Edit

Bork Group

Publications

Showing results out of

Publication year

A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.

Chechi K, Chakaroun R, Myridakis A, Forslund-Startceva SK, Fromentin S, Nielsen T, Aron-Wisneswky J, Belda E, Prifti E, Lassen PB, Falony G, Vieira-Silva S, Chilloux J, Sonomura K, Hoyles L, Martinez-Gili L, Pallotti F, Andrikopoulos P, Puig-Castellví F, Tapia RP, Castro-Dionicio I, Roume H, Pons N, Le Chatelier E, Quinquis B, Galleron N, Berland M, Olanipekun MT, Jia M, Manolias A, Holmes B, Adriouch S, Blüher M, Coelho LP, Da Silva K, Galan P, Ji B, Neves AL, Rouault C, Salem JE, Tremaroli V, Hansen TH, Søndertoft NB, Lewinter C, Pedersen HK, MetaCardis Consortium, Mark PD, Goetze JP, Køber L, Vestergaard H, Hansen T, Zucker JD, Sato TA, Hercberg S, Bäckhed F, Letunic I, Oppert JM, Nielsen J, Raes J, Tzoulaki I, Dehghan A, Zuber V, Bouzigon E, Lathrop M, Raina P, Froguel P, Matsuda F, Demenais F, Gauguier D, Stumvoll M, Bork P, Pedersen O, Ehrlich SD, Clément K, Dumas ME

Nature communications, 2026

doi:10.1038/s41467-026-69405-0.

Associations of Adiposity With Gut Microbiota Composition Among Adults-Results From a Federated Analysis of Individual Participant Data From Eight European Observational Studies.

Schwedhelm C, Pinart M, Forslund-Startceva SK, Oluwagbemigun K, Dötsch A, Schlicht K, Schwarz F, Siampani SM, Avraam D, De Angelis M, Bouwman J, Brigidi P, Caderni G, Calabrese FM, Cuadrat RRC, De Filippo C, De Filippis F, Ercolini D, Fabbrini M, Laudes M, Nöthlings U, Özsezen S, Sharon I, Schulze MB, Turroni S, Vitali F, Pischon T, Nimptsch K

Obesity reviews : an official journal of the International Association for the Study of Obesity, 2026

doi:10.1111/obr.70106.

Metalog: curated and harmonised contextual data for global metagenomics samples.

Kuhn M, Schmidt TSB, Ferretti P, Głazek A, Robbani SM, Akanni W, Fullam A, Schudoma C, Cetin E, Hassan M, Noack K, Schwarz A, Thielemann R, Thomas L, von Stetten M, Alves R, Iyappan A, Kartal E, Kel I, Keller MI, Maistrenko O, Mankowski A, Nishijima S, Podlesny D, Schiller J, Schulz S, Van Rossum T, Bork P

Nucleic acids research, 2026

doi:10.1093/nar/gkaf1118.

Prominent mediatory role of gut microbiome in the effect of lifestyle on host metabolic phenotypes.

Adriouch S, Belda E, Swartz TD, Forslund S, Prifti E, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Poitou C, Bel-Lassen P, Rouault C, Le Roy T, Andrikopoulos P, Chechi K, Puig-Castellví F, Dionicio IC, Froguel P, Holmes B, Alili R, Andreelli F, Soula H, Salem JE, Falony G, Vieira-Silva S, MetaCardis Consortium†Cecile Ciangura Resources, Arne Dietrich Resources, Morad Djebbar Resources, Angélique Doré Resources, Line Engelbrechtsen Resources, Leopold Fezeu Resources, Sebastien Fromentin Resources, Nathalie Galleron Resources, Marianne Grain Resources, Karoline Grunemann Resources, Agnes Hartemann Resources, Bolette Hartmann Resources, Gerald Helft Resources, Malene Hornbak Resources, Charlott Kranepuhl Resources, Julien Chilloux Resources, Antonis Myridakis Resources, Lesley Hoyles Resources, Richard Isnard Resources, Sophie Jaqueminet Resources, Niklas Rye Jørgensen Resources, Hanna Julienne Resources, Johanne Justesen Resources, Judith Kammer Resources, Nikolaj Krarup Resources, Lars Køber Resources, Michael Kuhn Resources, Veronique Lejard Resources, Ivica Letunic Resources, Florence Levenez Resources, Lajos MarkÓ Resources, Laura Martinez-Gili Resources, Nicolas Maziers Resources, Lucas Moitinho-Silva Resources, Gilles Montalescot Resources, Ana Luisa Neves Resources, Michael Olanipekun Resources, Laetitia Pasero Le Pavin Resources, Luis Pedro Coelho Resources, Nicolas Pons Resources, Benoit Quinquis Resources, Andrea Rodriguez-Martinez Resources, Hugo Roume Resources, Sebastien Schmidt Resources, Tatjana Schütz Resources, Johanne Silvain Resources, Mathilde Svendstrup Resources, Thierry Vanduyvenboden Resources, Stefanie Walther Resources, Jeroen Raes Conceptualization Funding acquisition Investigation Methodology Resources Writing – review & editing, Peer Bork Conceptualization Data curation Funding acquisition Methodology Resources Writing – review & editing, Michael Stumvoll Conceptualization Funding acquisition Investigation Resources Writing – review & editing, Oluf Pedersen Conceptualization Funding acquisition Investigation Resources Writing – review & editing, Stanislav Dusko Ehrlich Conceptualization Funding acquisition Resources Writing – review & editing, Marc-Emmanuel Dumas Conceptualization Data curation Funding acquisition Investigation Methodology Resources Writing – review & editing, Jean-Michel Oppert Conceptualization Funding acquisition Investigation Methodology Resources Writing – review & editing, Maria Dao Methodology Writing – review & editing, Jean-Daniel ZUCKER Conceptualization Formal analysis Funding acquisition Methodology Supervision Writing – original draft Writing – review & editing, Karine Clément Conceptualization Data curation Formal analysis Funding acquisition Methodology Supervision Writing – original draft Writing – review & editing, Renato Alves Resources, Ehm Astrid Andersson Galijatovic Resources, Olivier Barthelemy Resources, Jean-Philippe Bastard Resources, Jean-Paul Batisse Resources, Randa Bittar Resources, Matthias Blüher Resources, Frederic Bosquet Resources, Olivier Bourron Resources & Mickael Camus Resources, Raes J, Bork P, Stumvoll M, Pedersen O, Ehrlich SD, Dumas ME, Oppert JM, Dao MC, Zucker JD, Clément K

