and networks

Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P

Nucleic acids research 2006

doi:10.1093/nar/gkj079.

Environments shape the nucleotide composition of genomes

Foerstner KU, von Mering C, Hooper SD, Bork P

EMBO reports 2005

doi:10.1038/sj.embor.7400538.

Medusa: a simple tool for interaction graph analysis

Hooper SD, Bork P

Bioinformatics (Oxford, England) 2005

doi:10.1093/bioinformatics/bti696.

Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases

Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, Bork P, Wiese S, Gessler M, Kerkhoff E

Gene expression patterns : GEP 2005

doi:10.1016/j.modgep.2005.04.015.

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D

Science (New York, N.Y.) 2005

doi:10.1126/science.1119089.

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system

Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M

The Journal of cell biology 2005

doi:10.1083/jcb.200507168.

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets

Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E

RNA (New York, N.Y.) 2005

doi:10.1261/rna.2160905.

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii

Suyama M, Lathe WC 3rd, Bork P

FEBS letters 2005

doi:10.1016/j.febslet.2005.08.051.

Initial sequence of the chimpanzee genome and comparison with the human genome

Chimpanzee Sequencing and Analysis Consortium

Nature 2005

doi:10.1038/nature04072.

Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones

Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U

Microbial Cell Factories 2005

doi:10.1186/1475-2859-4-21.

Extraction of transcript diversity from scientific literature

Shah PK, Jensen LJ, Boué S, Bork P

PLoS computational biology 2005

doi:10.1371/journal.pcbi.0010010.

Consistency of genome-based methods in measuring Metazoan evolution

Zdobnov EM, von Mering C, Letunic I, Bork P

FEBS letters 2005

doi:10.1016/j.febslet.2005.04.006.

Towards cellular systems in 4D

Bork P, Serrano L

Cell 2005

doi:10.1016/j.cell.2005.05.001.

Systematic association of genes to phenotypes by genome and literature mining

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P

PLoS biology 2005

doi:10.1371/journal.pbio.0030134.

Structural similarity to bridge sequence space: finding new families on the bridges

Shah PK, Aloy P, Bork P, Russell RB

Protein science : a publication of the Protein Society 2005

doi:10.1110/ps.041187405.

The WHy domain mediates the response to desiccation in plants and bacteria

Ciccarelli FD, Bork P

Bioinformatics (Oxford, England) 2005

doi:10.1093/bioinformatics/bti221.

Comparison of computational methods for the identification of cell cycle-regulated genes

de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S

Bioinformatics (Oxford, England) 2005

doi:10.1093/bioinformatics/bti093.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK

Nature 2005

doi:10.1038/nature03466.

Comparative metagenomics of microbial communities

Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM

Science (New York, N.Y.) 2005

doi:10.1126/science.1107851.

Complex genomic rearrangements lead to novel primate gene function

Ciccarelli FD, von Mering C, Suyama M, Harrington ED, Izaurralde E, Bork P

Genome research 2005

doi:10.1101/gr.3266405.

Dynamic complex formation during the yeast cell cycle

de Lichtenberg U, Jensen LJ, Brunak S, Bork P

Science (New York, N.Y.) 2005

doi:10.1126/science.1105103.

Is there biological research beyond Systems Biology? A comparative analysis of terms

Bork P

Molecular systems biology 2005

doi:10.1038/msb4100016.

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G

Genome research 2005

doi:10.1101/gr.3002305.

InterPro, progress and status in 2005

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH

Nucleic acids research 2005

doi:10.1093/nar/gki106.

G2D: a tool for mining genes associated with disease

Perez-Iratxeta C, Wjst M, Bork P, Andrade MA

BMC genetics 2005

doi:10.1186/1471-2156-6-45.

DCD - a novel plant specific domain in proteins involved in development and programmed cell death

Tenhaken R, Doerks T, Bork P

BMC bioinformatics 2005

doi:10.1186/1471-2105-6-169.

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P

Nucleic acids research 2005

doi:10.1093/nar/gki005.

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes

Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P

Nucleic acids research 2005

doi:10.1093/nar/gki236.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium

Nature 2004

doi:10.1038/nature03154.

Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression

Koehl A, Schmidt N, Rieger A, Pilgram SM, Letunic I, Bork P, Soto F, Friauf E, Nothwang HG

The European journal of neuroscience 2004

doi:10.1111/j.1460-9568.2004.03791.x.

Shared components of protein complexes--versatile building blocks or biochemical artefacts?

Krause R, von Mering C, Bork P, Dandekar T

BioEssays : news and reviews in molecular, cellular and developmental biology 2004

doi:10.1002/bies.20141.

Estimating rates of alternative splicing in mammals and invertebrates

Kim H, Klein R, Majewski J, Ott J

Nature genetics 2004

doi:10.1038/ng0904-915.

Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome

Liska AJ, Popov AV, Sunyaev S, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A

Proteomics 2004

doi:10.1002/pmic.200300813.

Gene annotation from scientific literature using mappings between keyword systems

Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA

Bioinformatics (Oxford, England) 2004

doi:10.1093/bioinformatics/bth207.

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments

Suyama M, Torrents D, Bork P

Bioinformatics (Oxford, England) 2004

doi:10.1093/bioinformatics/bth172.

ArrayProspector: a web resource of functional associations inferred from microarray expression data

Jensen LJ, Lagarde J, von Mering C, Bork P

Nucleic acids research 2004

doi:10.1093/nar/gkh407.

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

Korbel JO, Jensen LJ, von Mering C, Bork P

Nature biotechnology 2004

doi:10.1038/nbt988.

Protein interaction networks from yeast to human

Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM

Current opinion in structural biology 2004

doi:10.1016/j.sbi.2004.05.003.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium

Nature 2004

doi:10.1038/nature02426.

Structure-based assembly of protein complexes in yeast

Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB

Science (New York, N.Y.) 2004

doi:10.1126/science.1092645.

Global analysis of bacterial transcription factors to predict cellular target processes

Doerks T, Andrade MA, Lathe W 3rd, von Mering C, Bork P

Trends in genetics : TIG 2004

doi:10.1016/j.tig.2004.01.006.

RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export

Forler D, Rabut G, Ciccarelli FD, Herold A, Köcher T, Niggeweg R, Bork P, Ellenberg J, Izaurralde E

Molecular and cellular biology 2004

doi:10.1128/mcb.24.3.1155-1167.2004.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R

Nature biotechnology 2004

doi:10.1038/nbt926.

Sequences and topology - Genes and structures in context - Editorial overview

Bork P, Orengo CA

Current opinion in structural biology 2004

doi:.

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources

Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gössling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Müller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E, Zimmer R

Bioinformatics (Oxford, England) 2004

doi:10.1093/bioinformatics/btg398.

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

Doerks T, von Mering C, Bork P

Nucleic acids research 2004

doi:10.1093/nar/gkh973.

Quality analysis and integration of large-scale molecular data sets

Jensen LJ, Bork P

Drug discovery today 2004

doi:.

SMART 4.0: towards genomic data integration

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P

Nucleic acids research 2004

doi:10.1093/nar/gkh088.

Extracting Regulatory Gene Expression Networks From Pubmed

Saric J, Jensen LJ, Bork P, Ouzounova R, Rojas I

2004

doi:.

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold

Ciccarelli FD, Izaurralde E, Bork P

BMC bioinformatics 2003

doi:10.1186/1471-2105-4-64.

Impact of selection, mutation rate and genetic drift on human genetic variation

Sunyaev S, Kondrashov FA, Bork P, Ramensky V

Human molecular genetics 2003

doi:10.1093/hmg/ddg359.

A genome-wide survey of human pseudogenes

Torrents D, Suyama M, Zdobnov E, Bork P

Genome research 2003

doi:10.1101/gr.1455503.

Genome evolution reveals biochemical networks and functional modules

von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P

Proceedings of the National Academy of Sciences of the United States of America 2003

doi:10.1073/pnas.2136809100.

Alternative splicing and evolution

Boue S, Letunic I, Bork P

BioEssays : news and reviews in molecular, cellular and developmental biology 2003

doi:10.1002/bies.10371.

Protein disorder prediction: implications for structural proteomics

Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB

Structure (London, England : 1993) 2003

doi:10.1016/j.str.2003.10.002.

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens

Krause R, von Mering C, Bork P

Bioinformatics (Oxford, England) 2003

doi:10.1093/bioinformatics/btg344.

Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways

Gatfield D, Unterholzner L, Ciccarelli FD, Bork P, Izaurralde E

The EMBO journal 2003

doi:10.1093/emboj/cdg371.

The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold

Ciccarelli FD, Bork P, Kerkhoff E

Trends in biochemical sciences 2003

doi:10.1016/s0968-0004(03)00116-6.

The DNA sequence of human chromosome 7

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK

Nature 2003

doi:10.1038/nature01782.

Systematic discovery of analogous enzymes in thiamin biosynthesis

Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P

Nature biotechnology 2003

doi:10.1038/nbt834.

Update on XplorMed: A web server for exploring scientific literature

Perez-Iratxeta C, Pérez AJ, Bork P, Andrade MA

Nucleic acids research 2003

doi:10.1093/nar/gkg538.

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ

Nucleic acids research 2003

doi:10.1093/nar/gkg545.

Metabolites: a helping hand for pathway evolution?

Schmidt S, Sunyaev S, Bork P, Dandekar T

Trends in biochemical sciences 2003

doi:10.1016/s0968-0004(03)00114-2.

The way we write

Netzel R, Perez-Iratxeta C, Bork P, Andrade MA

EMBO reports 2003

doi:10.1038/sj.embor.embor833.

Information extraction from full text scientific articles: where are the keywords?

Shah PK, Perez-Iratxeta C, Bork P, Andrade MA

BMC bioinformatics 2003

doi:10.1186/1471-2105-4-20.

The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia

Ciccarelli FD, Proukakis C, Patel H, Cross H, Azam S, Patton MA, Bork P, Crosby AH

Genomics 2003

doi:10.1016/s0888-7543(03)00011-9.

Function prediction and protein networks

Huynen MA, Snel B, von Mering C, Bork P

Current opinion in cell biology 2003

doi:10.1016/s0955-0674(03)00009-7.

Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes

Woerner SM, Benner A, Sutter C, Schiller M, Yuan YP, Keller G, Bork P, Doeberitz Mv, Gebert JF

Oncogene 2003

doi:10.1038/sj.onc.1206421.

Bioinformatics in the post-sequence era

Kanehisa M, Bork P

Nature genetics 2003

doi:10.1038/ng1109.

Increase of functional diversity by alternative splicing

Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S

Trends in genetics : TIG 2003

doi:10.1016/s0168-9525(03)00023-4.

High Rate of Gene Displacement in Vitamin Biosynthesis Pathways

Morett E, Saab G, Merino E, Bork P, Rajan E, Olvera L, Olvera M

2003

doi:.

The InterPro Database, 2003 brings increased coverage and new features

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM

Nucleic acids research 2003

doi:10.1093/nar/gkg046.

A protocol for the update of references to scientific literature in biological databases

Perez-Iratxeta C, Astola N, Ciccarelli FD, Sha PK, Bork P, Andrade MA

Applied bioinformatics 2003

doi:.

Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes

Shevchenko A, Sunyaev S, Liska A, Bork P, Shevchenko A

Methods in molecular biology (Clifton, N.J.) 2003

doi:.

Pseudogenes and Genomes

Torrents D, Suyama M, Bork P

2003

doi:.

STRING: a database of predicted functional associations between proteins

von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B

Nucleic acids research 2003

doi:10.1093/nar/gkg034.

The human genome: genes, pseudogenes, and variation on chromosome 7

Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK

Cold Spring Harbor symposia on quantitative biology 2003

doi:10.1101/sqb.2003.68.13.

Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes

Kloor M, Bork P, Duwe A, Klaes R, von Knebel Doeberitz M, Ridder R

Biochimica et biophysica acta 2002

doi:10.1016/s0167-4781(02)00543-2.

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES

Nature 2002

doi:10.1038/nature01262.

Immunity-related genes and gene families in Anopheles gambiae

Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Müller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P, Kafatos FC

Science (New York, N.Y.) 2002

doi:10.1126/science.1077136.

The genome sequence of the malaria mosquito Anopheles gambiae

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL

Science (New York, N.Y.) 2002

doi:10.1126/science.1076181.

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F

Proceedings of the National Academy of Sciences of the United States of America 2002

doi:10.1073/pnas.212527599.

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P

Science (New York, N.Y.) 2002

doi:10.1126/science.1077061.

InterPro: an integrated documentation resource for protein families, domains and functional sites

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ, InterPro Consortium

Briefings in bioinformatics 2002

doi:10.1093/bib/3.3.225.

Human non-synonymous SNPs: server and survey

Ramensky V, Bork P, Sunyaev S

Nucleic acids research 2002

doi:10.1093/nar/gkf493.

NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria

Andrade MA, Ciccarelli FD, Perez-Iratxeta C, Bork P

Genome biology 2002

doi:10.1186/gb-2002-3-9-research0047.

The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations

Bordo D, Bork P

EMBO reports 2002

doi:10.1093/embo-reports/kvf150.

Predicting protein cellular localization using a domain projection method

Mott R, Schultz J, Bork P, Ponting CP

Genome research 2002

doi:10.1101/gr.96802.

SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia

Patel H, Cross H, Proukakis C, Hershberger R, Bork P, Ciccarelli FD, Patton MA, McKusick VA, Crosby AH

Nature genetics 2002

doi:10.1038/ng937.

A complex prediction: three-dimensional model of the yeast exosome

Aloy P, Ciccarelli FD, Leutwein C, Gavin AC, Superti-Furga G, Bork P, Bottcher B, Russell RB

EMBO reports 2002

doi:10.1093/embo-reports/kvf135.

Association of genes to genetically inherited diseases using data mining

Perez-Iratxeta C, Bork P, Andrade MA

Nature genetics 2002

doi:10.1038/ng895.

Common exon duplication in animals and its role in alternative splicing

Letunic I, Copley RR, Bork P

Human molecular genetics 2002

doi:10.1093/hmg/11.13.1561.

Exploring MEDLINE abstracts with XplorMed

Perez-Iratxeta C, Bork P, Andrade MA

Drugs of today (Barcelona, Spain : 1998) 2002

doi:10.1358/dot.2002.38.6.678344.

Computing fuzzy associations for the analysis of biological literature

Perez-Iratxeta C, Keer HS, Bork P, Andrade MA

BioTechniques 2002

doi:10.2144/02326bc03.

Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae

Thomasova D, Ton LQ, Copley RR, Zdobnov EM, Wang X, Hong YS, Sim C, Bork P, Kafatos FC, Collins FH

Proceedings of the National Academy of Sciences of the United States of America 2002

doi:10.1073/pnas.082235599.

Proteinkomplexe und Netzwerke: Neue Herausforderungen für die Proteomik

Von Mering C, Bork P

2002

doi:.

Teamed up for transcription

von Mering C, Bork P

Nature 2002

doi:10.1038/417797a.

Comparative assessment of large-scale data sets of protein-protein interactions

von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P

Nature 2002

doi:10.1038/nature750.

BSD: a novel domain in transcription factors and synapse-associated proteins

Doerks T, Huber S, Buchner E, Bork P

Trends in biochemical sciences 2002

doi:10.1016/s0968-0004(01)02042-4.

The identification of functional modules from the genomic association of genes

Snel B, Bork P, Huynen MA

Proceedings of the National Academy of Sciences of the United States of America 2002

doi:10.1073/pnas.092632599.

AMOP, a protein module alternatively spliced in cancer cells

Ciccarelli FD, Doerks T, Bork P

Trends in biochemical sciences 2002

doi:10.1016/s0968-0004(01)02049-7.

SHOT: a web server for the construction of genome phylogenies

Korbel JO, Snel B, Huynen MA, Bork P

Trends in genetics : TIG 2002

doi:10.1016/s0168-9525(01)02597-5.

CASH--a beta-helix domain widespread among carbohydrate-binding proteins

Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P

Trends in biochemical sciences 2002

doi:10.1016/s0968-0004(01)02046-1.

Protein domain analysis in the era of complete genomes

Copley RR, Doerks T, Letunic I, Bork P

FEBS letters 2002

doi:10.1016/s0014-5793(01)03289-6.

Genome and protein evolution in eukaryotes

Copley RR, Letunic I, Bork P

Current opinion in chemical biology 2002

doi:10.1016/s1367-5931(01)00278-2.

Comparative analysis of protein interaction networks

Bork P

Bioinformatics (Oxford, England) 2002

doi:10.1093/bioinformatics/18.suppl_2.S64.

Alternative splicing and genome complexity

Brett D, Pospisil H, Valcárcel J, Reich J, Bork P

Nature genetics 2002

doi:10.1038/ng803.

Sequence analysis of multidomain proteins: past perspectives and future directions

Copley RR, Ponting CP, Schultz J, Bork P

Advances in protein chemistry 2003

doi:10.1016/s0065-3233(02)61002-2.

Comparative genome analysis of the mollicutes

Dandekar T, Snel B, Schmidt S, Lathe W, Suyama M, Huynen M, Bork P

2002

doi:10.1007/0-306-47606-1_11.

Systematic identification of novel protein domain families associated with nuclear functions

Doerks T, Copley RR, Schultz J, Ponting CP, Bork P

Genome research 2002

doi:10.1101/gr.203201.

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources

Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ

Nucleic acids research 2002

doi:10.1093/nar/30.1.387.

Functional organization of the yeast proteome by systematic analysis of protein complexes

Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G

Nature 2002

doi:10.1038/415141a.

Recent improvements to the SMART domain-based sequence annotation resource

Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P

Nucleic acids research 2002

doi:10.1093/nar/30.1.242.

A versatile structural domain analysis server using profile weight matrices

Schmidt S, Bork P, Dandekar T

Journal of chemical information and computer sciences 2002

doi:10.1021/ci010374r.

Genomes in flux: the evolution of archaeal and proteobacterial gene content

Snel B, Bork P, Huynen MA

Genome research 2002

doi:10.1101/gr.176501.

The Spir actin organizers are involved in vesicle transport processes

Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R

Current biology : CB 2001

doi:10.1016/s0960-9822(01)00602-9.

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution

Ponting CP, Mott R, Bork P, Copley RR

Genome research 2001

doi:10.1101/gr.198701.

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

Huynen MA, Snel B, Bork P, Gibson TJ

Human molecular genetics 2001

doi:10.1093/hmg/10.21.2463.