Gut microbes, 2025

doi:10.1080/19490976.2025.2599565.

Continent-wide differentiation of fitness traits and patterns of climate adaptation among European populations of Drosophila melanogaster.

Durmaz Mitchell E, Kerdaffrec E, Harney E, Paulo TF, Veselinovic MS, Tanaskovic M, Tyukmaeva V, de Arcaya TAF, Aksoy C, Argyridou E, Bailly TPM, Can D, Cobanoglu E, Cook N, Coşkun S, Davidovic S, Demir E, Dias T, Rasouli-Dogaheh S, Duque P, Eric K, Eric P, Erickson P, Filipovski F, Fishman B, Glaser-Schmitt A, Goldfischer A, Green L, Janillon S, Jelic M, Kostic H, Kreiman LE, Kremer N, Lyrakis M, Maistrenko OM, Marti SL, McGunnigle M, Merenciano M, Mira MS, Montbel V, Mouton L, Mukha DV, Murali S, Patenkovic A, Protsenko O, Putero FA, Reis M, Roshina NV, Rybina OY, Schou MF, Schowing T, Senkal SS, Serga S, Trieu V, Symonenko AV, Trostnikov MV, Tsybul'ko EA, van den Heuvel J, van Waarde D, Veselkina ER, Vieira CP, Wang X, Zandveld J, Abbott J, Billeter JC, Colinet H, Ebrahimi M, Gibert P, Hrcek J, Kankare M, Kozeretska I, Loeschcke V, Mensch J, Onder BS, Parsch J, Pasyukova EG, Stamenkovic-Radak M, Tauber E, Vieira C, Wegener C, Hoedjes KM, Zwaan BJ, Betancourt AJ, Fricke C, Grath S, Posnien N, Vieira J, Kapun M, Schlötterer C, Schmidt P, Sucena É, González J, Bergland A, Ritchie MG, Flatt T

Evolution letters, 2025

doi:10.1093/evlett/qraf014.

The postbiotic ReFerm® versus standard nutritional support in advanced alcohol-related liver disease (GALA-POSTBIO): a randomized controlled phase 2 trial.

Hansen JK, Israelsen M, Nishijima S, Stinson SE, Andersen P, Johansen S, Hansen CD, Brol MJ, Klein S, Schierwagen R, Uschner FE, Sulek K, Villesen IF, Lindvig KP, Thorhauge KH, Torp N, Jensen JM, Keller MI, Jensen GH, Detlefsen S, Leeming DJ, Stankevic E, Suvitaival T, Zawadzki A, Kuhn M, Jensen LJ, Karsdal M, Trebicka J, Israelsen H, Legido-Quigley C, Bork P, Arumugam M, Hansen T, Thiele M, Krag A

Nature communications, 2025

doi:10.1038/s41467-025-60755-9.

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.

Nishijima S, Stankevic E, Aasmets O, Schmidt TSB, Nagata N, Keller MI, Ferretti P, Juel HB, Fullam A, Robbani SM, Schudoma C, Hansen JK, Holm LA, Israelsen M, Schierwagen R, Torp N, Telzerow A, Hercog R, Kandels S, Hazenbrink DHM, Arumugam M, Bendtsen F, Brøns C, Fonvig CE, Holm JC, Nielsen T, Pedersen JS, Thiele MS, Trebicka J, Org E, Krag A, Hansen T, Kuhn M, Bork P, GALAXY and MicrobLiver Consortia

Cell, 2025

doi:10.1016/j.cell.2024.10.022.

InterPro: the protein sequence classification resource in 2025.

Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, Pinto BL, Orr A, Paysan-Lafosse T, Ponamareva I, Salazar GA, Bordin N, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Llinares-López F, Marchler-Bauer A, Meng-Papaxanthos L, Mi H, Natale DA, Orengo CA, Pandurangan AP, Piovesan D, Rivoire C, Sigrist CJA, Thanki N, Thibaud-Nissen F, Thomas PD, Tosatto SCE, Wu CH, Bateman A

Nucleic acids research, 2025

doi:10.1093/nar/gkae1082.

Bifidobacterium and Lactobacillus probiotics and gut dysbiosis in preterm infants: The PRIMAL randomized clinical trial.

Van Rossum T, Haiß A, Knoll RL, Marißen J, Podlesny D, Pagel J, Bleskina M, Vens M, Fortmann I, Siller B, Ricklefs I, Klopp J, Hilbert K, Meyer C, Thielemann R, Goedicke-Fritz S, Kuntz M, Wieg C, Teig N, Körner T, Kribs A, Hudalla H, Knuf M, Stein A, Gille C, Bagci S, Dohle F, Proquitté H, Olbertz DM, Schmidt E, Koch L, Pirr S, Rupp J, Spiegler J, Kopp MV, Göpel W, Herting E, Forslund SK, Viemann D, Zemlin M, Bork P, Gehring S, König IR, Henneke P, Härtel C

JAMA pediatrics, 2024

doi:10.1001/jamapediatrics.2024.2626.

A clinical protocol for a German birth cohort study of the Maturation of Immunity Against respiratory viral Infections (MIAI).

Hartmann CR, Khan R, Schöning J, Richter M, Willers M, Pirr S, Heckmann J, Dirks J, Morbach H, Konrad M, Fries E, Winkler M, Büchel J, Seidenspinner S, Fischer J, Vollmuth C, Meinhardt M, Marissen J, Schmolke M, Haid S, Pietschmann T, Backes S, Dölken L, Löber U, Keil T, Heuschmann PU, Wöckel A, Sagar, Ulas T, Forslund-Startceva SK, Härtel C, Viemann D

Frontiers in immunology, 2024

doi:10.3389/fimmu.2024.1443665.

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.

Essex M, Millet Pascual-Leone B, Löber U, Kuhring M, Zhang B, Brüning U, Fritsche-Guenther R, Krzanowski M, Fiocca Vernengo F, Brumhard S, Röwekamp I, Anna Bielecka A, Lesker TR, Wyler E, Landthaler M, Mantei A, Meisel C, Caesar S, Thibeault C, Corman VM, Marko L, Suttorp N, Strowig T, Kurth F, Sander LE, Li Y, Kirwan JA, Forslund SK, Opitz B

NPJ biofilms and microbiomes, 2024

doi:10.1038/s41522-024-00538-0.

Paternal microbiome perturbations impact offspring fitness.

Argaw-Denboba A, Schmidt TSB, Di Giacomo M, Ranjan B, Devendran S, Mastrorilli E, Lloyd CT, Pugliese D, Paribeni V, Dabin J, Pisaniello A, Espinola S, Crevenna A, Ghosh S, Humphreys N, Boruc O, Sarkies P, Zimmermann M, Bork P, Hackett JA

Nature, 2024

doi:10.1038/s41586-024-07336-w.

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung.

Dörner PJ, Anandakumar H, Röwekamp I, Fiocca Vernengo F, Millet Pascual-Leone B, Krzanowski M, Sellmaier J, Brüning U, Fritsche-Guenther R, Pfannkuch L, Kurth F, Milek M, Igbokwe V, Löber U, Gutbier B, Holstein M, Heinz GA, Mashreghi MF, Schulte LN, Klatt AB, Caesar S, Wienhold SM, Offermanns S, Mack M, Witzenrath M, Jordan S, Beule D, Kirwan JA, Forslund SK, Wilck N, Bartolomaeus H, Heimesaat MM, Opitz B

Nature communications, 2024

doi:10.1038/s41467-024-47149-z.

Opportunities and barriers for omics-based biomarker discovery in steatotic liver diseases.