XplorMed: a tool for exploring MEDLINE abstracts

Perez-Iratxeta C, Bork P, Andrade MA

Trends in biochemical sciences 2001

doi:10.1016/s0968-0004(01)01926-0.

Evolution of tuf genes: ancient duplication, differential loss and gene conversion

Lathe WC 3rd, Bork P

FEBS letters 2001

doi:10.1016/s0014-5793(01)02639-4.

Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens

Linnebacher M, Gebert J, Rudy W, Woerner S, Yuan YP, Bork P, von Knebel Doeberitz M

International journal of cancer. Journal international du cancer 2001

doi:10.1002/ijc.1298.

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells

Woerner SM, Gebert J, Yuan YP, Sutter C, Ridder R, Bork P, von Knebel Doeberitz M

International journal of cancer. Journal international du cancer 2001

doi:10.1002/ijc.1299.

Inversions and the dynamics of eukaryotic gene order

Huynen MA, Snel B, Bork P

Trends in genetics : TIG 2001

doi:10.1016/s0168-9525(01)02302-2.

Comparison of ARM and HEAT protein repeats

Andrade MA, Petosa C, O'Donoghue SI, Müller CW, Bork P

Journal of molecular biology 2001

doi:10.1006/jmbi.2001.4624.

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching

Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG

Analytical chemistry 2001

doi:10.1021/ac0013709.

DDT -- a novel domain in different transcription and chromosome remodeling factors

Doerks T, Copley R, Bork P

Trends in biochemical sciences 2001

doi:10.1016/s0968-0004(00)01769-2.

Prediction of deleterious human alleles

Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, Bork P

Human molecular genetics 2001

doi:10.1093/hmg/10.6.591.

Genome speak

Bork P, Copley R

Nature 2001

doi:10.1038/35057269.

The draft sequences. Filling in the gaps

Bork P, Copley R

Nature 2001

doi:10.1038/35057274.

Initial sequencing and analysis of the human genome

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, International Human Genome Sequencing Consortium

Nature 2001

doi:10.1038/35057062.

Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35]

Schultz J, Jones T, Bork P, Sheer D, Blencke S, Steyrer S, Wellbrock U, Bevec D, Ullrich A, Wallasch C

Genomics 2001

doi:10.1006/geno.2000.6447.

Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms

Sunyaev S, Lathe W 3rd, Bork P

Current opinion in structural biology 2001

doi:10.1016/s0959-440x(00)00175-5.

The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival

Becker S, Gehrsitz A, Bork P, Buchner S, Buchner E

Gene 2001

doi:10.1016/s0378-1119(00)00548-5.

Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes

Eisenhaber B, Bork P, Eisenhaber F

Protein engineering 2001

doi:10.1093/protein/14.1.17.

Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences

Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB, Koonin EV

Genome biology 2001

doi:.

Evolution of prokaryotic gene order: genome rearrangements in closely related species

Suyama M, Bork P

Trends in genetics : TIG 2001

doi:10.1016/s0168-9525(00)02159-4.

TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture

Herold A, Suyama M, Rodrigues JP, Braun IC, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E

Molecular and cellular biology 2000

doi:10.1128/mcb.20.23.8996-9008.2000.

Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways

Copley RR, Bork P

Journal of molecular biology 2000

doi:10.1006/jmbi.2000.4152.

Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III

Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlü N, Bork P, Hyman AA

Nature 2000

doi:10.1038/35042526.

GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins

Doerks T, Strauss M, Brendel M, Bork P

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01664-9.

Gene context conservation of a higher order than operons

Lathe WC 3rd, Snel B, Bork P

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01663-7.

EST analysis online: WWW tools for detection of SNPs and alternative splice forms

Brett D, Lehmann G, Hanke J, Gross S, Reich J, Bork P

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(00)02089-8.

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames

Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P

Nucleic acids research 2000

doi:10.1093/nar/28.17.3278.

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

Snel B, Lehmann G, Bork P, Huynen MA

Nucleic acids research 2000

doi:10.1093/nar/28.18.3442.

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

Huynen M, Snel B, Lathe W 3rd, Bork P

Genome research 2000

doi:10.1101/gr.10.8.1204.

SNP frequencies in human genes an excess of rare alleles and differing modes of selection

Sunyaev SR, Lathe WC 3rd, Ramensky VE, Bork P

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(00)02058-8.

L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7

Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01599-1.

Automated annotation of GPI anchor sites: case study C. elegans

Eisenhaber B, Bork P, Yuan Y, Löffler G, Eisenhaber F

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01601-7.

NAIL-Network Analysis Interface for Linking HMMER results

Sánchez-Pulido L, Yuan YP, Andrade MA, Bork P

Bioinformatics (Oxford, England) 2000

doi:10.1093/bioinformatics/16.7.656.

Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins

Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P

EMBO reports 2000

doi:10.1093/embo-reports/kvd009.

Automated extraction of information in molecular biology

Andrade MA, Bork P

FEBS letters 2000

doi:10.1016/s0014-5793(00)01661-6.

Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines

Dimopoulos G, Casavant TL, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares MB, Kafatos FC

Proceedings of the National Academy of Sciences of the United States of America 2000

doi:10.1073/pnas.97.12.6619.

Exploitation of gene context

Huynen M, Snel B, Lathe W, Bork P

Current opinion in structural biology 2000

doi:10.1016/s0959-440x(00)00098-1.

More than 1,000 putative new human signalling proteins revealed by EST data mining

Schultz J, Doerks T, Ponting CP, Copley RR, Bork P

Nature genetics 2000

doi:10.1038/76069.

Homology-based method for identification of protein repeats using statistical significance estimates

Andrade MA, Ponting CP, Gibson TJ, Bork P

Journal of molecular biology 2000

doi:10.1006/jmbi.2000.3684.

EST comparison indicates 38% of human mRNAs contain possible alternative splice forms

Brett D, Hanke J, Lehmann G, Haase S, Delbrück S, Krueger S, Reich J, Bork P

FEBS letters 2000

doi:10.1016/s0014-5793(00)01581-7.

Towards a structural basis of human non-synonymous single nucleotide polymorphisms

Sunyaev S, Ramensky V, Bork P

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(00)01988-0.

Powers and pitfalls in sequence analysis: the 70% hurdle

Bork P

Genome research 2000

doi:10.1101/gr.10.4.398.

REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export

Stutz F, Bachi A, Doerks T, Braun IC, Séraphin B, Wilm M, Bork P, Izaurralde E

RNA (New York, N.Y.) 2000

doi:10.1017/s1355838200000078.

The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization

Otto IM, Raabe T, Rennefahrt UE, Bork P, Rapp UR, Kerkhoff E

Current biology : CB 2000

doi:10.1016/s0960-9822(00)00388-2.

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem

Isaksson A, Landegren U, Syvänen AC, Bork P, Stein C, Ortigao F, Brookes AJ

European journal of human genetics : EJHG 2000

doi:10.1038/sj.ejhg.5200424.

Analysis of Amino Acid Sequences

Bork P

2000

doi:.

Advances in Protein Chemistry

Bork P (ed)

2000

doi:.

Genome and proteome informatics - Editorial overview

Bork P, Eisenberg D

Current opinion in structural biology 2000

doi:10.1016/S0959-440X(00)00093-2.

Comparative genome analysis: exploiting the context of genes to infer evolution and predict function

Bork P, Snel B, Lehmann G, Suyama M, Dandekar T, Lathe W III, Huynen M

2000

doi:10.1007/978-94-011-4309-7_25.

HGBASE: a database of SNPs and other variations in and around human genes

Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F

Nucleic acids research 2000

doi:10.1093/nar/28.1.356.

Evolution of domain families

Ponting CP, Schultz J, Copley RR, Andrade MA, Bork P

Advances in protein chemistry 2000

doi:10.1016/s0065-3233(00)54007-8.

SMART: a web-based tool for the study of genetically mobile domains

Schultz J, Copley RR, Doerks T, Ponting CP, Bork P

Nucleic acids research 2000

doi:10.1093/nar/28.1.231.

Genome evolution. Gene fusion versus gene fission

Snel B, Bork P, Huynen M

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(99)01924-1.

Individual variation in protein-coding sequences of human genome

Sunyaev S, Hanke J, Brett D, Aydin A, Zastrow I, Lathe W, Bork P, Reich J

Advances in protein chemistry 2000

doi:10.1016/s0065-3233(00)54012-1.

The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins

Liu Z, Macias MJ, Bottomley MJ, Stier G, Linge JP, Nilges M, Bork P, Sattler M

Structure (London, England : 1993) 1999

doi:10.1016/s0969-2126(00)88346-x.

A point of entry into genomics

Bork P, Huynen MA

Nature genetics 1999

doi:10.1038/15453.

Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes

Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P

Journal of molecular medicine (Berlin, Germany) 1999

doi:10.1007/s001099900059.

A lipid-binding domain in Wnt: a case of mistaken identity?

Barnes MR, Russell RB, Copley RR, Ponting CP, Bork P, Cumberledge S, Reichsman F, Moore HM

Current biology : CB 1999

doi:10.1016/s0960-9822(99)80465-5.

Phospholipases A2 and Wnts are unlikely to share a common ancestor

Copley RR, Ponting CP, Bork P

Current biology : CB 1999

doi:10.1016/s0960-9822(99)80466-7.

Pathway alignment: application to the comparative analysis of glycolytic enzymes

Dandekar T, Schuster S, Snel B, Huynen M, Bork P

The Biochemical journal 1999

doi:10.1042/0264-6021:3430115.

Alternative splicing of human genes: more the rule than the exception?

Hanke J, Brett D, Zastrow I, Aydin A, Delbrück S, Lehmann G, Luft F, Reich J, Bork P

Trends in genetics : TIG 1999

doi:10.1016/s0168-9525(99)01830-2.

Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites

Smalla M, Schmieder P, Kelly M, Ter Laak A, Krause G, Ball L, Wahl M, Bork P, Oschkinat H

Protein science : a publication of the Protein Society 1999

doi:10.1110/ps.8.10.1954.

Prediction of potential GPI-modification sites in proprotein sequences

Eisenhaber B, Bork P, Eisenhaber F

Journal of molecular biology 1999

doi:10.1006/jmbi.1999.3069.

Associative database of protein sequences

Hanke J, Lehmann G, Bork P, Reich JG

Bioinformatics (Oxford, England) 1999

doi:10.1093/bioinformatics/15.9.741.

Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures

Müller SA, Sasaki T, Bork P, Wolpensinger B, Schulthess T, Timpl R, Engel A, Engel J

Journal of molecular biology 1999

doi:10.1006/jmbi.1999.2996.

A latrophilin/CL-1-like GPS domain in polycystin-1

Ponting CP, Hofmann K, Bork P

Current biology : CB 1999

doi:10.1016/s0960-9822(99)80379-0.

Genome comparisons to monitor molecular evolution

Bork P, Dandekar T, Snel B, Huynen MA

1999

doi:.

Domains in plexins: links to integrins and transcription factors

Bork P, Doerks T, Springer TA, Snel B

Trends in biochemical sciences 1999

doi:10.1016/s0968-0004(99)01416-4.

Variation and evolution of the citric-acid cycle: a genomic perspective

Huynen MA, Dandekar T, Bork P

Trends in microbiology 1999

doi:10.1016/s0966-842x(99)01539-5.

Protein families in multicellular organisms

Copley RR, Schultz J, Ponting CP, Bork P

Current opinion in structural biology 1999

doi:10.1016/s0959-440x(99)80055-4.

A novel transactivation domain in parkin

Morett E, Bork P

Trends in biochemical sciences 1999

doi:10.1016/s0968-0004(99)01381-x.

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer

Ponting CP, Aravind L, Schultz J, Bork P, Koonin EV

Journal of molecular biology 1999

doi:10.1006/jmbi.1999.2827.

No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho

Ponting CP, Bork P, Schultz J, Aravind L

Trends in biochemical sciences 1999

doi:10.1016/s0968-0004(99)01379-1.

The mahogany protein is a receptor involved in suppression of obesity

Nagle DL, McGrail SH, Vitale J, Woolf EA, Dussault BJ Jr, DiRocco L, Holmgren L, Montagno J, Bork P, Huszar D, Fairchild-Huntress V, Ge P, Keilty J, Ebeling C, Baldini L, Gilchrist J, Burn P, Carlson GA, Moore KJ

Nature 1999

doi:10.1038/18210.

Applying logic programming ro derive novel functional information of genomes.

Bansal AK, Bork P

1999

doi:.

Bioinformatik... (editorial)

Bork P

1999

doi:.

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries

Eisenhaber F, Bork P

Bioinformatics (Oxford, England) 1999

doi:10.1093/bioinformatics/15.7.528.

Sequence analysis, dotplot, aligning sequences, indels and gap-penalty

Gibson T, Bork P

1999

doi:.

Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes

Huynen M, Snel B, Bork P

Science (New York, N.Y.) 1999

doi:.

SMART: identification and annotation of domains from signalling and extracellular protein sequences

Ponting CP, Schultz J, Milpetz F, Bork P

Nucleic acids research 1999

doi:10.1093/nar/27.1.229.

Genome phylogeny based on gene content

Snel B, Bork P, Huynen MA

Nature genetics 1999

doi:10.1038/5052.

Homology-based gene prediction using neural nets

Cai Y, Bork P

Analytical biochemistry 1998

doi:10.1006/abio.1998.2876.

Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase

Eisenhaber B, Bork P, Eisenhaber F

Protein engineering 1998

doi:10.1093/protein/11.12.1155.

Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues

Willeke F, Ridder R, Bork P, Klaes R, Mechtersheimer G, Schwarzbach M, Zimmer D, Kloor M, Lehnert T, Herfarth C, von Knebel Doeberitz M

Molecular carcinogenesis 1998

doi:10.1002/(sici)1098-2744(199812)23:4<195::aid-mc1>3.3.co;2-7.

Predicting function: from genes to genomes and back

Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y

Journal of molecular biology 1998

doi:10.1006/jmbi.1998.2144.

Conservation of gene order: a fingerprint of proteins that physically interact

Dandekar T, Snel B, Huynen M, Bork P

Trends in biochemical sciences 1998

doi:10.1016/s0968-0004(98)01274-2.

Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC

Morett E, Bork P

FEBS letters 1998

doi:10.1016/s0014-5793(98)00888-6.

Homology-based fold predictions for Mycoplasma genitalium proteins

Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P

Journal of molecular biology 1998

doi:10.1006/jmbi.1998.1884.

Protein annotation: detective work for function prediction

Doerks T, Bairoch A, Bork P

Trends in genetics : TIG 1998

doi:10.1016/s0168-9525(98)01486-3.

Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries

Kharrat A, Millevoi S, Baraldi E, Ponting CP, Bork P, Pastore A

Biochimica et biophysica acta 1998

doi:10.1016/s0167-4838(98)00041-7.

AUTOMATED PAIR-WISE COMPARISONS OF MICROBIAL GENOMES

Bansal A , Bork P, Stuckey P

1998

doi:.

Measuring genome evolution

Huynen MA, Bork P

Proceedings of the National Academy of Sciences of the United States of America 1998

doi:10.1073/pnas.95.11.5849.

SMART, a simple modular architecture research tool: identification of signaling domains

Schultz J, Milpetz F, Bork P, Ponting CP

Proceedings of the National Academy of Sciences of the United States of America 1998

doi:10.1073/pnas.95.11.5857.

Predicting functions from protein sequences--where are the bottlenecks?

Bork P, Koonin EV

Nature genetics 1998

doi:10.1038/ng0498-313.

Wanted: subcellular localization of proteins based on sequence

Eisenhaber F, Bork P

Trends in cell biology 1998

doi:10.1016/s0962-8924(98)01226-4.

Differential genome analysis applied to the species-specific features of Helicobacter pylori

Huynen M, Dandekar T, Bork P

FEBS letters 1998

doi:10.1016/s0014-5793(98)00276-2.

Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins

Beckmann G, Hanke J, Bork P, Reich JG

Journal of molecular biology 1998

doi:10.1006/jmbi.1997.1510.

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases

Bork P, Dandekar T, Eisenhaber F, Huynen M

Journal of molecular medicine (Berlin, Germany) 1998

doi:10.1007/s001090050194.

Sequences and topology - Deriving biological knowledge from genomic sequences

Bork P, Eisenberg D

Current opinion in structural biology 1998

doi:10.1016/S0959-440X(98)80066-3.

Frame: detection of genomic sequencing errors

Brown NP, Sander C, Bork P

Bioinformatics (Oxford, England) 1998

doi:10.1093/bioinformatics/14.4.367.

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches

Dandekar T, Beyer K, Bork P, Kenealy MR, Pantopoulos K, Hentze M, Sonntag-Buck V, Flouriot G, Gannon F, Schreiber S

Bioinformatics (Oxford, England) 1998

doi:10.1093/bioinformatics/14.3.271.

Elementary modes analysis illustrated with human red cell metabolism

Schuster S, Fell DA, Pfeiffer T, Dandekar T, Bork, P

1998

doi:.

Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis

Schwirzke M, Gnirke A, Bork P, Tarin D, Weidle UH

Anticancer research 1998

doi:.

Towards detection of orthologues in sequence databases

Yuan YP, Eulenstein O, Vingron M, Bork P

Bioinformatics (Oxford, England) 1998

doi:10.1093/bioinformatics/14.3.285.

The Sequence Alerting Server--a new WEB server

Hegyi H, Lai JM, Bork P

Computer applications in the biosciences : CABIOS 1997

doi:.

A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases

Morozov V, Mushegian AR, Koonin EV, Bork P

Trends in biochemical sciences 1997

doi:10.1016/s0968-0004(97)01128-6.

Genome maps 8. Building gene families. Wall chart

Green EA, Pietrokovski S, Henikoff S, Bork P, Attwood T, Hood L, Bairoch A

Science (New York, N.Y.) 1997

doi:10.1126/science.278.5338.615.

Gene families: the taxonomy of protein paralogs and chimeras

Henikoff S, Greene EA, Pietrokovski S, Bork P, Attwood TK, Hood L

Science (New York, N.Y.) 1997

doi:10.1126/science.278.5338.609.

Differential genome display

Huynen MA, Diaz-Lazcoz Y, Bork P

Trends in genetics : TIG 1997

doi:10.1016/s0168-9525(97)01255-9.

Cytoplasmic signalling domains: the next generation

Bork P, Schultz J, Ponting CP

Trends in biochemical sciences 1997

doi:10.1016/s0968-0004(97)01084-0.

A novel class of RanGTP binding proteins

Görlich D, Dabrowski M, Bischoff FR, Kutay U, Bork P, Hartmann E, Prehn S, Izaurralde E

The Journal of cell biology 1997

doi:10.1083/jcb.138.1.65.

On the classification and evolution of protein modules

Hegyi H, Bork P

Journal of protein chemistry 1997

doi:10.1023/a:1026382032119.

The breast cancer gene product TSG101: a regulator of ubiquitination?

Ponting CP, Cai YD, Bork P

Journal of molecular medicine (Berlin, Germany) 1997

doi:.

SPRY domains in ryanodine receptors (Ca(2+)-release channels)

Ponting C, Schultz J, Bork P

Trends in biochemical sciences 1997

doi:10.1016/s0968-0004(97)01049-9.

Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs

Mushegian AR, Bassett DE Jr, Boguski MS, Bork P, Koonin EV

Proceedings of the National Academy of Sciences of the United States of America 1997

doi:10.1073/pnas.94.11.5831.

Bioinformatics and molecular medicine--introduction and call for papers

Bork P

Journal of molecular medicine (Berlin, Germany) 1997

doi:.

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins

Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1997

doi:.

SAM as a protein interaction domain involved in developmental regulation

Schultz J, Ponting CP, Hofmann K, Bork P

Protein science : a publication of the Protein Society 1997

doi:10.1002/pro.5560060128.

Secreted fringe-like signaling molecules may be glycosyltransferases

Yuan YP, Schultz J, Mlodzik M, Bork P

Cell 1997

doi:10.1016/s0092-8674(00)81852-8.

Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction

Gibson TJ, Koonin EV, Musco G, Pastore A, Bork P

Trends in neurosciences 1996

doi:10.1016/s0166-2236(96)20054-2.

Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome

Nagle DL, Karim MA, Woolf EA, Holmgren L, Bork P, Misumi DJ, McGrail SH, Dussault BJ Jr, Perou CM, Boissy RE, Duyk GM, Spritz RA, Moore KJ

Nature genetics 1996

doi:10.1038/ng1196-307.

Go hunting in sequence databases but watch out for the traps

Bork P, Bairoch A

Trends in genetics : TIG 1996

doi:10.1016/0168-9525(96)60040-7.

On the classification of modular proteins

Henrissat B, Bork P

Protein engineering 1996

doi:10.1093/protein/9.9.725.

Non-orthologous gene displacement

Koonin EV, Mushegian AR, Bork P

Trends in genetics : TIG 1996

doi:10.1016/0168-9525(96)20010-1.

Comparison of CD45 extracellular domain sequences from divergent vertebrate species suggests the conservation of three fibronectin type III domains

Okumura M, Matthews RJ, Robb B, Litman GW, Bork P, Thomas ML

Journal of immunology (Baltimore, Md. : 1950) 1996

doi:.

The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues

Bork P, Brown NP, Hegyi H, Schultz J

Protein science : a publication of the Protein Society 1996

doi:10.1002/pro.5560050720.

BRCA1 protein products ... Functional motifs..

Koonin EV, Altschul SF, Bork P

Nature genetics 1996

doi:10.1038/ng0796-266.

Pleckstrin's repeat performance: a novel domain in G-protein signaling?

Ponting CP, Bork P

Trends in biochemical sciences 1996

doi:10.1016/0968-0004(96)30027-3.

Protein sequence motifs

Bork P, Koonin EV

Current opinion in structural biology 1996

doi:10.1016/s0959-440x(96)80057-1.

Internal repeats in the BRCA2 protein sequence

Bork P, Blomberg N, Nilges M

Nature genetics 1996

doi:10.1038/ng0596-22.

Structure and distribution of modules in extracellular proteins

Bork P, Downing AK, Kieffer B, Campbell ID

Quarterly reviews of biophysics 1996

doi:10.1017/s0033583500005783.

Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes

Koonin EV, Bork P

Trends in biochemical sciences 1996

doi:10.1016/0968-0004(96)30007-8.

Sperm-egg binding protein or proto-oncogene?

Bork P

Science (New York, N.Y.) 1996

doi:10.1126/science.271.5254.1431.

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV

Current biology : CB 1996

doi:10.1016/s0960-9822(02)00478-5.

Applying motif and profile searches

Bork P, Gibson TJ

Methods in enzymology 1996

doi:10.1016/s0076-6879(96)66013-3.

Self-organizing hierarchic networks for pattern recognition in protein sequence

Hanke J, Beckmann G, Bork P, Reich JG

Protein science : a publication of the Protein Society 1996

doi:10.1002/pro.5560050109.

Structural motifs of the PKD1 protein

Löhning C, Pohlschmidt M, Glücksmann-Kuis MA, Duyk G, Bork P, Schneider MO, Reeders ST, Frischauf AM

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 1996

doi:.

Identification of residues within the SHC phosphotyrosine binding/phosphotyrosine interaction domain crucial for phosphopeptide interaction

Yajnik V, Blaikie P, Bork P, Margolis B

The Journal of biological chemistry 1996

doi:10.1074/jbc.271.4.1813.

New protein functions in yeast chromosome VIII

Ouzounis C, Bork P, Casari G, Sander C

Protein science : a publication of the Protein Society 1995

doi:10.1002/pro.5560041121.

HEAT repeats in the Huntington's disease protein

Andrade MA, Bork P

Nature genetics 1995

doi:10.1038/ng1095-115.

Challenging times for bioinformatics

Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C

Nature 1995

doi:10.1038/376647a0.

Characterization of a novel protein-binding module--the WW domain

Sudol M, Chen HI, Bougeret C, Einbond A, Bork P

FEBS letters 1995

doi:10.1016/0014-5793(95)00550-s.

The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction

Bork P, Holm L, Koonin EV, Sander C

Proteins 1995

doi:10.1002/prot.340220306.

The SEA module: a new extracellular domain associated with O-glycosylation

Bork P, Patthy L

Protein science : a publication of the Protein Society 1995

doi:10.1002/pro.5560040716.

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology

Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM

Molecular microbiology 1995

doi:10.1111/j.1365-2958.1995.tb02321.x.

Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain

Sudol M, Bork P, Einbond A, Kastury K, Druck T, Negrini M, Huebner K, Lehman D

The Journal of biological chemistry 1995

doi:10.1074/jbc.270.24.14733.

A phosphotyrosine interaction domain

Bork P, Margolis B

Cell 1995

doi:10.1016/0092-8674(95)90347-x.

Ready for a motif submission? A proposed checklist

Bork P, Ouzounis C, McEntyre J

Trends in biochemical sciences 1995

doi:10.1016/s0968-0004(00)88974-4.

Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search

Bork P, Gellerich J, Groth H, Hooft R, Martin F

Protein science : a publication of the Protein Society 1995

doi:10.1002/pro.5560040213.

A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity

Bork P, Koonin EV

Proteins 1994

doi:10.1002/prot.340200407.

Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure

Meitinger T, Meindl A, Bork P, Rost B, Sander C, Haasemann M, Murken J

Nature genetics 1993

doi:10.1038/ng1293-376.

Prokaryotic members of a new family of putative helicases with similarity to transcription activator SNF2

Kolstø AB, Bork P, Kvaløy K, Lindback T, Grønstadt A, Kristensen T, Sander C

Journal of molecular biology 1993

doi:10.1006/jmbi.1993.1185.

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III

Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E

Protein science : a publication of the Protein Society 1992

doi:10.1002/pro.5560011216.

Cloning of a gene from Bacillus cereus with homology to the mreB gene from Escherichia coli

Narahara A, Naterstad K, Kristensen T, Lopez R, Bork P, Kolstø AB

Gene 1992

doi:10.1016/0378-1119(92)90047-s.

Proposed acquisition of an animal protein domain by bacteria

Bork P, Doolittle RF

Proceedings of the National Academy of Sciences of the United States of America 1992

doi:10.1073/pnas.89.19.8990.

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins

Bork P, Sander C, Valencia A

Proceedings of the National Academy of Sciences of the United States of America 1992

doi:10.1073/pnas.89.16.7290.

The modular architecture of vertebrate collagens

Bork P

FEBS letters 1992

doi:10.1016/0014-5793(92)80900-2.

What's in a genome?

Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E

Nature 1992

doi:10.1038/358287a0.

A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor

Bork P, Sander C

FEBS letters 1992

doi:10.1016/0014-5793(92)80853-9.

A module of the DnaJ heat shock proteins found in malaria parasites

Bork P, Sander C, Valencia A, Bukau B

Trends in biochemical sciences 1992

doi:10.1016/0968-0004(92)90319-5.

More von Willebrand factor type A domains? Sequence similarities with malaria thrombospondin-related anonymous protein, dihydropyridine-sensitive calcium channel and inter-alpha-trypsin inhibitor

Bork P, Rohde K

The Biochemical journal 1991

doi:10.1042/bj2790908.

On alpha-helices terminated by glycine. 2. Recognition by sequence patterns

Bork P, Preissner R

Biochemical and biophysical research communications 1991

doi:10.1016/s0006-291x(05)81117-9.

On alpha-helices terminated by glycine. 1. Identification of common structural features

Preissner R, Bork P

Biochemical and biophysical research communications 1991

doi:10.1016/s0006-291x(05)81116-7.

Shuffled domains in extracellular proteins

Bork P

FEBS letters 1991

doi:10.1016/0014-5793(91)80937-x.

Complement components C1r/C1s, bone morphogenic protein 1 and Xenopus laevis developmentally regulated protein UVS.2 share common repeats

Bork P

FEBS letters 1991

doi:10.1016/0014-5793(91)80433-4.

Sequence similarities between tryptophan synthase beta subunit and other pyridoxal-phosphate-dependent enzymes

Bork P, Rohde K

Biochemical and biophysical research communications 1990

doi:10.1016/0006-291x(90)90830-g.

Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach

Bork P, Grunwald C

European journal of biochemistry / FEBS 1990

doi:10.1111/j.1432-1033.1990.tb19129.x.

Recognition of functional regions in primary structures using a set of property patterns

Bork P

FEBS letters 1989

doi:10.1016/0014-5793(89)81818-6.


Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.

Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P

PloS one 2021

doi:10.1371/journal.pone.0254429.

eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale.

Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J

Molecular biology and evolution 2021

doi:10.1093/molbev/msab293.

Correction to 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets'.

Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2021

doi:10.1093/nar/gkab835.

Protein intake, metabolic status and the gut microbiota in different ethnicities: results from two independent cohorts.

Bel Lassen P, Attaye I, Adriouch S, Nicolaou M, Aron-Wisnewsky J, Nielsen T, Chakaroun R, Le Chatelier E, Forslund S, Belda E, Bork P, Bäckhed F, Stumvoll M, Pedersen O, Herrema H, Groen AK, Pinto-Sietsma SJ, Zwinderman AH, Nieuwdorp M, Clement K, On Behalf Of Metacardis Consortium

Nutrients 2021

doi:10.3390/nu13093159.

Bioaccumulation of therapeutic drugs by human gut bacteria.

Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature 2021

doi:10.1038/s41586-021-03891-8.

Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a Lynch syndrome mouse model.

Gebert J, Gelincik O, Oezcan-Wahlbrink M, Marshall JD, Hernandez-Sanchez A, Urban K, Long M, Cortes E, Tosti E, Katzenmaier EM, Song Y, Elsaadi A, Deng N, Vilar E, Fuchs V, Nelius N, Yuan, Ahadova A, Sei S, Shoemaker RH, Umar A, Wei L, Liu S, Bork P, Edelmann W, von Knebel Doeberitz M, Lipkin SM, Kloor M

Gastroenterology 2021

doi:10.1053/j.gastro.2021.06.073.

GUNC: detection of chimerism and contamination in prokaryotic genomes.

Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, Schmidt TSB, Bork P

Genome biology 2021

doi:10.1186/s13059-021-02393-0.

Dispersal strategies shape persistence and evolution of human gut bacteria.

Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P

Cell host & microbe 2021

doi:10.1016/j.chom.2021.05.008.

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.

Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM

Communications biology 2021

doi:10.1038/s42003-021-02112-2.

Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.

Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Olanipekun M, Hoyles L, Djouadi F, Neves AL, Rodriguez-Martinez A, Mouawad GI, Pons N, Forslund S, Le-Chatelier E, Le Lay A, Nicholson J, Hansen T, Hyötyläinen T, Clément K, Oresic M, Bork P, Ehrlich SD, Raes J, Pedersen OB, Gauguier D, Dumas ME

Gut 2021

doi:10.1136/gutjnl-2020-323314.

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.

Letunic I, Bork P

Nucleic acids research 2021

doi:10.1093/nar/gkab301.

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.

Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G

Genome biology 2021

doi:10.1186/s13059-021-02306-1.

A 12-genus bacterial signature identifies a group of severe autistic children with differential sensory behavior and brain structures.

Shi K, Zhang L, Yu J, Chen Z, Lai S, Zhao X, Li WG, Luo Q, Lin W, Feng J, Bork P, Zhao XM, Li F

Clinical and translational medicine 2021

doi:10.1002/ctm2.314.

The InterPro protein families and domains database: 20 years on.

Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD

Nucleic acids research 2020

doi:10.1093/nar/gkaa977.

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.

Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH

Nucleic acids research 2020

doi:10.1093/nar/gkaa884.

SMART: recent updates, new developments and status in 2020.

Letunic I, Khedkar S, Bork P

Nucleic acids research 2020

doi:10.1093/nar/gkaa937.

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.

Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2020

doi:10.1093/nar/gkaa1074.

Polarization of microbial communities between competitive and cooperative metabolism.

Machado D, Maistrenko OM, Andrejev S, Kim Y, Bork P, Patil KR, Patil KR

Nature ecology & evolution 2021

doi:10.1038/s41559-020-01353-4.

Author correction: imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.

Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F

Nature communications 2020

doi:10.1038/s41467-020-20412-9.

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.

Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisneswky J, Clément K, Bäckhed F

Nature communications 2020

doi:10.1038/s41467-020-19589-w.

Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure.

Trebicka J, Bork P, Krag A, Arumugam M

Nature reviews. Gastroenterology & hepatology 2020

doi:10.1038/s41575-020-00376-3.

Metagenomic assessment of the global distribution of bacteria and fungi.

Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F

Environmental microbiology 2020

doi:10.1111/1462-2920.15314.

(Phospho)proteomic profiling of microsatellite unstable CRC cells reveals alterations in nuclear signaling and cholesterol metabolism caused by frameshift mutation of NMD regulator UPF3A.

Michalak M, Katzenmaier EM, Roeckel N, Woerner SM, Fuchs V, Warnken U, Yuan YP, Bork P, Neu-Yilik G, Kulozik A, von Knebel Doeberitz M, Kloor M, Kopitz J, Gebert J

International journal of molecular sciences 2020

doi:10.3390/ijms21155234.

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.

Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, Bastard JP, Andreelli F, Galleron N, Coelho LP, Hulot JS, Hansen TH, Pedersen HK, Lewinter C, Rouault C, Quinquis B, Salem JE, Roume H, Touch S, Søndertoft NB, Dumas ME, Touch S, Gøtze JP, Hansen T, Ehrlich SD, Galan P, Letunic I, Nielsen J, Holst JJ, Køber L, Vestergaard H, Zucker JD, Oppert JM, Stumvoll M, Bäckhed F, Clément K, Bork P, Pedersen O, Raes J

Nature 2020

doi:10.1038/s41586-020-2269-x.

Diversity within species: interpreting strains in microbiomes.

Van Rossum T, Ferretti P, Maistrenko OM, Bork P

Nature reviews. Microbiology 2020

doi:10.1038/s41579-020-0368-1.

Tara Oceans: towards global ocean ecosystems biology.

Sunagawa S, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C

Nature reviews. Microbiology 2020

doi:10.1038/s41579-020-0364-5.

Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.

Bahram M, Netherway T, Hildebrand F, Pritsch K, Drenkhan R, Loit K, Anslan S, Bork P, Tedersoo L

The New phytologist 2020

doi:10.1111/nph.16598.

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.

Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P

The ISME journal 2020

doi:10.1038/s41396-020-0600-z.

Dissecting the collateral damage of antibiotics on gut microbes.

Maier L, Goemans CV, Pruteanu M, Wirbel J, Kuhn M, Cacace E, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KP, Zeller G, Bork P, Typas A

2020

doi:10.1101/2020.01.09.893560.

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.

Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P

Nucleic acids research 2019

doi:10.1093/nar/gkz1002.

Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells.

Poisa-Beiro L, Thoma J, Landry J, Sauer S, Yamamoto A, Eckstein V, Romanov N, Raffel S, Hoffmann GF, Bork P, Benes V, Gavin AC, Tanaka M, Ho AD

2020

doi:10.1038/s41598-020-68396-2.

Efficacy of Bifidobacterium longum, B. infantis and Lactobacillus acidophilus probiotics to prevent gut dysbiosis in preterm infants of 28+0–32+6 weeks of gestation: a randomised, placebo-controlled, double-blind, multicentre trial: the PRIMAL Clinical Study protocol.

Marißen J, Haiß A, Meyer C, Van Rossum T, Bünte LM, Frommhold D, Gille C, Goedicke-Fritz S, Göpel W, Hudalla H, Pagel J, Pirr S, Siller B, Viemann D, Vens M, Herting E, König I, Gehring S, Zemlin M, Henneke P, Bork P, Härtel C, Härtel C

BMJ open 2019

doi:10.1136/bmjopen-2019-032617.

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.

Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Sánchez P, Roux S, Zayed AA, Uehara H, Carmichael M, Zeller G, Ferland J, Dimier C, Picheral M, Kandels S, Poulain J, Pisarev S, Acinas SG, Poulain J, Bork P, Babin M, Guidi L, Hingamp P, Bowler C, de Vargas C, Karsenti E, Ogata H, Iudicone D, Karp-Boss L, Sullivan MB, Wincker P, Pesant S, Speich S, Sunagawa S

Cell 2019

doi:10.1016/j.cell.2019.10.014.

Quantitative proteome landscape of the NCI-60 cancer cell lines.

Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Iskar M, Ori A, Bi R, Gillet L, Zhang H, Zhang J, Zhong Q, Yu C, Schmitt U, Varma S, Zhang Q, Qiu P, Wild PJ, Zhu Y, Bork P, Garnett MJ, Saez-Rodriguez J, Elloumi F, Beck M, Liu K, Pommier Y, Aebersold R, Reinhold WC, Sander C

iScience 2019

doi:10.1016/j.isci.2019.10.059.

Author correction: metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, , Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N

Nature medicine 2019

doi:10.1038/s41591-019-0663-4.

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.

Li Y, Kuhn M, Gavin AC, Bork P

Bioinformatics (Oxford, England) 2019

doi:10.1093/bioinformatics/btz736.

Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome.

Hickl O, Heintz-Buschart A, Trautwein-Schult A, Hercog R, Bork P, Wilmes P, Becher D

Microorganisms 2019

doi:10.3390/microorganisms7090367.

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology.

Hildebrand F, Pallen MJ, Bork P

Gut 2019

doi:10.1136/gutjnl-2019-319045.

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P

Microbiome 2019

doi:10.1186/s40168-019-0684-8.

Ice-age climate adaptations trap the alpine marmot in a state of low genetic diversity.

Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Griffin JL, Zelezniak A, Allaine D, Bork P, Welch JJ, Cohas A, Ralser M, Timmermann B

Current biology : CB 2019

doi:10.1016/j.cub.2019.04.020.

Consent insufficient for data release–Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Munoz AR, Roberts RJ, Rossello-Mora R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I, Xenarios I, Whitman WB

SCIENCE 2019

doi:10.1126/science.aax7509.

Disentangling genetic and environmental effects on the proteotypes of individuals.

Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P

Cell 2019

doi:10.1016/j.cell.2019.03.015.

Marine DNA viral macro- and microdiversity from pole to pole.

Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Pesant S, Marec C, Pisarev S, Picheral M, Tremblay JÉ, Poulain J, Vik D, Vik D, Bowler C, Babin M, de Vargas C, Culley AI, Iudicone D, Dutilh BE, Roux S, Karp-Boss L, Sullivan MB, Sunagawa S, Wincker P

Cell 2019

doi:10.1016/j.cell.2019.03.040.

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.

Letunic I, Bork P

Nucleic acids research 2019

doi:10.1093/nar/gkz239.

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, , Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N

Nature medicine 2019

doi:10.1038/s41591-019-0405-7.

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.

Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G

Nature medicine 2019

doi:10.1038/s41591-019-0406-6.

Microbial abundance, activity and population genomic profiling with mOTUs2.

Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S

Nature communications 2019

doi:10.1038/s41467-019-08844-4.

Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Caputi L, Carradec Q, Eveillard D, Kirilovsky A, Pelletier E, Karlusich JJP, Vieira FRJ, Villar E, Chaffron S, Malviya S, Scalco E, Acinas SG, Alberti A, Aury JM, Benoiston AS, Bertrand A, Biard T, Bittner L, Boccara M, Brum JR, Brunet C, Busseni G, Carratala A, Claustre H, Coelho LP, Colin S, D'Aniello S, Da Silva C, Del Core M, Dore H, Gasparini S, Kokoszka F, Jamet JL, Lejeusne C, Lepoivre C, Lescot M, Lima-Mendez G, Lombard F, Lukes J, Maillet N, Madoui MA, Martinez E, Mazzocchi MG, Neou MB, Paz-Yepes J, Poulain J, Ramondenc S, Romagnan JB, Roux S, Manta DS, Sanges R, Speich S, Sprovieri M, Sunagawa S, Taillandier V, Tanaka A, Tirichine L, Trottier C, Uitz J, Veluchamy A, Vesela J, Vincent F, Yau S, Kandels-Lewis S, Searson S, Dimier C, Picheral M, Bork P, Boss E, De Vargas C, Follows MJ, Grimsley N, Guidi L, Hingamp P, Karsenti E, Sordino P, Stemmann L, Sullivan MB, Tagliabue A, Zingone A, Garczarek L, d'Ortenzio F, Testor P, Not F, d'Alcala MR, Wincker P, Bowler C, Iudicone D, Gorsky G, Jaillon O, Karp-Boss L, Krzic U, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Velayoudon D, Weissenbach J, Weissenbach J, Sieracki M, Velayoudon D

Global Biogeochemical Cycles 2019

doi:10.1029/2018GB006022.

Extensive transmission of microbes along the gastrointestinal tract.

Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P

eLife 2019

doi:10.7554/eLife.42693.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Munoz AR, Roberts RJ, Rossello-Mora R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I, Xenarios I, Whitman WB

Science (New York, N.Y.) 2019

doi:10.1126/science.aaw1280.

Antibiotics-induced monodominance of a novel gut bacterial order.

Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Huerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Belzer C, Aalvink S, Sunagawa S, Forslund SK, Merten C, Hentschel U, Benes V, Patil KR, Bork P

Gut 2019

doi:10.1136/gutjnl-2018-317715.

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2018

doi:10.1093/nar/gky1085.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Madeira F, Luciani A, Mi H, Marchler-Bauer A, Necci M, Natale DA, Orengo C, Nuka G, Paysan-Lafosse T, Pandurangan AP, Potter SC, Pesseat S, Rawlings ND, Qureshi MA, Richardson LJ, Redaschi N, Sangrador-Vegas A, Sigrist CJA, Rivoire C, Salazar GA, Thanki N, Thomas PD, Sillitoe I, Sutton GG, Tosatto SCE, Yong SY, Finn RD

Nucleic acids research 2018

doi:10.1093/nar/gky1100.

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2018

doi:10.1093/nar/gky1131.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Daly RA, Cochrane GR, Duhaime MB, Desnues C, Enault F, Emerson JB, Hingamp P, Fuhrman JA, Hurwitz BL, Hugenholtz P, Labonté JM, Ivanova NN, Malmstrom RR, Lee KB, Mizrachi IK, Martinez-Garcia M, Petit MA, Putonti C, Ogata H, Páez-Espino D, Rodriguez-Valera F, Rosario K, Rattei T, Reyes A, Steward GF, Sullivan MB, Schriml L, Schulz F, Temperton B, Tringe SG, Sunagawa S, Suttle CA, Wilhelm SW, Whiteson KL, Webster NS, Thurber RV, Yilmaz P, Wrighton KC, Woyke T, Wommack KE, Allen LZ, Yutin N, Young MJ, Yoshida T, Eloe-Fadrosh EA, Kyrpides NC

Nature biotechnology 2018

doi:10.1038/nbt.4306.

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes.

Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, Moebus S, Bork P, Fischer S, Herms S, Aretz S, Hoffmann P, Steinke-Lange V

International journal of cancer 2018

doi:10.1002/ijc.31725.

Recovery of gut microbiota of healthy adults following antibiotic exposure.

Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen HB, Nielsen MF, Wang J, Bork P, Hansen T, Vilsbøll T, Arumugam M, Knop FK, Pedersen O

Nature microbiology 2018

doi:10.1038/s41564-018-0257-9.

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.

Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB

Nature protocols 2018

doi:10.1038/s41596-018-0064-z.

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.

Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Aloy P, Bork P, Gavin AC, Ho AD

Nature communications 2018

doi:10.1038/s41467-018-06353-4.

Das Darmmikrobiom bei der Parkinson-Krankheit.

Bedarf JR, Hildebrand F, Goeser F, Bork P, Wüllner U

Der Nervenarzt 2018

doi:10.1007/s00115-018-0601-6.

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.

Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J

Gut 2018

doi:10.1136/gutjnl-2018-316106.

Structure and function of the global topsoil microbiome.

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Põlme S, Pent M, Ryberg M, Sunagawa S, Tedersoo L, Bork P

Nature 2018

doi:10.1038/s41586-018-0386-6.

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.

Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L

Environmental microbiology reports 2018

doi:10.1111/1758-2229.12684.

Metagenomic analysis of gut microbial communities from a Central Asian population.

Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P

BMJ open 2018

doi:10.1136/bmjopen-2018-021682.

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Cologna M, Clementi R, Cusumano G, Crifò T, Innamorati C, Gottardi S, Postai D, Masè C, Duranti S, Savoi D, Mancabelli L, Lugli GA, Ferrario C, Turroni F, Mangifesta M, Milani C, Yassour M, Vlamakis H, Anzalone R, Viappiani A, Koren O, Tateo S, Xavier R, Collado CM, Ventura M, Huttenhower C, Soffiati M, Pedrotti A, Bork P, Segata N

Cell host & microbe 2018

doi:10.1016/j.chom.2018.06.005.

Species-specific activity of antibacterial drug combinations.

Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Bork P, Savitski MM, Göttig S, Typas A

Nature 2018

doi:10.1038/s41586-018-0278-9.

iPath3.0: interactive pathways explorer v3.

Darzi Y, Letunic I, Bork P, Yamada T

Nucleic acids research 2018

doi:10.1093/nar/gky299.

Quantifying compartment-associated variations of protein abundance in proteomics data.

Parca L, Beck M, Bork P, Ori A

Molecular systems biology 2018

doi:10.15252/msb.20178131.

Pervasive protein thermal stability variation during the cell cycle.

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM

Cell 2018

doi:10.1016/j.cell.2018.03.053.

The gut microbiome is associated with behavioural task in honey bees.

Jones JC, Fruciano C, Marchant J, Hildebrand F, Forslund S, Bork P, Engel P, Hughes WOH

Insectes sociaux 2018

doi:10.1007/s00040-018-0624-9.

Selective maternal seeding and environment shape the human gut microbiome.

Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P

Genome research 2018

doi:10.1101/gr.233940.117.

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR

Nature microbiology 2018

doi:10.1038/s41564-018-0123-9.

Similarity of the dog and human gut microbiomes in gene content and response to diet.

Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P

Microbiome 2018

doi:10.1186/s40168-018-0450-3.

Extensive impact of non-antibiotic drugs on human gut bacteria.

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A

Nature 2018

doi:10.1038/nature25979.

Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.

Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O

Cell 2018

doi:10.1016/j.cell.2018.02.032.

The Human Gut Microbiome: From Association to Modulation.

Schmidt TSB, Raes J, Bork P

Cell 2018

doi:10.1016/j.cell.2018.02.044.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Birren B, Malmstrom RR, Bork P, Podar M, Garrity GM, Weinstock GM, Yooseph S, Dodsworth JA, Glöckner FO, Sutton G, Nelson WC, Gilbert JA, Jungbluth SP, Hallam SJ, Tighe S, Ettema TJG, Baker BJ, Rattei T, Konstantinidis KT, Liu WT, McMahon KD, Fierer N, Eisen JA, Hedlund B, Cochrane G, Karsch-Mizrachi I, Knight R, Finn R, Rinke C, Lapidus A, Tyson GW, Rinke C, Eren AM, Parks DH, Yilmaz P, Meyer F, Woyke T, Hugenholtz P, Banfield JF, Schriml L

Nature biotechnology 2018

doi:10.1038/nbt0218-196a.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P

Nature microbiology 2018

doi:10.1038/s41564-018-0114-x.

Gut microbiota composition is associated with environmental landscape in honey bees.

Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO

Ecology and evolution 2017

doi:10.1002/ece3.3597.

A global ocean atlas of eukaryotic genes.

Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Searson S, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P

Nature communications 2018

doi:10.1038/s41467-017-02342-1.

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.

Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Searson S, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P

Nature communications 2018

doi:10.1038/s41467-017-02235-3.

MVP: a microbe-phage interaction database.

Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH

Nucleic acids research 2017

doi:10.1093/nar/gkx1124.

20 years of the SMART protein domain annotation resource.

Letunic I, Bork P

Nucleic acids research 2017

doi:10.1093/nar/gkx922.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P

Nature microbiology 2017

doi:10.1038/s41564-017-0072-8.

Subspecies in the global human gut microbiome.

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P

Molecular systems biology 2017

doi:10.15252/msb.20177589.

Salt-responsive gut commensal modulates TH17 axis and disease.

Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN

Nature 2017

doi:10.1038/nature24628.

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.

Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC

Scientific reports 2017

doi:10.1038/s41598-017-16353-x.

Towards standards for human fecal sample processing in metagenomic studies.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P

Nature biotechnology 2017

doi:10.1038/nbt.3960.

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.

Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C

eLife 2017

doi:10.7554/eLife.26066.

RTK: efficient rarefaction analysis of large datasets.

Saary P, Forslund K, Bork P, Hildebrand F

Bioinformatics (Oxford, England) 2017

doi:10.1093/bioinformatics/btx206.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T

Nature biotechnology 2017

doi:10.1038/nbt.3893.

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.

Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P

Molecular biology and evolution 2017

doi:10.1093/molbev/msx148.

metaSNV: A tool for metagenomic strain level analysis.

Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P

PloS one 2017

doi:10.1371/journal.pone.0182392.

Capturing protein communities by structural proteomics in a thermophilic eukaryote.

Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC

Molecular systems biology 2017

doi:10.15252/msb.20167412.

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U

Genome medicine 2017

doi:10.1186/s13073-017-0451-z.

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U

Genome medicine 2017

doi:10.1186/s13073-017-0428-y.

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition – a metagenomic analysis.

Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S

American journal of physiology. Gastrointestinal and liver physiology 2016

doi:10.1152/ajpgi.00293.2016.

Systematic identification of phosphorylation-mediated protein interaction switches.

Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB

PLoS computational biology 2017

doi:10.1371/journal.pcbi.1005462.

GEAR: A database of Genomic Elements Associated with drug Resistance.

Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM

Scientific reports 2017

doi:10.1038/srep44085.

Metabolic anchor reactions for robust biorefining.

Jouhten P, Huerta-Cepas J, Bork P, Patil KR

Metabolic engineering 2017

doi:10.1016/j.ymben.2017.02.010.

Bioinformatics Analysis of Functional Associations of PTMs.

Minguez P, Bork P

Methods in molecular biology (Clifton, N.J.) 2017

doi:10.1007/978-1-4939-6783-4_14.

[Microbial Biomarkers for Early Cancer Detection].

Voigt AY, Zeller G, Bork P

Deutsche medizinische Wochenschrift (1946) 2017

doi:10.1055/s-0042-110193.

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.

Chen WH, Lu G, Chen X, Zhao XM, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw1013.

InterPro in 2017-beyond protein family and domain annotations.

Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Yong SY, Mitchell AL

Nucleic acids research 2016

doi:10.1093/nar/gkw1107.

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw989.

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2016

doi:10.1093/nar/gkw937.

Global genetic capacity for mixotrophy in marine picocyanobacteria.

Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW

The ISME journal 2016

doi:10.1038/ismej.2016.64.

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.

Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R

The Journal of cell biology 2016

doi:10.1083/jcb.201601090.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Bork P, Acinas SG, Wincker P, Sullivan MB

NATURE 2016

doi:10.1038/nature19366.

CART – a chemical annotation retrieval toolkit.

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P

Bioinformatics (Oxford, England) 2016

doi:10.1093/bioinformatics/btw233.

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Dore J, Machado AMD, de Evgrafov MCR, Hansen T, Jorgensen T, Bork P, Guarner F, Pedersen O, Sommer MOA, Ehrlich SD, Sicheritz-Ponten T, Brunak S, Nielsen HB

Nature microbiology 2016

doi:10.1038/nmicrobiol.2016.152.

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P

Bioinformatics (Oxford, England) 2016

doi:10.1093/bioinformatics/btw183.

Human gut microbes impact host serum metabolome and insulin sensitivity.

Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K, Consortium M, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O

Nature 2016

doi:10.1038/nature18646.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Letunic I, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw290.

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.

Huerta-Cepas J, Serra F, Bork P

Molecular biology and evolution 2016

doi:10.1093/molbev/msw046.

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC

Nature protocols 2016

doi:10.1038/nprot.2016.059.

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R

PloS one 2016

doi:10.1371/journal.pone.0155362.

Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C

Nature methods 2016

doi:10.1038/nmeth.3830.

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P

Science (New York, N.Y.) 2016

doi:10.1126/science.aad8852.

Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Chen WH, Lu G, Bork P, Hu S, Lercher MJ

Nature communications 2016

doi:10.1038/ncomms11334.

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG

NATURE COMMUNICATIONS 2016

doi:10.1038/ncomms11071.

Spatiotemporal variation of mammalian protein complex stoichiometries.

Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M

Genome biology 2016

doi:10.1186/s13059-016-0912-5.

Gut Microbiota Linked to Sexual Preference and HIV Infection.

Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R

EBioMedicine 2016

doi:10.1016/j.ebiom.2016.01.032.

Bacterial antisense RNAs are mainly the product of transcriptional noise.

Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M

Science Advances 2016

doi:10.1126/sciadv.1501363.

Plankton networks driving carbon export in the oligotrophic ocean.

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans Consortium Coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G

Nature 2016

doi:10.1038/nature16942.

The exploration of network motifs as potential drug targets from post-translational regulatory networks.

Zhang XD, Song J, Bork P, Zhao XM

Scientific reports 2016

doi:10.1038/srep20558.

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM

Nature communications 2016

doi:10.1038/ncomms10410.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P

Nucleic acids research 2016

doi:10.1093/nar/gkw004.

The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex.

Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW

PloS one 2016

doi:10.1371/journal.pone.0146457.

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2015

doi:10.1093/nar/gkv1248.

The SIDER database of drugs and side effects.

Kuhn M, Letunic I, Jensen LJ, Bork P

Nucleic acids research 2015

doi:10.1093/nar/gkv1075.

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M

Nucleic acids research 2015

doi:10.1093/nar/gkv1277.

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Igor Costea P, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O

Nature 2015

doi:10.1038/nature15766.

Operon structure and cotranslational subunit association direct protein assembly in bacteria.

Shieh YW, Minguez P, Bork P, Auburger JJ, Guilbride DL, Kramer G, Bukau B

Science (New York, N.Y.) 2015

doi:10.1126/science.aac8171.

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.

Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M

2015

doi:10.1016/j.cels.2015.08.012.

In situ structural analysis of the human nuclear pore complex.

von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M

Nature 2015

doi:10.1038/nature15381.

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC

Cell reports 2015

doi:10.1016/j.celrep.2015.07.054.

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.

Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L

EBioMedicine 2015

doi:10.1016/j.ebiom.2015.07.007.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldon T

GENOME BIOLOGY AND EVOLUTION 2015

doi:10.1093/gbe/evv121.

Tara Oceans. Tara Oceans studies plankton at planetary scale. Introduction.

Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P

Science (New York, N.Y.) 2015

doi:10.1126/science.aac5605.

Computational eco-systems biology in Tara Oceans: translating data into knowledge.