Thiele M, Villesen IF, Niu L, Johansen S, Sulek K, Nishijima S, Van Espen L, Keller M, Israelsen M, Suvitaival T, de Zawadzki A, Juel HB, Brol MJ, Stinson SE, Huang Y, Alvarez Silva MC, Kuhn M, Anastasiadou E, Leeming DJ, Karsdal M, Matthijnssens J, Arumugam M, Dalgaard LT, Legido-Quigley C, Mann M, Trebicka J, Bork P, Jensen LJ, Hansen T, Krag A, MicrobLiver and GALAXY consortia, GALAXY consortium, MicrobLiver consortium

Journal of hepatology, 2024

doi:10.1016/j.jhep.2024.03.035.

Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.

Mücke MM, Hernández-Tejero M, Gu W, Kuhn M, Janz M, Keller MI, Fullam A, Altepeter L, Mücke VT, Finkelmeier F, Schwarzkopf KM, Cremonese C, Hunyady PM, Heilani MW, Uschner FE, Schierwagen R, Brol MJ, Fischer J, Klein S, Peiffer KH, Hogardt M, Shoaie S, Coenraad MJ, Bojunga J, Arroyo V, Zeuzem S, Kempf VAJ, Welsch C, Laleman W, Bork P, Fernandez J, Trebicka J, MICROB-PREDICT and PREDICT Study Group of the EASL-CLIF Consortium

Alimentary Pharmacology and Therapeutics, 2024

doi:10.1111/apt.17899.

Genomic attributes of airway commensal bacteria and mucosa.

Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, Lewis KE, Hopkin JM, Chung KF, O'Carroll O, Faul J, Creaser-Thomas J, Andrews M, Ghosal R, Piatek S, Willis-Owen SAG, Bartolomaeus TUP, Birkner T, Dwyer S, Kumar N, Turek EM, William Musk A, Hui J, Hunter M, James A, Dumas ME, Filippi S, Cox MJ, Lawley TD, Forslund SK, Moffatt MF, Cookson WOC

Communications biology, 2024

doi:10.1038/s42003-024-05840-3.

Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean.

Fabien L, Lionel G, Brandão MC, Pedro CL, Sébastien C, Richard DJ, Amanda E, Gasol JM, Luc GP, Nicolas H, Ibarbalz FM, Laëtitia J, Michel L, Séverinne M, Zoé M, Marc P, Pierella Karlusich JJ, Pepperkok R, Jean-Baptiste R, Lucie Z, Lars S, Acinas SG, Lee K, Emmanuel B, Sullivan MB, de Vargas C, Chris B, Eric K, Gabriel G, Tara Oceans Coordinators

bioRxiv, 2024

doi:10.1101/2024.02.09.579612.

Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.

Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D'Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, Pascual-Anaya J

Nature ecology & evolution, 2024

doi:10.1038/s41559-023-02299-z.

Dominantly inherited micro-satellite instable cancer - the four Lynch syndromes - an EHTG, PLSD position statement.

Møller P, Seppälä TT, Ahadova A, Crosbie EJ, Holinski-Feder E, Scott R, Haupt S, Möslein G, Winship I, Broeke SWB, Kohut KE, Ryan N, Bauerfeind P, Thomas LE, Evans DG, Aretz S, Sijmons RH, Half E, Heinimann K, Horisberger K, Monahan K, Engel C, Cavestro GM, Fruscio R, Abu-Freha N, Zohar L, Laghi L, Bertario L, Bonanni B, Tibiletti MG, Lino-Silva LS, Vaccaro C, Valle AD, Rossi BM, da Silva LA, de Oliveira Nascimento IL, Rossi NT, Dębniak T, Mecklin JP, Bernstein I, Lindblom A, Sunde L, Nakken S, Heuveline V, Burn J, Hovig E, Kloor M, Sampson JR, Dominguez-Valentin M, Prospective Lynch Syndrome Database (www.plsd.eu) and The European Hereditary Tumour Group (www.ehtg.org)

Hereditary Cancer in Clinical Practice, 2023

doi:10.1186/s13053-023-00263-3.

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide.

Andrikopoulos P, Aron-Wisnewsky J, Chakaroun R, Myridakis A, Forslund SK, Nielsen T, Adriouch S, Holmes B, Chilloux J, Vieira-Silva S, Falony G, Salem JE, Andreelli F, Belda E, Kieswich J, Chechi K, Puig-Castellvi F, Chevalier M, Le Chatelier E, Olanipekun MT, Hoyles L, Alves R, Helft G, Isnard R, Køber L, Coelho LP, Rouault C, Gauguier D, Gøtze JP, Prifti E, Froguel P, MetaCardis Consortium, Zucker JD, Bäckhed F, Vestergaard H, Hansen T, Oppert JM, Blüher M, Nielsen J, Raes J, Bork P, Yaqoob MM, Stumvoll M, Pedersen O, Ehrlich SD, Clément K, Dumas ME

Nature communications, 2023

doi:10.1038/s41467-023-39824-4.

Ocean-wide comparisons of mesopelagic planktonic community structures.