Sunagawa S, Karsenti E, Bowler C, Bork P

Molecular systems biology 2015

doi:10.15252/msb.20156272.

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi.

Tedersoo L, Anslan S, Bahram M, Polme S, Riit T, Liiv I, Koljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K

MycoKeys 2015

doi:10.3897/mycokeys.10.4852.

Metabolic dependencies drive species co-occurrence in diverse microbial communities.

Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR

Proceedings of the National Academy of Sciences of the United States of America 2015

doi:10.1073/pnas.1421834112.

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Tara Oceans Coordinators, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB

Science (New York, N.Y.) 2015

doi:10.1126/science.1261498.

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E

Science (New York, N.Y.) 2015

doi:10.1126/science.1261605.

Ocean plankton. Determinants of community structure in the global plankton interactome.

Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J

Science (New York, N.Y.) 2015

doi:10.1126/science.1262073.

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).

Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M

Molecular & cellular proteomics : MCP 2015

doi:10.1074/mcp.m114.042499.

Ocean plankton. Structure and function of the global ocean microbiome.

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P

Science (New York, N.Y.) 2015

doi:10.1126/science.1261359.

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D

Science (New York, N.Y.) 2015

doi:10.1126/science.1261447.

Inter-individual differences in the gene content of human gut bacterial species.

Zhu A, Sunagawa S, Mende DR, Bork P

Genome biology 2015

doi:10.1186/s13059-015-0646-9.

Temporal and technical variability of human gut metagenomes.

Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P

Genome biology 2015

doi:10.1186/s13059-015-0639-8.

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

Betts MJ, Lu Q, Jiang Y, Drusko A, Wichmann O, Utz M, Valtierra-Gutiérrez IA, Schlesner M, Jaeger N, Jones DT, Pfister S, Lichter P, Eils R, Siebert R, Bork P, Apic G, Gavin AC, Russell RB

Nucleic acids research 2014

doi:10.1093/nar/gku1094.

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L

Molecular systems biology 2015

doi:10.15252/msb.20145558.

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P

Nucleic acids research 2014

doi:10.1093/nar/gku1081.

The InterPro protein families database: the classification resource after 15 years.

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD

Nucleic acids research 2014

doi:10.1093/nar/gku1243.

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2014

doi:10.1093/nar/gku1003.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P

Nucleic acids research 2014

doi:10.1093/nar/gku1147.

Potential of fecal microbiota for early-stage detection of colorectal cancer.

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P

Molecular systems biology 2014

doi:10.15252/msb.20145645.

Luminal signalling links cell communication to tissue architecture during organogenesis.

Durdu S, Iskar M, Revenu C, Schieber N, Kunze A, Bork P, Schwab Y, Gilmour D

Nature 2014

doi:10.1038/nature13852.

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P

PloS one 2014

doi:10.1371/journal.pone.0111122.

Correction: LotuS: an efficient and user-friendly OTU processing pipeline.

Hildebrand F, Tito RY, Voigt AY, Bork P, Raes J

Microbiome 2014

doi:10.1186/2049-2618-2-37.

LotuS: an efficient and user-friendly OTU processing pipeline.

Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J

Microbiome 2014

doi:10.1186/2049-2618-2-30.

Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors

Woerner SM, Tosti E, Yuan YP, Kloor M, Bork P, Edelmann W, Gebert J

Molecular carcinogenesis 2014

doi:10.1002/mc.22213.

An integrated catalog of reference genes in the human gut microbiome

Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD, Bork P, Wang J

Nature biotechnology 2014

doi:10.1038/nbt.2942.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD

Nature biotechnology 2014

doi:10.1038/nbt.2939.

Comments on "human dominant disease genes are enriched in paralogs originating from whole genome duplication"

Chen WH, Zhao XM, van Noort V, Bork P

PLoS computational biology 2014

doi:10.1371/journal.pcbi.1003758.

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene expression profiling

van Noort VV, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P

Cancer research 2014

doi:10.1158/0008-5472.CAN-13-3540.

Classification and quantification of bacteriophage taxa in human gut metagenomes

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P

The ISME journal 2014

doi:10.1038/ismej.2014.30.

Classification and quantification of bacteriophage taxa in human gut metagenomes.

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P

The ISME journal 2014

doi:10.1038/ismej.2014.66.

A fair comparison

Costea PI, Zeller G, Sunagawa S, Bork P

Nature methods 2014

doi:10.1038/nmeth.2897.

Metagenomic insights into the human gut resistome and the forces that shape it

Forslund K, Sunagawa S, Coelho LP, Bork P

BioEssays : news and reviews in molecular, cellular and developmental biology 2014

doi:10.1002/bies.201300143.

Enterotypes of the human gut microbiome (vol 473, pg 174, 2011)

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin JJ, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Weissenbach J, Ehrlich SD, Bork P

NATURE 2014

doi:10.1038/nature13075.

Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs

Gallina AM, Bork P, Bordo D

Journal of molecular recognition : JMR 2014

doi:10.1002/jmr.2332.

STITCH 4: integration of protein-chemical interactions with user data

Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P

Nucleic acids research 2013

doi:10.1093/nar/gkt1207.

eggNOG v4.0: nested orthology inference across 3686 organisms

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2013

doi:10.1093/nar/gkt1253.

A quantitative liposome microarray to systematically characterize protein-lipid interactions

Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin AC

Nature methods 2013

doi:10.1038/nmeth.2734.

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P

Nature methods 2013

doi:10.1038/nmeth.2693.

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H

The ISME journal 2013

doi:10.1038/ismej.2013.59.

Accurate and universal delineation of prokaryotic species

Mende DR, Sunagawa S, Zeller G, Bork P

Nature methods 2013

doi:10.1038/nmeth.2575.

Richness of human gut microbiome correlates with metabolic markers

Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O

Nature 2013

doi:10.1038/nature12506.

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG

Environmental microbiology 2013

doi:10.1111/1462-2920.12250.

Experimental characterization of the human non-sequence-specific nucleic acid interactome

Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J

Genome biology 2013

doi:10.1186/gb-2013-14-7-r81.

Country-specific antibiotic use practices impact the human gut resistome

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P

Genome research 2013

doi:10.1101/gr.155465.113.

The microbiome explored: recent insights and future challenges

Blaser M, Bork P, Fraser C, Knight R, Wang J

Nature reviews. Microbiology 2013

doi:10.1038/nrmicro2973.

Orthologous gene clusters and taxon signature genes for viruses of prokaryotes

Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV

Journal of bacteriology 2013

doi:10.1128/jb.01801-12.

Evolution and functional cross-talk of protein post-translational modifications

Beltrao P, Bork P, Krogan NJ, van Noort V

Molecular systems biology 2013

doi:10.1002/msb.201304521.

Human monogenic disease genes have frequently functionally redundant paralogs

Chen WH, Zhao XM, van Noort V, Bork P

PLoS computational biology 2013

doi:10.1371/journal.pcbi.1003073.

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ

Nucleic acids research 2013

doi:10.1093/nar/gks1094.

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P

Molecular systems biology 2013

doi:10.1038/msb.2013.20.

Systematic identification of proteins that elicit drug side effects

Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P

Molecular systems biology 2013

doi:10.1038/msb.2013.10.

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Minguez P, Letunic I, Parca L, Bork P

Nucleic acids research 2013

doi:10.1093/nar/gks1230.

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.

Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M

Molecular systems biology 2013

doi:10.1038/msb.2013.4.

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data

Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J

Bioinformatics (Oxford, England) 2013

doi:10.1093/bioinformatics/bts656.

Genomic variation landscape of the human gut microbiome

Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P

Nature 2013

doi:10.1038/nature11711.

Consistent mutational paths predict eukaryotic thermostability

van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P

BMC evolutionary biology 2013

doi:10.1186/1471-2148-13-7.

Role for urea in nitrification by polar marine Archaea

Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay JÉ, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedrós-Alió C, Bertilsson S

Proceedings of the National Academy of Sciences of the United States of America 2012

doi:10.1073/pnas.1201914109.

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

Iskar M, Zeller G, Zhao XM, van Noort V, Bork P

Current opinion in biotechnology 2012

doi:10.1016/j.copbio.2011.11.010.

Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age

Chen WH, Trachana K, Lercher MJ, Bork P

Molecular biology and evolution 2012

doi:10.1093/molbev/mss014.

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M

The ISME journal 2012

doi:10.1038/ismej.2011.212.

A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL

Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JW, Jauch A, Bartram CR, Reinhardt D, Koch KA, Bandapalli OR, Kulozik AE

British journal of haematology 2012

doi:10.1111/j.1365-2141.2012.09028.x.

OGEE: an online gene essentiality database

Chen WH, Minguez P, Lercher MJ, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr986.

The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). Introduction

Chen YP, Bork P

BMC genomics 2012

doi:10.1186/1471-2164-13-s1-i1.

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins

Doerks T, van Noort V, Minguez P, Bork P

PloS one 2012

doi:10.1371/journal.pone.0034302.

InterPro in 2011: new developments in the family and domain prediction database

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY

Nucleic acids research 2012

doi:10.1093/nar/gkr948.

STITCH 3: zooming in on protein-chemical interactions

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr1011.

MOCAT: a metagenomics assembly and gene prediction toolkit

Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P

PloS one 2012

doi:10.1371/journal.pone.0047656.

SMART 7: recent updates to the protein domain annotation resource

Letunic I, Doerks T, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr931.

Assessment of metagenomic assembly using simulated next generation sequencing data

Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P

PloS one 2012

doi:10.1371/journal.pone.0031386.

Deciphering a global network of functionally associated post-translational modifications

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P

Molecular systems biology 2012

doi:10.1038/msb.2012.31.

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P

Nucleic acids research 2012

doi:10.1093/nar/gkr1060.

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium

van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC

Molecular systems biology 2012

doi:10.1038/msb.2012.4.

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P

Molecular systems biology 2012

doi:10.1038/msb.2012.13.

Transcription start site associated RNAs in bacteria

Yus E, Güell M, Vivancos AP, Chen WH, Lluch-Senar M, Delgado J, Gavin AC, Bork P, Serrano L

Molecular systems biology 2012

doi:10.1038/msb.2012.16.

Identifying single copy orthologs in Metazoa

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P

PLoS computational biology 2011

doi:10.1371/journal.pcbi.1002269.

Prediction of drug combinations by integrating molecular and pharmacological data

Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P

PLoS computational biology 2011

doi:10.1371/journal.pcbi.1002323.

A holistic approach to marine eco-systems biology

Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P, Tara Oceans Consortium

PLoS biology 2011

doi:10.1371/journal.pbio.1001177.

Orthology prediction methods: a quality assessment using curated protein families

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P

BioEssays : news and reviews in molecular, cellular and developmental biology 2011

doi:10.1002/bies.201100062.

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile

Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E

Cell 2011

doi:10.1016/j.cell.2011.06.039.

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Letunic I, Bork P

Nucleic acids research 2011

doi:10.1093/nar/gkr201.

iPath2.0: interactive pathway explorer

Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P

Nucleic acids research 2011

doi:10.1093/nar/gkr313.

Enterotypes of the human gut microbiome

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P

Nature 2011

doi:10.1038/nature09944.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO

Nature biotechnology 2011

doi:10.1038/nbt.1823.

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

Raes J, Letunic I, Yamada T, Jensen LJ, Bork P

Molecular systems biology 2011

doi:10.1038/msb.2011.6.

The ecoresponsive genome of Daphnia pulex

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL

Science (New York, N.Y.) 2011

doi:10.1126/science.1197761.

Network neighbors of drug targets contribute to drug side-effect similarity

Brouwers L, Iskar M, Zeller G, van Noort V, Bork P

PloS one 2011

doi:10.1371/journal.pone.0022187.

Universally distributed single-copy genes indicate a constant rate of horizontal transfer

Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P

PloS one 2011

doi:10.1371/journal.pone.0022099.

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C

Nucleic acids research 2011

doi:10.1093/nar/gkq973.

SmashCommunity: a metagenomic annotation and analysis tool

Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P

Bioinformatics (Oxford, England) 2010

doi:10.1093/bioinformatics/btq536.

SmashCell: a software framework for the analysis of single-cell amplified genome sequences

Harrington ED, Arumugam M, Raes J, Bork P, Relman DA

Bioinformatics (Oxford, England) 2010

doi:10.1093/bioinformatics/btq564.

A network of conserved co-occurring motifs for the regulation of alternative splicing

Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkq705.

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae

Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC

Molecular systems biology 2010

doi:10.1038/msb.2010.87.

[Metagenomics of the intestinal microbiota: potential applications]

Dusko Ehrlich S, MetaHIT consortium

Gastroenterologie clinique et biologique 2010

doi:10.1016/s0399-8320(10)70017-8.

Ontologies in quantitative biology: a basis for comparison, integration, and discovery

Jensen LJ, Bork P

PLoS biology 2010

doi:10.1371/journal.pbio.1000374.

A method and server for predicting damaging missense mutations

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR

Nature methods 2010

doi:10.1038/nmeth0410-248.

A human gut microbial gene catalogue established by metagenomic sequencing

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J

Nature 2010

doi:10.1038/nature08821.

Evolution and regulation of cellular periodic processes: a role for paralogues

Trachana K, Jensen LJ, Bork P

EMBO reports 2010

doi:10.1038/embor.2010.9.

Ancient animal microRNAs and the evolution of tissue identity

Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D

Nature 2010

doi:10.1038/nature08744.

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM

Genome biology 2010

doi:10.1186/gb-2010-11-3-r24.

Drug-induced regulation of target expression

Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P

PLoS computational biology 2010

doi:10.1371/journal.pcbi.1000925.

A side effect resource to capture phenotypic effects of drugs

Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P

Molecular systems biology 2010

doi:10.1038/msb.2009.98.

STITCH 2: an interaction network database for small molecules and proteins

Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkp937.

AQUA: automated quality improvement for multiple sequence alignments

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P

Bioinformatics (Oxford, England) 2010

doi:10.1093/bioinformatics/btp651.

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkp951.

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA

Science (New York, N.Y.) 2010

doi:10.1126/science.1178028.

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology

Woerner SM, Yuan YP, Benner A, Korff S, von Knebel Doeberitz M, Bork P

Nucleic acids research 2010

doi:10.1093/nar/gkp839.

Transcriptome complexity in a genome-reduced bacterium

Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L

Science (New York, N.Y.) 2009

doi:10.1126/science.1176951.

Proteome organization in a genome-reduced bacterium

Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC

Science (New York, N.Y.) 2009

doi:10.1126/science.1176343.

Evolution of biomolecular networks: lessons from metabolic and protein interactions

Yamada T, Bork P

Nature reviews. Molecular cell biology 2009

doi:10.1038/nrm2787.

Impact of genome reduction on bacterial metabolism and its regulation

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L

Science (New York, N.Y.) 2009

doi:10.1126/science.1177263.

ASTD: The Alternative Splicing and Transcript Diversity database

Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D

Genomics 2009

doi:10.1016/j.ygeno.2008.11.003.

Quantifying environmental adaptation of metabolic pathways in metagenomics

Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB

Proceedings of the National Academy of Sciences of the United States of America 2009

doi:10.1073/pnas.0808022106.

InterPro: the integrative protein signature database

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C

Nucleic acids research 2009

doi:10.1093/nar/gkn785.

STRING 8–a global view on proteins and their functional interactions in 630 organisms

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C

Nucleic acids research 2009

doi:10.1093/nar/gkn760.

Sequence-based feature prediction and annotation of proteins

Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S

Genome biology 2009

doi:10.1186/gb-2009-10-2-206.

SMART 6: recent updates and new developments

Letunic I, Doerks T, Bork P

Nucleic acids research 2009

doi:10.1093/nar/gkn808.

Discovering functional novelty in metagenomes: examples from light-mediated processes

Singh AH, Doerks T, Letunic I, Raes J, Bork P

Journal of bacteriology 2009

doi:10.1128/jb.01084-08.

Biochemistry. Not comparable, but complementary

Jensen LJ, Bork P

Science (New York, N.Y.) 2008

doi:10.1126/science.1164801.

Sircah: a tool for the detection and visualization of alternative transcripts

Harrington ED, Bork P

Bioinformatics (Oxford, England) 2008

doi:10.1093/bioinformatics/btn361.

Molecular eco-systems biology: towards an understanding of community function

Raes J, Bork P

Nature reviews. Microbiology 2008

doi:10.1038/nrmicro1935.

Drug target identification using side-effect similarity

Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P

Science (New York, N.Y.) 2008

doi:10.1126/science.1158140.

KEGG Atlas mapping for global analysis of metabolic pathways

Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M

Nucleic acids research 2008

doi:10.1093/nar/gkn282.

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

Pincus D, Letunic I, Bork P, Lim WA

Proceedings of the National Academy of Sciences of the United States of America 2008

doi:10.1073/pnas.0803161105.

Predicting biological networks from genomic data

Harrington ED, Jensen LJ, Bork P

FEBS letters 2008

doi:10.1016/j.febslet.2008.02.033.

Large-scale prediction of drug-target relationships

Kuhn M, Campillos M, González P, Jensen LJ, Bork P

FEBS letters 2008

doi:10.1016/j.febslet.2008.02.024.

The genome of the model beetle and pest Tribolium castaneum

Tribolium Genome Sequencing Consortium, Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G

Nature 2008

doi:10.1038/nature06784.

Sequence and Structure of Proteins

Eisenhaber F, Bork P

1998

doi:DOI: 10.1002/9783527620869.

iPath: interactive exploration of biochemical pathways and networks

Letunic I, Yamada T, Kanehisa M, Bork P

Trends in biochemical sciences 2008

doi:10.1016/j.tibs.2008.01.001.

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D

Nature 2008

doi:10.1038/nature06617.

A computational screen for type I polyketide synthases in metagenomics shotgun data

Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P

PloS one 2008

doi:10.1371/journal.pone.0003515.

A nitrile hydratase in the eukaryote Monosiga brevicollis

Foerstner KU, Doerks T, Muller J, Raes J, Bork P

PloS one 2008

doi:10.1371/journal.pone.0003976.

SuperTarget and Matador: resources for exploring drug-target relationships

Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R

Nucleic acids research 2008

doi:10.1093/nar/gkm862.

4DXpress: a database for cross-species expression pattern comparisons

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T

Nucleic acids research 2008

doi:10.1093/nar/gkm797.

A molecular study of microbe transfer between distant environments

Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P

PloS one 2008

doi:10.1371/journal.pone.0002607.

Circular reasoning rather than cyclic expression

Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P

Genome biology 2008

doi:10.1186/gb-2008-9-6-403.

eggNOG: automated construction and annotation of orthologous groups of genes

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P

Nucleic acids research 2008

doi:10.1093/nar/gkm796.

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability

Korff S, Woerner SM, Yuan YP, Bork P, von Knebel Doeberitz M, Gebert J

BMC cancer 2008

doi:10.1186/1471-2407-8-329.

STITCH: interaction networks of chemicals and proteins

Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P

Nucleic acids research 2008

doi:10.1093/nar/gkm795.

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P

Molecular systems biology 2008

doi:10.1038/msb.2008.35.

NetworKIN: a resource for exploring cellular phosphorylation networks

Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T

Nucleic acids research 2008

doi:10.1093/nar/gkm902.

Linear motif atlas for phosphorylation-dependent signaling

Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R

Science signaling 2008

doi:10.1126/scisignal.1159433.

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

Pallejà A, Harrington ED, Bork P

BMC genomics 2008

doi:10.1186/1471-2164-9-335.

Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation

Perotti C, Liu R, Parusel CT, Böcher N, Schultz J, Bork P, Pfitzner E, Groner B, Shemanko CS

Breast cancer research : BCR 2008

doi:10.1186/bcr2193.

Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution

Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M

Genome biology 2008

doi:10.1186/gb-2008-9-12-r176.

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families

Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R

Gene 2008

doi:10.1016/j.gene.2007.10.012.

Non-random retention of protein-coding overlapping genes in Metazoa

Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD

BMC genomics 2008

doi:10.1186/1471-2164-9-174.

MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects

Wiemann S, Mehrle A, Hahne F, Hermjakob H, Apweiler R, Arlt D, Bechtel S, Bielke W, Birmingham A, Smith Q, Bork P, Buchholz F, Cai X, Camon E, Carninci P, Chanda SK, Chen Z, Cusick M, Echeverri C, Eils J, Eils R, Frank R, Fraser A, Girod A, Haedrich B, Hannus M, Harris M, Hayashizaki Y, Hide W, Hofmann O, Huber P, Hyman A, Jensen L, Kallioniemi O, Khvorova A, Koski L, Kraybill B, LaBaer J, Landegren U, Lawerenz C, Lehrach H, Liu F-F, Majety M, Mathey-Prevot B, Medico E, Mills GB, Nomura N, The OBI Consortium, Perrimon N, Pizarro A, Poustka A, Quackenbush J, Rosenfelder H, Sahin O, Salehi-Ashtiani K, Sasse F, Sauermann M, Schimmer AD, Schmidt C, Selfors L, Shamu C, Sönnichsen B, Taylor C, Temple G, Vidal M, Weidlich M, Wrobel DJ, Zhang J

2008

doi:.

Genome-wide experimental determination of barriers to horizontal gene transfer

Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM

Science (New York, N.Y.) 2007

doi:10.1126/science.1147112.

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing

Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E

Genes & development 2007

doi:10.1101/gad.443107.

Get the most out of your metagenome: computational analysis of environmental sequence data

Raes J, Foerstner KU, Bork P

Current opinion in microbiology 2007

doi:10.1016/j.mib.2007.09.001.

Evolution of cell cycle control: same molecular machines, different regulation

de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ

Cell cycle (Georgetown, Tex.) 2007

doi:10.4161/cc.6.15.4537.

Quantitative assessment of protein function prediction from metagenomics shotgun sequences

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P

Proceedings of the National Academy of Sciences of the United States of America 2007

doi:10.1073/pnas.0702636104.

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism

Pachkov M, Dandekar T, Korbel J, Bork P, Schuster S

Gene 2007

doi:10.1016/j.gene.2007.02.033.

Update of the G2D tool for prioritization of gene candidates to inherited diseases

Perez-Iratxeta C, Bork P, Andrade-Navarro MA

Nucleic acids research 2007

doi:10.1093/nar/gkm223.

Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals

Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE

The EMBO journal 2007

doi:10.1038/sj.emboj.7601699.

Systematic discovery of in vivo phosphorylation networks

Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T

Cell 2007

doi:10.1016/j.cell.2007.05.052.

Protein function space: viewing the limits or limited by our view?

Raes J, Harrington ED, Singh AH, Bork P

Current opinion in structural biology 2007

doi:10.1016/j.sbi.2007.05.010.

Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris–A comparative view on 79 human genes

Boettner M, Steffens C, von Mering C, Bork P, Stahl U, Lang C

Journal of biotechnology 2007

doi:10.1016/j.jbiotec.2007.02.019.

Quantitative phylogenetic assessment of microbial communities in diverse environments

von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P

Science (New York, N.Y.) 2007

doi:10.1126/science.1133420.

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P

Molecular systems biology 2007

doi:10.1038/msb4100112.

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Letunic I, Bork P

Bioinformatics (Oxford, England) 2007

doi:10.1093/bioinformatics/btl529.

New developments in the InterPro database

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C

Nucleic acids research 2007

doi:10.1093/nar/gkl841.

Prediction of effective genome size in metagenomic samples

Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P

Genome biology 2007

doi:10.1186/gb-2007-8-1-r10.

STRING 7–recent developments in the integration and prediction of protein interactions

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P

Nucleic acids research 2007

doi:10.1093/nar/gkl825.

Quantification of insect genome divergence

Zdobnov EM, Bork P

Trends in genetics : TIG 2007

doi:10.1016/j.tig.2006.10.004.

Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome

Raible F, Tessmar-Raible K, Arboleda E, Kaller T, Bork P, Arendt D, Arnone MI

Developmental biology 2006

doi:10.1016/j.ydbio.2006.08.070.

Computational characterization of multiple Gag-like human proteins

Campillos M, Doerks T, Shah PK, Bork P

Trends in genetics : TIG 2006

doi:10.1016/j.tig.2006.09.006.

Insights into social insects from the genome of the honeybee Apis mellifera

Honeybee Genome Sequencing Consortium

Nature 2006

doi:10.1038/nature05260.

Co-evolution of transcriptional and post-translational cell-cycle regulation

Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P

Nature 2006

doi:10.1038/nature05186.

Assessing systems properties of yeast mitochondria through an interaction map of the organelle

Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM

PLoS genetics 2006

doi:10.1371/journal.pgen.0020170.

mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes

Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E

Genes & development 2006

doi:10.1101/gad.1424106.

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Suyama M, Torrents D, Bork P

Nucleic acids research 2006

doi:10.1093/nar/gkl315.

A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development

Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE

Developmental cell 2006

doi:10.1016/j.devcel.2006.04.009.

Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes

Suyama M, Harrington E, Bork P, Torrents D

PLoS computational biology 2006

doi:10.1371/journal.pcbi.0020076.

LSAT: learning about alternative transcripts in MEDLINE

Shah PK, Bork P

Bioinformatics (Oxford, England) 2006

doi:10.1093/bioinformatics/btk044.

Identification and analysis of evolutionarily cohesive functional modules in protein networks

Campillos M, von Mering C, Jensen LJ, Bork P

Genome research 2006

doi:10.1101/gr.4336406.

Toward automatic reconstruction of a highly resolved tree of life

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P

Science (New York, N.Y.) 2006

doi:10.1126/science.1123061.

Comparative analysis of environmental sequences: potential and challenges

Foerstner KU, von Mering C, Bork P

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006

doi:10.1098/rstb.2005.1809.

Proteome survey reveals modularity of the yeast cell machinery

Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G

Nature 2006

doi:10.1038/nature04532.

Extraction of regulatory gene/protein networks from Medline

Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P

Bioinformatics (Oxford, England) 2006

doi:10.1093/bioinformatics/bti597.

Similar gene expression profiles do not imply similar tissue functions

Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ

Trends in genetics : TIG 2006

doi:10.1016/j.tig.2006.01.006.

Literature mining for the biologist: from information retrieval to biological discovery

Jensen LJ, Saric J, Bork P

Nature reviews. Genetics 2006

doi:10.1038/nrg1768.

SMART 5: domains in the context of genomes and networks

Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P

Nucleic acids research 2006

doi:10.1093/nar/gkj079.

Environments shape the nucleotide composition of genomes

Foerstner KU, von Mering C, Hooper SD, Bork P

EMBO reports 2005

doi:10.1038/sj.embor.7400538.

Medusa: a simple tool for interaction graph analysis

Hooper SD, Bork P

Bioinformatics (Oxford, England) 2005

doi:10.1093/bioinformatics/bti696.

Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases

Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, Bork P, Wiese S, Gessler M, Kerkhoff E

Gene expression patterns : GEP 2005

doi:10.1016/j.modgep.2005.04.015.

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D

Science (New York, N.Y.) 2005

doi:10.1126/science.1119089.

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system

Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M

The Journal of cell biology 2005

doi:10.1083/jcb.200507168.

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets

Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E

RNA (New York, N.Y.) 2005

doi:10.1261/rna.2160905.

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii

Suyama M, Lathe WC 3rd, Bork P

FEBS letters 2005

doi:10.1016/j.febslet.2005.08.051.

Initial sequence of the chimpanzee genome and comparison with the human genome

Chimpanzee Sequencing and Analysis Consortium

Nature 2005

doi:10.1038/nature04072.

Structural genomics of human proteins–target selection and generation of a public catalogue of expression clones

Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U

Microbial Cell Factories 2005

doi:10.1186/1475-2859-4-21.

Extraction of transcript diversity from scientific literature

Shah PK, Jensen LJ, Boué S, Bork P

PLoS computational biology 2005

doi:10.1371/journal.pcbi.0010010.

Consistency of genome-based methods in measuring Metazoan evolution

Zdobnov EM, von Mering C, Letunic I, Bork P

FEBS letters 2005

doi:10.1016/j.febslet.2005.04.006.

Towards cellular systems in 4D

Bork P, Serrano L

Cell 2005

doi:10.1016/j.cell.2005.05.001.

Systematic association of genes to phenotypes by genome and literature mining

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P

PLoS biology 2005

doi:10.1371/journal.pbio.0030134.

Structural similarity to bridge sequence space: finding new families on the bridges

Shah PK, Aloy P, Bork P, Russell RB

Protein science : a publication of the Protein Society 2005

doi:10.1110/ps.041187405.

The WHy domain mediates the response to desiccation in plants and bacteria

Ciccarelli FD, Bork P

Bioinformatics (Oxford, England) 2005

doi:10.1093/bioinformatics/bti221.

Comparison of computational methods for the identification of cell cycle-regulated genes

de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S

Bioinformatics (Oxford, England) 2005

doi:10.1093/bioinformatics/bti093.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK

Nature 2005

doi:10.1038/nature03466.

Comparative metagenomics of microbial communities

Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM

Science (New York, N.Y.) 2005

doi:10.1126/science.1107851.

Complex genomic rearrangements lead to novel primate gene function

Ciccarelli FD, von Mering C, Suyama M, Harrington ED, Izaurralde E, Bork P

Genome research 2005

doi:10.1101/gr.3266405.

Dynamic complex formation during the yeast cell cycle

de Lichtenberg U, Jensen LJ, Brunak S, Bork P

Science (New York, N.Y.) 2005

doi:10.1126/science.1105103.

Is there biological research beyond Systems Biology? A comparative analysis of terms

Bork P

Molecular systems biology 2005

doi:10.1038/msb4100016.

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G

Genome research 2005

doi:10.1101/gr.3002305.

InterPro, progress and status in 2005

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH

Nucleic acids research 2005

doi:10.1093/nar/gki106.

G2D: a tool for mining genes associated with disease

Perez-Iratxeta C, Wjst M, Bork P, Andrade MA

BMC genetics 2005

doi:10.1186/1471-2156-6-45.

DCD – a novel plant specific domain in proteins involved in development and programmed cell death

Tenhaken R, Doerks T, Bork P

BMC bioinformatics 2005

doi:10.1186/1471-2105-6-169.

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P

Nucleic acids research 2005

doi:10.1093/nar/gki005.

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes

Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P

Nucleic acids research 2005

doi:10.1093/nar/gki236.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium

Nature 2004

doi:10.1038/nature03154.

Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression

Koehl A, Schmidt N, Rieger A, Pilgram SM, Letunic I, Bork P, Soto F, Friauf E, Nothwang HG

The European journal of neuroscience 2004

doi:10.1111/j.1460-9568.2004.03791.x.

Shared components of protein complexes–versatile building blocks or biochemical artefacts?

Krause R, von Mering C, Bork P, Dandekar T

BioEssays : news and reviews in molecular, cellular and developmental biology 2004

doi:10.1002/bies.20141.

Estimating rates of alternative splicing in mammals and invertebrates

Kim H, Klein R, Majewski J, Ott J

Nature genetics 2004

doi:10.1038/ng0904-915.

Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome

Liska AJ, Popov AV, Sunyaev S, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A

Proteomics 2004

doi:10.1002/pmic.200300813.

Gene annotation from scientific literature using mappings between keyword systems

Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA

Bioinformatics (Oxford, England) 2004

doi:10.1093/bioinformatics/bth207.

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments

Suyama M, Torrents D, Bork P

Bioinformatics (Oxford, England) 2004

doi:10.1093/bioinformatics/bth172.

ArrayProspector: a web resource of functional associations inferred from microarray expression data

Jensen LJ, Lagarde J, von Mering C, Bork P

Nucleic acids research 2004

doi:10.1093/nar/gkh407.

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

Korbel JO, Jensen LJ, von Mering C, Bork P

Nature biotechnology 2004

doi:10.1038/nbt988.

Protein interaction networks from yeast to human

Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM

Current opinion in structural biology 2004

doi:10.1016/j.sbi.2004.05.003.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium

Nature 2004

doi:10.1038/nature02426.

Structure-based assembly of protein complexes in yeast

Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB

Science (New York, N.Y.) 2004

doi:10.1126/science.1092645.

Global analysis of bacterial transcription factors to predict cellular target processes

Doerks T, Andrade MA, Lathe W 3rd, von Mering C, Bork P

Trends in genetics : TIG 2004

doi:10.1016/j.tig.2004.01.006.

RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export

Forler D, Rabut G, Ciccarelli FD, Herold A, Köcher T, Niggeweg R, Bork P, Ellenberg J, Izaurralde E

Molecular and cellular biology 2004

doi:10.1128/mcb.24.3.1155-1167.2004.

The HUPO PSI's molecular interaction format–a community standard for the representation of protein interaction data

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R

Nature biotechnology 2004

doi:10.1038/nbt926.

Sequences and topology – Genes and structures in context – Editorial overview

Bork P, Orengo CA

Current opinion in structural biology 2004

doi:.

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources

Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gössling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Müller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E, Zimmer R

Bioinformatics (Oxford, England) 2004

doi:10.1093/bioinformatics/btg398.

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

Doerks T, von Mering C, Bork P

Nucleic acids research 2004

doi:10.1093/nar/gkh973.

Quality analysis and integration of large-scale molecular data sets

Jensen LJ, Bork P

Drug discovery today 2004

doi:.

SMART 4.0: towards genomic data integration

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P

Nucleic acids research 2004

doi:10.1093/nar/gkh088.

Extracting Regulatory Gene Expression Networks From Pubmed

Saric J, Jensen LJ, Bork P, Ouzounova R, Rojas I

2004

doi:.

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold

Ciccarelli FD, Izaurralde E, Bork P

BMC bioinformatics 2003

doi:10.1186/1471-2105-4-64.

Impact of selection, mutation rate and genetic drift on human genetic variation

Sunyaev S, Kondrashov FA, Bork P, Ramensky V

Human molecular genetics 2003

doi:10.1093/hmg/ddg359.

A genome-wide survey of human pseudogenes

Torrents D, Suyama M, Zdobnov E, Bork P

Genome research 2003

doi:10.1101/gr.1455503.

Genome evolution reveals biochemical networks and functional modules

von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P

Proceedings of the National Academy of Sciences of the United States of America 2003

doi:10.1073/pnas.2136809100.

Alternative splicing and evolution

Boue S, Letunic I, Bork P

BioEssays : news and reviews in molecular, cellular and developmental biology 2003

doi:10.1002/bies.10371.

Protein disorder prediction: implications for structural proteomics

Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB

Structure (London, England : 1993) 2003

doi:10.1016/j.str.2003.10.002.

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens

Krause R, von Mering C, Bork P

Bioinformatics (Oxford, England) 2003

doi:10.1093/bioinformatics/btg344.

Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways

Gatfield D, Unterholzner L, Ciccarelli FD, Bork P, Izaurralde E

The EMBO journal 2003

doi:10.1093/emboj/cdg371.

The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold

Ciccarelli FD, Bork P, Kerkhoff E

Trends in biochemical sciences 2003

doi:10.1016/s0968-0004(03)00116-6.

The DNA sequence of human chromosome 7

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK

Nature 2003

doi:10.1038/nature01782.

Systematic discovery of analogous enzymes in thiamin biosynthesis

Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P

Nature biotechnology 2003

doi:10.1038/nbt834.

Update on XplorMed: A web server for exploring scientific literature

Perez-Iratxeta C, Pérez AJ, Bork P, Andrade MA

Nucleic acids research 2003

doi:10.1093/nar/gkg538.

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ

Nucleic acids research 2003

doi:10.1093/nar/gkg545.

Metabolites: a helping hand for pathway evolution?

Schmidt S, Sunyaev S, Bork P, Dandekar T

Trends in biochemical sciences 2003

doi:10.1016/s0968-0004(03)00114-2.

The way we write

Netzel R, Perez-Iratxeta C, Bork P, Andrade MA

EMBO reports 2003

doi:10.1038/sj.embor.embor833.

Information extraction from full text scientific articles: where are the keywords?

Shah PK, Perez-Iratxeta C, Bork P, Andrade MA

BMC bioinformatics 2003

doi:10.1186/1471-2105-4-20.

The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia

Ciccarelli FD, Proukakis C, Patel H, Cross H, Azam S, Patton MA, Bork P, Crosby AH

Genomics 2003

doi:10.1016/s0888-7543(03)00011-9.

Function prediction and protein networks

Huynen MA, Snel B, von Mering C, Bork P

Current opinion in cell biology 2003

doi:10.1016/s0955-0674(03)00009-7.

Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes

Woerner SM, Benner A, Sutter C, Schiller M, Yuan YP, Keller G, Bork P, Doeberitz Mv, Gebert JF

Oncogene 2003

doi:10.1038/sj.onc.1206421.

Bioinformatics in the post-sequence era

Kanehisa M, Bork P

Nature genetics 2003

doi:10.1038/ng1109.