Rigonato J, Budinich M, Murillo AA, Brandão MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Frémont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E, Tara Oceans coordinators, Bork P, Bowler C, de Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O

ISME communications, 2023

doi:10.1038/s43705-023-00279-9.

Sphingolipids are depleted in alcohol-related liver fibrosis.

Thiele M, Suvitaival T, Trošt K, Kim M, de Zawadzki A, Kjaergaard M, Rasmussen DN, Lindvig KP, Israelsen M, Detlefsen S, Andersen P, Juel HB, Nielsen T, Georgiou S, Filippa V, Kuhn M, Nishijima S, Moitinho-Silva L, Rossing P, Trebicka J, Anastasiadou E, Bork P, Hansen T, Quigley CL, Krag A, MicrobLiver, GALAXY Consortia

Gastroenterology, 2023

doi:10.1053/j.gastro.2023.02.023.

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.

Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J

Nature, 2023

doi:10.1038/s41586-022-05546-8.

InterPro in 2022.

Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunić I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A

Nucleic acids research, 2023

doi:10.1093/nar/gkac993.

Deep phenotyping of two pre-clinical mouse models and a cohort of RBM20 mutation carriers reveals no sex-dependent disease severity in RBM20 cardiomyopathy.

Lennermann DC, Pepin ME, Grosch M, Konrad L, Kemmling E, Hartmann J, Nolte JL, Clauder-Münster S, Kayvanpour E, Sedaghat-Hamedani F, Haas J, Meder B, van den Boogaard M, Amin AS, Dewenter M, Krüger M, Steinmetz LM, Backs J, van den Hoogenhof MMG

American Journal of Physiology - Heart and Circulatory Physiology, 2022

doi:10.1152/ajpheart.00328.2022.

Mutant phosphodiesterase 3A protects from hypertension-induced cardiac damage.

Ercu M, Mücke MB, Pallien T, Markó L, Sholokh A, Schächterle C, Aydin A, Kidd A, Walter S, Esmati Y, McMurray BJ, Lato DF, Yumi Sunaga-Franze D, Dierks PH, Flores BIM, Walker-Gray R, Gong M, Merticariu C, Zühlke K, Russwurm M, Liu T, Batolomaeus TUP, Pautz S, Schelenz S, Taube M, Napieczynska H, Heuser A, Eichhorst J, Lehmann M, Miller DC, Diecke S, Qadri F, Popova E, Langanki R, Movsesian MA, Herberg FW, Forslund SK, Müller DN, Borodina T, Maass PG, Bähring S, Hübner N, Bader M, Klussmann E

Circulation, 2022

doi:10.1161/circulationaha.122.060210.

Inflammation in children with CKD linked to gut dysbiosis and metabolite imbalance.

Holle J, Bartolomaeus H, Löber U, Behrens F, Bartolomaeus TUP, Anandakumar H, Wimmer MI, Vu DL, Kuhring M, Brüning U, Maifeld A, Geisberger S, Kempa S, Schumacher F, Kleuser B, Bufler P, Querfeld U, Kitschke S, Engler D, Kuhrt LD, Drechsel O, Eckardt KU, Forslund SK, Thürmer A, McParland V, Kirwan JA, Wilck N, Müller D

Journal of the American Society of Nephrology : JASN, 2022

doi:10.1681/asn.2022030378.

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems.

Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, Tara Oceans Coordinators, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcalà M, Iudicone D, Jaillon O

eLife, 2022

doi:10.7554/elife.78129.

Priorities for ocean microbiome research.

Tara Ocean Foundation, Tara Oceans, European Molecular Biology Laboratory (EMBL), European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC)

Nature microbiology, 2022

doi:10.1038/s41564-022-01145-5.

Biosynthetic potential of the global ocean microbiome.

Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlström CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sánchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL, Piel J, Sunagawa S

Nature, 2022

doi:10.1038/s41586-022-04862-3.

A faecal microbiota signature with high specificity for pancreatic cancer.

Kartal E, Schmidt TSB, Molina-Montes E, Rodríguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gómez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Márquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K, MAGIC Study investigators, PanGenEU Study investigators, Benes V, Zeller G, Trebicka J, Real FX, Malats N, Bork P

Gut, 2022

doi:10.1136/gutjnl-2021-324755.

Microbiome and metabolome features of the cardiometabolic disease spectrum.

Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves R, Adiouch S, Bar N, Talmor-Barkan Y, Belda E, Caesar R, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Le Chatelier E, Julienne H, Olsson L, Pedersen HK, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Schmidt TSB, Vieira-Silva S, Li P, Zimmermann-Kogadeeva M, Lewinter C, Søndertoft NB, Hansen TH, Gauguier D, Gøtze JP, Køber L, Kornowski R, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Letunic I, Bäckhed F, Oppert JM, Nielsen J, Raes J, Bork P, Stumvoll M, Segal E, Clément K, Dumas ME, Ehrlich SD, Pedersen O

Nature medicine, 2022

doi:10.1038/s41591-022-01688-4.

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.

Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann KE, Prifiti E, Aron-Wisnewsky J, Debédat J, Le Roy T, Nielsen T, Amouyal C, André S, Andreelli F, Blüher M, Chakaroun R, Chilloux J, Coelho LP, Dao MC, Das P, Fellahi S, Forslund S, Galleron N, Hansen TH, Holmes B, Ji B, Krogh Pedersen H, Le P, Le Chatelier E, Lewinter C, Mannerås-Holm L, Marquet F, Myridakis A, Pelloux V, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Sokolovska N, Søndertoft NB, Touch S, Vieira-Silva S, MetaCardis Consortium, Galan P, Holst J, Gøtze JP, Køber L, Vestergaard H, Hansen T, Hercberg S, Oppert JM, Nielsen J, Letunic I, Dumas ME, Stumvoll M, Pedersen OB, Bork P, Ehrlich SD, Zucker JD, Bäckhed F, Raes J, Clément K

Gut, 2022

doi:10.1136/gutjnl-2021-325753.

Towards the biogeography of prokaryotic genes.

Coelho LP, Alves R, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P

Nature, 2021

doi:10.1038/s41586-021-04233-4.

Combinatorial, additive and dose-dependent drug-microbiome associations.

Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem JE, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Søndertoft NB, Pedersen HK, Hansen TH, MetaCardis Consortium*, Gøtze JP, Køber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert JM, Letunic I, Nielsen J, Bäckhed F, Ehrlich SD, Dumas ME, Raes J, Pedersen O, Clément K, Stumvoll M, Bork P

Nature, 2021

doi:10.1038/s41586-021-04177-9.

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution.

Musser JM, Schippers KJ, Nickel M, Mizzon G, Kohn AB, Pape C, Ronchi P, Papadopoulos N, Tarashansky AJ, Hammel JU, Wolf F, Liang C, Hernández-Plaza A, Cantalapiedra CP, Achim K, Schieber NL, Pan L, Ruperti F, Francis WR, Vargas S, Kling S, Renkert M, Polikarpov M, Bourenkov G, Feuda R, Gaspar I, Burkhardt P, Wang B, Bork P, Beck M, Schneider TR, Kreshuk A, Wörheide G, Huerta-Cepas J, Schwab Y, Moroz LL, Arendt D

Science (New York, N.Y.), 2021

doi:10.1126/science.abj2949.

Unravelling the collateral damage of antibiotics on gut bacteria.

Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A

Nature, 2021

doi:10.1038/s41586-021-03986-2.

Identification and characterization of human observational studies in nutritional epidemiology on gut microbiomics for joint data analysis.

Pinart M, Nimptsch K, Forslund SK, Schlicht K, Gueimonde M, Brigidi P, Turroni S, Ahrens W, Hebestreit A, Wolters M, Dötsch A, Nöthlings U, Oluwagbemigun K, Cuadrat RRC, Schulze MB, Standl M, Schloter M, De Angelis M, Iozzo P, Guzzardi MA, Vlaemynck G, Penders J, Jonkers DMAE, Stemmer M, Chiesa G, Cavalieri D, De Filippo C, Ercolini D, De Filippis F, Ribet D, Achamrah N, Tavolacci MP, Déchelotte P, Bouwman J, Laudes M, Pischon T

Nutrients, 2021

doi:10.3390/nu13093292.

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.

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.

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, 2021

doi:10.1093/nar/gkaa977.

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.

Primary mismatch repair deficient IDH-mutant astrocytoma (PMMRDIA) is a distinct type with a poor prognosis.

Suwala AK, Stichel D, Schrimpf D, Kloor M, Wefers AK, Reinhardt A, Maas SLN, Kratz CP, Schweizer L, Hasselblatt M, Snuderl M, Abedalthagafi MSJ, Abdullaev Z, Monoranu CM, Bergmann M, Pekrun A, Freyschlag C, Aronica E, Kramm CM, Hinz F, Sievers P, Korshunov A, Kool M, Pfister SM, Sturm D, Jones DTW, Wick W, Unterberg A, Hartmann C, Dodgshun A, Tabori U, Wesseling P, Sahm F, von Deimling A, Reuss DE

Acta neuropathologica, 2020

doi:10.1007/s00401-020-02243-6.

The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution.

Ballhausen A, Przybilla MJ, Jendrusch M, Haupt S, Pfaffendorf E, Seidler F, Witt J, Hernandez Sanchez A, Urban K, Draxlbauer M, Krausert S, Ahadova A, Kalteis MS, Pfuderer PL, Heid D, Stichel D, Gebert J, Bonsack M, Schott S, Bläker H, Seppälä T, Mecklin JP, Ten Broeke S, Nielsen M, Heuveline V, Krzykalla J, Benner A, Riemer AB, von Knebel Doeberitz M, Kloor M

Nature communications, 2020

doi:10.1038/s41467-020-18514-5.