Increase of functional diversity by alternative splicing

Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S

Trends in genetics : TIG 2003

doi:10.1016/s0168-9525(03)00023-4.

High Rate of Gene Displacement in Vitamin Biosynthesis Pathways

Morett E, Saab G, Merino E, Bork P, Rajan E, Olvera L, Olvera M

2003

doi:.

The InterPro Database, 2003 brings increased coverage and new features

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM

Nucleic acids research 2003

doi:10.1093/nar/gkg046.

A protocol for the update of references to scientific literature in biological databases

Perez-Iratxeta C, Astola N, Ciccarelli FD, Sha PK, Bork P, Andrade MA

Applied bioinformatics 2003

doi:.

Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes

Shevchenko A, Sunyaev S, Liska A, Bork P, Shevchenko A

Methods in molecular biology (Clifton, N.J.) 2003

doi:.

Pseudogenes and Genomes

Torrents D, Suyama M, Bork P

2003

doi:.

STRING: a database of predicted functional associations between proteins

von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B

Nucleic acids research 2003

doi:10.1093/nar/gkg034.

The human genome: genes, pseudogenes, and variation on chromosome 7

Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK

Cold Spring Harbor symposia on quantitative biology 2003

doi:10.1101/sqb.2003.68.13.

Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes

Kloor M, Bork P, Duwe A, Klaes R, von Knebel Doeberitz M, Ridder R

Biochimica et biophysica acta 2002

doi:10.1016/s0167-4781(02)00543-2.

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES

Nature 2002

doi:10.1038/nature01262.

Immunity-related genes and gene families in Anopheles gambiae

Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Müller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P, Kafatos FC

Science (New York, N.Y.) 2002

doi:10.1126/science.1077136.

The genome sequence of the malaria mosquito Anopheles gambiae

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL

Science (New York, N.Y.) 2002

doi:10.1126/science.1076181.

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F

Proceedings of the National Academy of Sciences of the United States of America 2002

doi:10.1073/pnas.212527599.

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P

Science (New York, N.Y.) 2002

doi:10.1126/science.1077061.

InterPro: an integrated documentation resource for protein families, domains and functional sites

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ, InterPro Consortium

Briefings in bioinformatics 2002

doi:10.1093/bib/3.3.225.

Human non-synonymous SNPs: server and survey

Ramensky V, Bork P, Sunyaev S

Nucleic acids research 2002

doi:10.1093/nar/gkf493.

NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria

Andrade MA, Ciccarelli FD, Perez-Iratxeta C, Bork P

Genome biology 2002

doi:10.1186/gb-2002-3-9-research0047.

The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations

Bordo D, Bork P

EMBO reports 2002

doi:10.1093/embo-reports/kvf150.

Predicting protein cellular localization using a domain projection method

Mott R, Schultz J, Bork P, Ponting CP

Genome research 2002

doi:10.1101/gr.96802.

SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia

Patel H, Cross H, Proukakis C, Hershberger R, Bork P, Ciccarelli FD, Patton MA, McKusick VA, Crosby AH

Nature genetics 2002

doi:10.1038/ng937.

A complex prediction: three-dimensional model of the yeast exosome

Aloy P, Ciccarelli FD, Leutwein C, Gavin AC, Superti-Furga G, Bork P, Bottcher B, Russell RB

EMBO reports 2002

doi:10.1093/embo-reports/kvf135.

Association of genes to genetically inherited diseases using data mining

Perez-Iratxeta C, Bork P, Andrade MA

Nature genetics 2002

doi:10.1038/ng895.

Common exon duplication in animals and its role in alternative splicing

Letunic I, Copley RR, Bork P

Human molecular genetics 2002

doi:10.1093/hmg/11.13.1561.

Exploring MEDLINE abstracts with XplorMed

Perez-Iratxeta C, Bork P, Andrade MA

Drugs of today (Barcelona, Spain : 1998) 2002

doi:10.1358/dot.2002.38.6.678344.

Computing fuzzy associations for the analysis of biological literature

Perez-Iratxeta C, Keer HS, Bork P, Andrade MA

BioTechniques 2002

doi:10.2144/02326bc03.

Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae

Thomasova D, Ton LQ, Copley RR, Zdobnov EM, Wang X, Hong YS, Sim C, Bork P, Kafatos FC, Collins FH

Proceedings of the National Academy of Sciences of the United States of America 2002

doi:10.1073/pnas.082235599.

Proteinkomplexe und Netzwerke: Neue Herausforderungen für die Proteomik

Von Mering C, Bork P

2002

doi:.

Teamed up for transcription

von Mering C, Bork P

Nature 2002

doi:10.1038/417797a.

Comparative assessment of large-scale data sets of protein-protein interactions

von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P

Nature 2002

doi:10.1038/nature750.

BSD: a novel domain in transcription factors and synapse-associated proteins

Doerks T, Huber S, Buchner E, Bork P

Trends in biochemical sciences 2002

doi:10.1016/s0968-0004(01)02042-4.

The identification of functional modules from the genomic association of genes

Snel B, Bork P, Huynen MA

Proceedings of the National Academy of Sciences of the United States of America 2002

doi:10.1073/pnas.092632599.

AMOP, a protein module alternatively spliced in cancer cells

Ciccarelli FD, Doerks T, Bork P

Trends in biochemical sciences 2002

doi:10.1016/s0968-0004(01)02049-7.

SHOT: a web server for the construction of genome phylogenies

Korbel JO, Snel B, Huynen MA, Bork P

Trends in genetics : TIG 2002

doi:10.1016/s0168-9525(01)02597-5.

CASH–a beta-helix domain widespread among carbohydrate-binding proteins

Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P

Trends in biochemical sciences 2002

doi:10.1016/s0968-0004(01)02046-1.

Protein domain analysis in the era of complete genomes

Copley RR, Doerks T, Letunic I, Bork P

FEBS letters 2002

doi:10.1016/s0014-5793(01)03289-6.

Genome and protein evolution in eukaryotes

Copley RR, Letunic I, Bork P

Current opinion in chemical biology 2002

doi:10.1016/s1367-5931(01)00278-2.

Comparative analysis of protein interaction networks

Bork P

Bioinformatics (Oxford, England) 2002

doi:10.1093/bioinformatics/18.suppl_2.S64.

Alternative splicing and genome complexity

Brett D, Pospisil H, Valcárcel J, Reich J, Bork P

Nature genetics 2002

doi:10.1038/ng803.

Sequence analysis of multidomain proteins: past perspectives and future directions

Copley RR, Ponting CP, Schultz J, Bork P

Advances in protein chemistry 2003

doi:10.1016/s0065-3233(02)61002-2.

Comparative genome analysis of the mollicutes

Dandekar T, Snel B, Schmidt S, Lathe W, Suyama M, Huynen M, Bork P

2002

doi:10.1007/0-306-47606-1_11.

Systematic identification of novel protein domain families associated with nuclear functions

Doerks T, Copley RR, Schultz J, Ponting CP, Bork P

Genome research 2002

doi:10.1101/gr.203201.

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources

Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ

Nucleic acids research 2002

doi:10.1093/nar/30.1.387.

Functional organization of the yeast proteome by systematic analysis of protein complexes

Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G

Nature 2002

doi:10.1038/415141a.

Recent improvements to the SMART domain-based sequence annotation resource

Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P

Nucleic acids research 2002

doi:10.1093/nar/30.1.242.

A versatile structural domain analysis server using profile weight matrices

Schmidt S, Bork P, Dandekar T

Journal of chemical information and computer sciences 2002

doi:10.1021/ci010374r.

Genomes in flux: the evolution of archaeal and proteobacterial gene content

Snel B, Bork P, Huynen MA

Genome research 2002

doi:10.1101/gr.176501.

The Spir actin organizers are involved in vesicle transport processes

Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R

Current biology : CB 2001

doi:10.1016/s0960-9822(01)00602-9.

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution

Ponting CP, Mott R, Bork P, Copley RR

Genome research 2001

doi:10.1101/gr.198701.

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

Huynen MA, Snel B, Bork P, Gibson TJ

Human molecular genetics 2001

doi:10.1093/hmg/10.21.2463.

XplorMed: a tool for exploring MEDLINE abstracts

Perez-Iratxeta C, Bork P, Andrade MA

Trends in biochemical sciences 2001

doi:10.1016/s0968-0004(01)01926-0.

Evolution of tuf genes: ancient duplication, differential loss and gene conversion

Lathe WC 3rd, Bork P

FEBS letters 2001

doi:10.1016/s0014-5793(01)02639-4.

Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens

Linnebacher M, Gebert J, Rudy W, Woerner S, Yuan YP, Bork P, von Knebel Doeberitz M

International journal of cancer. Journal international du cancer 2001

doi:10.1002/ijc.1298.

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells

Woerner SM, Gebert J, Yuan YP, Sutter C, Ridder R, Bork P, von Knebel Doeberitz M

International journal of cancer. Journal international du cancer 2001

doi:10.1002/ijc.1299.

Inversions and the dynamics of eukaryotic gene order

Huynen MA, Snel B, Bork P

Trends in genetics : TIG 2001

doi:10.1016/s0168-9525(01)02302-2.

Comparison of ARM and HEAT protein repeats

Andrade MA, Petosa C, O'Donoghue SI, Müller CW, Bork P

Journal of molecular biology 2001

doi:10.1006/jmbi.2001.4624.

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching

Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG

Analytical chemistry 2001

doi:10.1021/ac0013709.

DDT — a novel domain in different transcription and chromosome remodeling factors

Doerks T, Copley R, Bork P

Trends in biochemical sciences 2001

doi:10.1016/s0968-0004(00)01769-2.

Prediction of deleterious human alleles

Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, Bork P

Human molecular genetics 2001

doi:10.1093/hmg/10.6.591.

Genome speak

Bork P, Copley R

Nature 2001

doi:10.1038/35057269.

The draft sequences. Filling in the gaps

Bork P, Copley R

Nature 2001

doi:10.1038/35057274.

Initial sequencing and analysis of the human genome

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, International Human Genome Sequencing Consortium

Nature 2001

doi:10.1038/35057062.

Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35]

Schultz J, Jones T, Bork P, Sheer D, Blencke S, Steyrer S, Wellbrock U, Bevec D, Ullrich A, Wallasch C

Genomics 2001

doi:10.1006/geno.2000.6447.

Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms

Sunyaev S, Lathe W 3rd, Bork P

Current opinion in structural biology 2001

doi:10.1016/s0959-440x(00)00175-5.

The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival

Becker S, Gehrsitz A, Bork P, Buchner S, Buchner E

Gene 2001

doi:10.1016/s0378-1119(00)00548-5.

Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes

Eisenhaber B, Bork P, Eisenhaber F

Protein engineering 2001

doi:10.1093/protein/14.1.17.

Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences

Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB, Koonin EV

Genome biology 2001

doi:.

Evolution of prokaryotic gene order: genome rearrangements in closely related species

Suyama M, Bork P

Trends in genetics : TIG 2001

doi:10.1016/s0168-9525(00)02159-4.

TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture

Herold A, Suyama M, Rodrigues JP, Braun IC, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E

Molecular and cellular biology 2000

doi:10.1128/mcb.20.23.8996-9008.2000.

Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways

Copley RR, Bork P

Journal of molecular biology 2000

doi:10.1006/jmbi.2000.4152.

Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III

Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlü N, Bork P, Hyman AA

Nature 2000

doi:10.1038/35042526.

GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins

Doerks T, Strauss M, Brendel M, Bork P

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01664-9.

Gene context conservation of a higher order than operons

Lathe WC 3rd, Snel B, Bork P

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01663-7.

EST analysis online: WWW tools for detection of SNPs and alternative splice forms

Brett D, Lehmann G, Hanke J, Gross S, Reich J, Bork P

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(00)02089-8.

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames

Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P

Nucleic acids research 2000

doi:10.1093/nar/28.17.3278.

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

Snel B, Lehmann G, Bork P, Huynen MA

Nucleic acids research 2000

doi:10.1093/nar/28.18.3442.

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

Huynen M, Snel B, Lathe W 3rd, Bork P

Genome research 2000

doi:10.1101/gr.10.8.1204.

SNP frequencies in human genes an excess of rare alleles and differing modes of selection

Sunyaev SR, Lathe WC 3rd, Ramensky VE, Bork P

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(00)02058-8.

L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7

Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01599-1.

Automated annotation of GPI anchor sites: case study C. elegans

Eisenhaber B, Bork P, Yuan Y, Löffler G, Eisenhaber F

Trends in biochemical sciences 2000

doi:10.1016/s0968-0004(00)01601-7.

NAIL-Network Analysis Interface for Linking HMMER results

Sánchez-Pulido L, Yuan YP, Andrade MA, Bork P

Bioinformatics (Oxford, England) 2000

doi:10.1093/bioinformatics/16.7.656.

Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins

Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P

EMBO reports 2000

doi:10.1093/embo-reports/kvd009.

Automated extraction of information in molecular biology

Andrade MA, Bork P

FEBS letters 2000

doi:10.1016/s0014-5793(00)01661-6.

Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines

Dimopoulos G, Casavant TL, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares MB, Kafatos FC

Proceedings of the National Academy of Sciences of the United States of America 2000

doi:10.1073/pnas.97.12.6619.

Exploitation of gene context

Huynen M, Snel B, Lathe W, Bork P

Current opinion in structural biology 2000

doi:10.1016/s0959-440x(00)00098-1.

More than 1,000 putative new human signalling proteins revealed by EST data mining

Schultz J, Doerks T, Ponting CP, Copley RR, Bork P

Nature genetics 2000

doi:10.1038/76069.

Homology-based method for identification of protein repeats using statistical significance estimates

Andrade MA, Ponting CP, Gibson TJ, Bork P

Journal of molecular biology 2000

doi:10.1006/jmbi.2000.3684.

EST comparison indicates 38% of human mRNAs contain possible alternative splice forms

Brett D, Hanke J, Lehmann G, Haase S, Delbrück S, Krueger S, Reich J, Bork P

FEBS letters 2000

doi:10.1016/s0014-5793(00)01581-7.

Towards a structural basis of human non-synonymous single nucleotide polymorphisms

Sunyaev S, Ramensky V, Bork P

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(00)01988-0.

Powers and pitfalls in sequence analysis: the 70% hurdle

Bork P

Genome research 2000

doi:10.1101/gr.10.4.398.

REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export

Stutz F, Bachi A, Doerks T, Braun IC, Séraphin B, Wilm M, Bork P, Izaurralde E

RNA (New York, N.Y.) 2000

doi:10.1017/s1355838200000078.

The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization

Otto IM, Raabe T, Rennefahrt UE, Bork P, Rapp UR, Kerkhoff E

Current biology : CB 2000

doi:10.1016/s0960-9822(00)00388-2.

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem

Isaksson A, Landegren U, Syvänen AC, Bork P, Stein C, Ortigao F, Brookes AJ

European journal of human genetics : EJHG 2000

doi:10.1038/sj.ejhg.5200424.

Analysis of Amino Acid Sequences

Bork P

2000

doi:.

Advances in Protein Chemistry

Bork P (ed)

2000

doi:.

Genome and proteome informatics – Editorial overview

Bork P, Eisenberg D

Current opinion in structural biology 2000

doi:10.1016/S0959-440X(00)00093-2.

Comparative genome analysis: exploiting the context of genes to infer evolution and predict function

Bork P, Snel B, Lehmann G, Suyama M, Dandekar T, Lathe W III, Huynen M

2000

doi:10.1007/978-94-011-4309-7_25.

HGBASE: a database of SNPs and other variations in and around human genes

Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F

Nucleic acids research 2000

doi:10.1093/nar/28.1.356.

Evolution of domain families

Ponting CP, Schultz J, Copley RR, Andrade MA, Bork P

Advances in protein chemistry 2000

doi:10.1016/s0065-3233(00)54007-8.

SMART: a web-based tool for the study of genetically mobile domains

Schultz J, Copley RR, Doerks T, Ponting CP, Bork P

Nucleic acids research 2000

doi:10.1093/nar/28.1.231.

Genome evolution. Gene fusion versus gene fission

Snel B, Bork P, Huynen M

Trends in genetics : TIG 2000

doi:10.1016/s0168-9525(99)01924-1.

Individual variation in protein-coding sequences of human genome

Sunyaev S, Hanke J, Brett D, Aydin A, Zastrow I, Lathe W, Bork P, Reich J

Advances in protein chemistry 2000

doi:10.1016/s0065-3233(00)54012-1.

The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins

Liu Z, Macias MJ, Bottomley MJ, Stier G, Linge JP, Nilges M, Bork P, Sattler M

Structure (London, England : 1993) 1999

doi:10.1016/s0969-2126(00)88346-x.

A point of entry into genomics

Bork P, Huynen MA

Nature genetics 1999

doi:10.1038/15453.

Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes

Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P

Journal of molecular medicine (Berlin, Germany) 1999

doi:10.1007/s001099900059.

A lipid-binding domain in Wnt: a case of mistaken identity?

Barnes MR, Russell RB, Copley RR, Ponting CP, Bork P, Cumberledge S, Reichsman F, Moore HM

Current biology : CB 1999

doi:10.1016/s0960-9822(99)80465-5.

Phospholipases A2 and Wnts are unlikely to share a common ancestor

Copley RR, Ponting CP, Bork P

Current biology : CB 1999

doi:10.1016/s0960-9822(99)80466-7.

Pathway alignment: application to the comparative analysis of glycolytic enzymes

Dandekar T, Schuster S, Snel B, Huynen M, Bork P

The Biochemical journal 1999

doi:10.1042/0264-6021:3430115.

Alternative splicing of human genes: more the rule than the exception?

Hanke J, Brett D, Zastrow I, Aydin A, Delbrück S, Lehmann G, Luft F, Reich J, Bork P

Trends in genetics : TIG 1999

doi:10.1016/s0168-9525(99)01830-2.

Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites

Smalla M, Schmieder P, Kelly M, Ter Laak A, Krause G, Ball L, Wahl M, Bork P, Oschkinat H

Protein science : a publication of the Protein Society 1999

doi:10.1110/ps.8.10.1954.

Prediction of potential GPI-modification sites in proprotein sequences

Eisenhaber B, Bork P, Eisenhaber F

Journal of molecular biology 1999

doi:10.1006/jmbi.1999.3069.