Multi-omics analysis reveals adipose-tumor crosstalk in colorectal cancer patients.

Holowatyj AN, Haffa M, Lin T, Scherer D, Gigic B, Ose J, Warby CA, Himbert C, Abbenhardt-Martin C, Achaintre D, Boehm J, Boucher KM, Gicquiau A, Gsur A, Habermann N, Kauczor HU, Herpel E, Kloor M, Keski-Rahkonen P, Kok DE, von Knebel Doeberitz M, Schirmacher P, Nattenmüller J, Schrotz-King P, Schneider M, Ueland PM, Simon T, Weijenberg MP, Viskochil R, Ulrich A, Scalbert A, Ulrich CM, Bowers LW, Hursting SD

Cancer Prevention Research, 2020

doi:10.1158/1940-6207.CAPR-19-0538.

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.

Phosphodiesterase 3A and arterial hypertension.

Ercu M, Markó L, Schächterle C, Tsvetkov D, Cui Y, Maghsodi S, Bartolomaeus TUP, Maass PG, Zühlke K, Gregersen N, Hübner N, Hodge R, Mühl A, Pohl B, Molé-Illas R, Walter S, Geelhaar A, Schelenz S, Napieczynska H, Heuser A, Taube M, Qadri F, Anistan YM, Plehm R, Todiras M, Langanki R, Popova E, Lehmann M, Eichhorst J, Russwurm M, Wiesner B, Müller DN, Gollasch M, Forslund SK, Kamer I, Bader M, Luft FC, Aydin A, Bähring S, Klussmann E

Circulation, 2020

doi:10.1161/CIRCULATIONAHA.119.043061.

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.

Orchestrating single-cell analysis with Bioconductor.

Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Martini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Hicks SC, Gottardo R

Nature methods, 2019

doi:10.1038/s41592-019-0654-x.

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.

Global trends in marine plankton diversity across kingdoms of life.

Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Soviadan D, Scalco E, Zingone A, Zayed AA, Ferland J, Labadie K, Kandels S, Marec C, Dimier C, Picheral M, Pisarev S, Poulain J, Pesant S, Carmichael M, Babin M, Pesant S, Jaillon O, Acinas SG, Boss E, Iudicone D, Stemmann L, Sullivan MB, Ogata H, Pelletier E, de Vargas C, Karp-Boss L, Sunagawa S, Bopp L, Bowler C, Zinger L, Wincker P, Lombard F

Cell, 2019

doi:10.1016/j.cell.2019.10.008.

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.

Ensembl 2020.

Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, Dodiya K, Davidson C, Gall A, Fatima R, Gil L, Giron CG, Haggerty L, Grego T, Hourlier T, Haskell E, Janacek SH, Izuogu OG, Kay M, Juettemann T, Le T, Lavidas I, Maurel T, McDowall M, Lemos D, Martinez JG, Moore B, Nuhn M, McMahon A, Mohanan S, Parton A, Patricio M, Oheh DN, Parker A, Schmitt BM, Schuilenburg H, Sakthivel MP, Abdul Salam AI, Taylor K, Szuba M, Sycheva M, Sheppard D, Walts B, Vullo A, Threadgold G, Thormann A, Flint B, Chakiachvili M, Zadissa A, Winterbottom A, Kostadima M, IIsley G, Hunt SE, Frankish A, Mudge JM, Muffato M, Perry E, Ruffier M, Langridge N, Loveland JE, Martin FJ, Morales J, Flicek P, Trevanion SJ, Cunningham F, Howe KL, Zerbino DR

Nucleic acids research, 2019

doi:10.1093/nar/gkz966.

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.

Ensembl Genomes 2020–enabling non-vertebrate genomic research.

Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Fexova S, Davis P, George N, Gall A, Gupta P, Gil L, Haskell E, Hammond-Kosack KE, Jaiswal P, Hunt SE, Kersey PJ, Janacek SH, Maheswari U, Langridge N, McDowall MD, Maurel T, Naamati G, Naithani S, Moore B, Muffato M, Patricio M, Paulini M, Olson A, Papatheodorou I, Preece J, Rosello M, Pedro H, Perry E, Staines DM, Stein J, Russell M, Sitnik V, Wei S, Urban M, Trevanion SJ, Tello-Ruiz MK, Flicek P, Yates AD, Williams G, Ware D

Nucleic acids research, 2019

doi:10.1093/nar/gkz890.

Advances and applications in the quest for orthologs.

Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD, Thomas PD

Molecular biology and evolution, 2019

doi:10.1093/molbev/msz150.

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.

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.

Short-chain fatty acid propionate protects from hypertensive cardiovascular damage.