Associative database of protein sequences

Hanke J, Lehmann G, Bork P, Reich JG

Bioinformatics (Oxford, England) 1999

doi:10.1093/bioinformatics/15.9.741.

Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures

Müller SA, Sasaki T, Bork P, Wolpensinger B, Schulthess T, Timpl R, Engel A, Engel J

Journal of molecular biology 1999

doi:10.1006/jmbi.1999.2996.

A latrophilin/CL-1-like GPS domain in polycystin-1

Ponting CP, Hofmann K, Bork P

Current biology : CB 1999

doi:10.1016/s0960-9822(99)80379-0.

Genome comparisons to monitor molecular evolution

Bork P, Dandekar T, Snel B, Huynen MA

1999

doi:.

Domains in plexins: links to integrins and transcription factors

Bork P, Doerks T, Springer TA, Snel B

Trends in biochemical sciences 1999

doi:10.1016/s0968-0004(99)01416-4.

Variation and evolution of the citric-acid cycle: a genomic perspective

Huynen MA, Dandekar T, Bork P

Trends in microbiology 1999

doi:10.1016/s0966-842x(99)01539-5.

Protein families in multicellular organisms

Copley RR, Schultz J, Ponting CP, Bork P

Current opinion in structural biology 1999

doi:10.1016/s0959-440x(99)80055-4.

A novel transactivation domain in parkin

Morett E, Bork P

Trends in biochemical sciences 1999

doi:10.1016/s0968-0004(99)01381-x.

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer

Ponting CP, Aravind L, Schultz J, Bork P, Koonin EV

Journal of molecular biology 1999

doi:10.1006/jmbi.1999.2827.

No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho

Ponting CP, Bork P, Schultz J, Aravind L

Trends in biochemical sciences 1999

doi:10.1016/s0968-0004(99)01379-1.

The mahogany protein is a receptor involved in suppression of obesity

Nagle DL, McGrail SH, Vitale J, Woolf EA, Dussault BJ Jr, DiRocco L, Holmgren L, Montagno J, Bork P, Huszar D, Fairchild-Huntress V, Ge P, Keilty J, Ebeling C, Baldini L, Gilchrist J, Burn P, Carlson GA, Moore KJ

Nature 1999

doi:10.1038/18210.

Applying logic programming ro derive novel functional information of genomes.

Bansal AK, Bork P

1999

doi:.

Bioinformatik… (editorial)

Bork P

1999

doi:.

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries

Eisenhaber F, Bork P

Bioinformatics (Oxford, England) 1999

doi:10.1093/bioinformatics/15.7.528.

Sequence analysis, dotplot, aligning sequences, indels and gap-penalty

Gibson T, Bork P

1999

doi:.

Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes

Huynen M, Snel B, Bork P

Science (New York, N.Y.) 1999

doi:.

SMART: identification and annotation of domains from signalling and extracellular protein sequences

Ponting CP, Schultz J, Milpetz F, Bork P

Nucleic acids research 1999

doi:10.1093/nar/27.1.229.

Genome phylogeny based on gene content

Snel B, Bork P, Huynen MA

Nature genetics 1999

doi:10.1038/5052.

Homology-based gene prediction using neural nets

Cai Y, Bork P

Analytical biochemistry 1998

doi:10.1006/abio.1998.2876.

Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase

Eisenhaber B, Bork P, Eisenhaber F

Protein engineering 1998

doi:10.1093/protein/11.12.1155.

Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues

Willeke F, Ridder R, Bork P, Klaes R, Mechtersheimer G, Schwarzbach M, Zimmer D, Kloor M, Lehnert T, Herfarth C, von Knebel Doeberitz M

Molecular carcinogenesis 1998

doi:10.1002/(sici)1098-2744(199812)23:4<195::aid-mc1>3.3.co;2-7.

Predicting function: from genes to genomes and back

Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y

Journal of molecular biology 1998

doi:10.1006/jmbi.1998.2144.

Conservation of gene order: a fingerprint of proteins that physically interact

Dandekar T, Snel B, Huynen M, Bork P

Trends in biochemical sciences 1998

doi:10.1016/s0968-0004(98)01274-2.

Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC

Morett E, Bork P

FEBS letters 1998

doi:10.1016/s0014-5793(98)00888-6.

Homology-based fold predictions for Mycoplasma genitalium proteins

Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P

Journal of molecular biology 1998

doi:10.1006/jmbi.1998.1884.

Protein annotation: detective work for function prediction

Doerks T, Bairoch A, Bork P

Trends in genetics : TIG 1998

doi:10.1016/s0168-9525(98)01486-3.

Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries

Kharrat A, Millevoi S, Baraldi E, Ponting CP, Bork P, Pastore A

Biochimica et biophysica acta 1998

doi:10.1016/s0167-4838(98)00041-7.

AUTOMATED PAIR-WISE COMPARISONS OF MICROBIAL GENOMES

Bansal A , Bork P, Stuckey P

1998

doi:.

Measuring genome evolution

Huynen MA, Bork P

Proceedings of the National Academy of Sciences of the United States of America 1998

doi:10.1073/pnas.95.11.5849.

SMART, a simple modular architecture research tool: identification of signaling domains

Schultz J, Milpetz F, Bork P, Ponting CP

Proceedings of the National Academy of Sciences of the United States of America 1998

doi:10.1073/pnas.95.11.5857.

Predicting functions from protein sequences–where are the bottlenecks?

Bork P, Koonin EV

Nature genetics 1998

doi:10.1038/ng0498-313.

Wanted: subcellular localization of proteins based on sequence

Eisenhaber F, Bork P

Trends in cell biology 1998

doi:10.1016/s0962-8924(98)01226-4.

Differential genome analysis applied to the species-specific features of Helicobacter pylori

Huynen M, Dandekar T, Bork P

FEBS letters 1998

doi:10.1016/s0014-5793(98)00276-2.

Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins

Beckmann G, Hanke J, Bork P, Reich JG

Journal of molecular biology 1998

doi:10.1006/jmbi.1997.1510.

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases

Bork P, Dandekar T, Eisenhaber F, Huynen M

Journal of molecular medicine (Berlin, Germany) 1998

doi:10.1007/s001090050194.

Sequences and topology – Deriving biological knowledge from genomic sequences

Bork P, Eisenberg D

Current opinion in structural biology 1998

doi:10.1016/S0959-440X(98)80066-3.

Frame: detection of genomic sequencing errors

Brown NP, Sander C, Bork P

Bioinformatics (Oxford, England) 1998

doi:10.1093/bioinformatics/14.4.367.

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches

Dandekar T, Beyer K, Bork P, Kenealy MR, Pantopoulos K, Hentze M, Sonntag-Buck V, Flouriot G, Gannon F, Schreiber S

Bioinformatics (Oxford, England) 1998

doi:10.1093/bioinformatics/14.3.271.

Elementary modes analysis illustrated with human red cell metabolism

Schuster S, Fell DA, Pfeiffer T, Dandekar T, Bork, P

1998

doi:.

Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis

Schwirzke M, Gnirke A, Bork P, Tarin D, Weidle UH

Anticancer research 1998

doi:.

Towards detection of orthologues in sequence databases

Yuan YP, Eulenstein O, Vingron M, Bork P

Bioinformatics (Oxford, England) 1998

doi:10.1093/bioinformatics/14.3.285.

The Sequence Alerting Server–a new WEB server

Hegyi H, Lai JM, Bork P

Computer applications in the biosciences : CABIOS 1997

doi:.

A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases

Morozov V, Mushegian AR, Koonin EV, Bork P

Trends in biochemical sciences 1997

doi:10.1016/s0968-0004(97)01128-6.

Genome maps 8. Building gene families. Wall chart

Green EA, Pietrokovski S, Henikoff S, Bork P, Attwood T, Hood L, Bairoch A

Science (New York, N.Y.) 1997

doi:10.1126/science.278.5338.615.

Gene families: the taxonomy of protein paralogs and chimeras

Henikoff S, Greene EA, Pietrokovski S, Bork P, Attwood TK, Hood L

Science (New York, N.Y.) 1997

doi:10.1126/science.278.5338.609.

Differential genome display

Huynen MA, Diaz-Lazcoz Y, Bork P

Trends in genetics : TIG 1997

doi:10.1016/s0168-9525(97)01255-9.

Cytoplasmic signalling domains: the next generation

Bork P, Schultz J, Ponting CP

Trends in biochemical sciences 1997

doi:10.1016/s0968-0004(97)01084-0.

A novel class of RanGTP binding proteins

Görlich D, Dabrowski M, Bischoff FR, Kutay U, Bork P, Hartmann E, Prehn S, Izaurralde E

The Journal of cell biology 1997

doi:10.1083/jcb.138.1.65.

On the classification and evolution of protein modules

Hegyi H, Bork P

Journal of protein chemistry 1997

doi:10.1023/a:1026382032119.

The breast cancer gene product TSG101: a regulator of ubiquitination?

Ponting CP, Cai YD, Bork P

Journal of molecular medicine (Berlin, Germany) 1997

doi:.

SPRY domains in ryanodine receptors (Ca(2+)-release channels)

Ponting C, Schultz J, Bork P

Trends in biochemical sciences 1997

doi:10.1016/s0968-0004(97)01049-9.

Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs

Mushegian AR, Bassett DE Jr, Boguski MS, Bork P, Koonin EV

Proceedings of the National Academy of Sciences of the United States of America 1997

doi:10.1073/pnas.94.11.5831.

Bioinformatics and molecular medicine–introduction and call for papers

Bork P

Journal of molecular medicine (Berlin, Germany) 1997

doi:.

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins

Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1997

doi:.

SAM as a protein interaction domain involved in developmental regulation

Schultz J, Ponting CP, Hofmann K, Bork P

Protein science : a publication of the Protein Society 1997

doi:10.1002/pro.5560060128.

Secreted fringe-like signaling molecules may be glycosyltransferases

Yuan YP, Schultz J, Mlodzik M, Bork P

Cell 1997

doi:10.1016/s0092-8674(00)81852-8.

Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction

Gibson TJ, Koonin EV, Musco G, Pastore A, Bork P

Trends in neurosciences 1996

doi:10.1016/s0166-2236(96)20054-2.

Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome

Nagle DL, Karim MA, Woolf EA, Holmgren L, Bork P, Misumi DJ, McGrail SH, Dussault BJ Jr, Perou CM, Boissy RE, Duyk GM, Spritz RA, Moore KJ

Nature genetics 1996

doi:10.1038/ng1196-307.

Go hunting in sequence databases but watch out for the traps

Bork P, Bairoch A

Trends in genetics : TIG 1996

doi:10.1016/0168-9525(96)60040-7.

On the classification of modular proteins

Henrissat B, Bork P

Protein engineering 1996

doi:10.1093/protein/9.9.725.

Non-orthologous gene displacement

Koonin EV, Mushegian AR, Bork P

Trends in genetics : TIG 1996

doi:10.1016/0168-9525(96)20010-1.

Comparison of CD45 extracellular domain sequences from divergent vertebrate species suggests the conservation of three fibronectin type III domains

Okumura M, Matthews RJ, Robb B, Litman GW, Bork P, Thomas ML

Journal of immunology (Baltimore, Md. : 1950) 1996

doi:.

The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues

Bork P, Brown NP, Hegyi H, Schultz J

Protein science : a publication of the Protein Society 1996

doi:10.1002/pro.5560050720.

BRCA1 protein products … Functional motifs..

Koonin EV, Altschul SF, Bork P

Nature genetics 1996

doi:10.1038/ng0796-266.

Pleckstrin's repeat performance: a novel domain in G-protein signaling?

Ponting CP, Bork P

Trends in biochemical sciences 1996

doi:10.1016/0968-0004(96)30027-3.

Protein sequence motifs

Bork P, Koonin EV

Current opinion in structural biology 1996

doi:10.1016/s0959-440x(96)80057-1.

Internal repeats in the BRCA2 protein sequence

Bork P, Blomberg N, Nilges M

Nature genetics 1996

doi:10.1038/ng0596-22.

Structure and distribution of modules in extracellular proteins

Bork P, Downing AK, Kieffer B, Campbell ID

Quarterly reviews of biophysics 1996

doi:10.1017/s0033583500005783.

Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes

Koonin EV, Bork P

Trends in biochemical sciences 1996

doi:10.1016/0968-0004(96)30007-8.

Sperm-egg binding protein or proto-oncogene?

Bork P

Science (New York, N.Y.) 1996

doi:10.1126/science.271.5254.1431.

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV

Current biology : CB 1996

doi:10.1016/s0960-9822(02)00478-5.

Applying motif and profile searches

Bork P, Gibson TJ

Methods in enzymology 1996

doi:10.1016/s0076-6879(96)66013-3.

Self-organizing hierarchic networks for pattern recognition in protein sequence

Hanke J, Beckmann G, Bork P, Reich JG

Protein science : a publication of the Protein Society 1996

doi:10.1002/pro.5560050109.

Structural motifs of the PKD1 protein

Löhning C, Pohlschmidt M, Glücksmann-Kuis MA, Duyk G, Bork P, Schneider MO, Reeders ST, Frischauf AM

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association – European Renal Association 1996

doi:.

Identification of residues within the SHC phosphotyrosine binding/phosphotyrosine interaction domain crucial for phosphopeptide interaction

Yajnik V, Blaikie P, Bork P, Margolis B

The Journal of biological chemistry 1996

doi:10.1074/jbc.271.4.1813.

New protein functions in yeast chromosome VIII

Ouzounis C, Bork P, Casari G, Sander C

Protein science : a publication of the Protein Society 1995

doi:10.1002/pro.5560041121.

HEAT repeats in the Huntington's disease protein

Andrade MA, Bork P

Nature genetics 1995

doi:10.1038/ng1095-115.

Challenging times for bioinformatics

Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C

Nature 1995

doi:10.1038/376647a0.

Characterization of a novel protein-binding module–the WW domain

Sudol M, Chen HI, Bougeret C, Einbond A, Bork P

FEBS letters 1995

doi:10.1016/0014-5793(95)00550-s.

The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction

Bork P, Holm L, Koonin EV, Sander C

Proteins 1995

doi:10.1002/prot.340220306.

The SEA module: a new extracellular domain associated with O-glycosylation

Bork P, Patthy L

Protein science : a publication of the Protein Society 1995

doi:10.1002/pro.5560040716.

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology

Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM

Molecular microbiology 1995

doi:10.1111/j.1365-2958.1995.tb02321.x.

Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain

Sudol M, Bork P, Einbond A, Kastury K, Druck T, Negrini M, Huebner K, Lehman D

The Journal of biological chemistry 1995

doi:10.1074/jbc.270.24.14733.

A phosphotyrosine interaction domain

Bork P, Margolis B

Cell 1995

doi:10.1016/0092-8674(95)90347-x.

Ready for a motif submission? A proposed checklist

Bork P, Ouzounis C, McEntyre J

Trends in biochemical sciences 1995

doi:10.1016/s0968-0004(00)88974-4.

Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search

Bork P, Gellerich J, Groth H, Hooft R, Martin F

Protein science : a publication of the Protein Society 1995

doi:10.1002/pro.5560040213.

A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity

Bork P, Koonin EV

Proteins 1994

doi:10.1002/prot.340200407.

Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure

Meitinger T, Meindl A, Bork P, Rost B, Sander C, Haasemann M, Murken J

Nature genetics 1993

doi:10.1038/ng1293-376.

Prokaryotic members of a new family of putative helicases with similarity to transcription activator SNF2

Kolstø AB, Bork P, Kvaløy K, Lindback T, Grønstadt A, Kristensen T, Sander C

Journal of molecular biology 1993

doi:10.1006/jmbi.1993.1185.

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III

Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E

Protein science : a publication of the Protein Society 1992

doi:10.1002/pro.5560011216.

Cloning of a gene from Bacillus cereus with homology to the mreB gene from Escherichia coli

Narahara A, Naterstad K, Kristensen T, Lopez R, Bork P, Kolstø AB

Gene 1992

doi:10.1016/0378-1119(92)90047-s.

Proposed acquisition of an animal protein domain by bacteria

Bork P, Doolittle RF

Proceedings of the National Academy of Sciences of the United States of America 1992

doi:10.1073/pnas.89.19.8990.

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins

Bork P, Sander C, Valencia A

Proceedings of the National Academy of Sciences of the United States of America 1992

doi:10.1073/pnas.89.16.7290.

The modular architecture of vertebrate collagens

Bork P

FEBS letters 1992

doi:10.1016/0014-5793(92)80900-2.

What's in a genome?

Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E

Nature 1992

doi:10.1038/358287a0.

A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor

Bork P, Sander C

FEBS letters 1992

doi:10.1016/0014-5793(92)80853-9.

A module of the DnaJ heat shock proteins found in malaria parasites

Bork P, Sander C, Valencia A, Bukau B

Trends in biochemical sciences 1992

doi:10.1016/0968-0004(92)90319-5.

More von Willebrand factor type A domains? Sequence similarities with malaria thrombospondin-related anonymous protein, dihydropyridine-sensitive calcium channel and inter-alpha-trypsin inhibitor

Bork P, Rohde K

The Biochemical journal 1991

doi:10.1042/bj2790908.

On alpha-helices terminated by glycine. 2. Recognition by sequence patterns

Bork P, Preissner R

Biochemical and biophysical research communications 1991

doi:10.1016/s0006-291x(05)81117-9.

On alpha-helices terminated by glycine. 1. Identification of common structural features

Preissner R, Bork P

Biochemical and biophysical research communications 1991

doi:10.1016/s0006-291x(05)81116-7.

Shuffled domains in extracellular proteins

Bork P

FEBS letters 1991

doi:10.1016/0014-5793(91)80937-x.

Complement components C1r/C1s, bone morphogenic protein 1 and Xenopus laevis developmentally regulated protein UVS.2 share common repeats

Bork P

FEBS letters 1991

doi:10.1016/0014-5793(91)80433-4.

Sequence similarities between tryptophan synthase beta subunit and other pyridoxal-phosphate-dependent enzymes

Bork P, Rohde K

Biochemical and biophysical research communications 1990

doi:10.1016/0006-291x(90)90830-g.

Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach

Bork P, Grunwald C

European journal of biochemistry / FEBS 1990

doi:10.1111/j.1432-1033.1990.tb19129.x.

Recognition of functional regions in primary structures using a set of property patterns

Bork P

FEBS letters 1989

doi:10.1016/0014-5793(89)81818-6.

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