Bartolomaeus H, Balogh A, Yakoub M, Homann S, Markó L, Höges S, Tsvetkov D, Krannich A, Wundersitz S, Avery EG, Haase N, Kräker K, Hering L, Maase M, Kusche-Vihrog K, Fielitz J, Grandoch M, Gollasch M, Kempa S, Kozhakhmetov S, Zhumadilov Z, Eckardt KU, Kushugulova A, Rump LC, Dechend R, Müller DN, Forslund SK, Wilck N, Stegbauer J

Circulation, 2019

doi:10.1161/CIRCULATIONAHA.118.036652.

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.

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.

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 J, Benoiston A, Bertrand A, Biard T, Bittner L, Boccara M, Brum JR, Brunet C, Busseni G, Carratalà A, Claustre H, Coelho LP, Colin S, Aniello S, Silva CD, Core MD, Doré H, Gasparini S, Kokoszka F, Jamet J, Lejeusne C, Lepoivre C, Lescot M, Lima-Mendez G, Lombard F, Lukeš J, Maillet N, Madoui M, Martinez E, Mazzocchi MG, Néou MB, Paz-Yepes J, Poulain J, Ramondenc S, Romagnan J, Roux S, Manta DS, Sanges R, Speich S, Sprovieri M, Sunagawa S, Taillandier V, Tanaka A, Tirichine L, Trottier C, Uitz J, Veluchamy A, Veselá J, Vincent F, Yau S, Kandels-Lewis S, Searson S, Dimier C, Picheral M, Bork P, Boss E, Vargas C, Follows MJ, Grimsley N, Guidi L, Hingamp P, Karsenti E, Sordino P, Stemmann L, Sullivan MB, Tagliabue A, Zingone A, Garczarek L, Ortenzio F, Testor P, Not F, Alcalà MR, Wincker P, Bowler C, Iudicone D, Acinas SG, Bork P, Boss E, Bowler C, Vargas C, Follows MJ, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P

Global Biogeochemical Cycles, 2019

doi:10.1029/2018gb006022.

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, 2019

doi:10.1093/nar/gky1100.

Function, evolution, and structure of J-domain proteins.

Kampinga HH, Andreasson C, Barducci A, Cheetham ME, Cyr D, Emanuelsson C, Genevaux P, Gestwicki JE, Goloubinoff P, Huerta-Cepas J, Kirstein J, Liberek K, Mayer MP, Nagata K, Nillegoda NB, Ramos C, Pulido P, Rospert S, De Los Rios P, Sahi C, Rosenzweig R, Tomiczek B, Taipale M, Young JC, Ushioda R, Zylicz A, Zimmermann R, Craig EA, Zylicz M, Marszalek J

Cell stress & chaperones, 2018

doi:10.1007/s12192-018-0948-4.

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.

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.

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.

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, 2018

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

Science Forum: The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim SK, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake SR, Reik W, Rozenblatt-Rosen O, Sanes JR, Satija R, Schumacher TN, Shalek AK, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton MR, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt FM, Weissman JS, Wold BJ, Xavier RJ, Yosef N, Yosef N

eLife, 2017

doi:10.7554/eLife.27041.

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.

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.

Genomic and transcriptomic heterogeneity of colorectal tumors arising in Lynch Syndrome.

Binder H, Hopp L, Schweiger MR, Hoffmann S, Jühling F, Kerick M, Timmermann B, Siebert S, Grimm C, Nersisyan L, Arakelyan A, Herberg M, Buske P, Loeffler-Wirth H, Rosolowski M, Engel C, Przybilla J, Peifer M, Friedrichs N, Moeslein G, Odenthal M, Hussong M, Peters S, Holzapfel S, Nattermann J, Hueneburg R, Schmiegel W, Royer-Pokora B, Aretz S, Kloth M, Kloor M, Buettner R, Galle J, Loeffler M

The Journal of pathology, 2017

doi:10.1002/path.4948.

Gearing up to handle the mosaic nature of life in the quest for orthologs.

Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Fernández Breis JT, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S

Bioinformatics (Oxford, England), 2017

doi:10.1093/bioinformatics/btx542.

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.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Hurwitz BL, Pesant S, Karsenti E, Wincker P

Scientific data, 2017

doi:10.1038/sdata.2017.93.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips A, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD

Genome research, 2017

doi:10.1101/gr.217117.116.

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, 2017

doi:10.1093/nar/gkw1107.

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.

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.

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.

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.

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.

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.

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.

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, 2015

doi:10.1126/science.1261605.

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, 2015

doi:10.1126/science.1262073.

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.

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, 2015

doi:10.1126/science.1261447.

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, 2015

doi:10.1093/nar/gku1243.

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.

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.

A fair comparison

Costea PI, Zeller G, Sunagawa S, Bork P

Nature methods, 2014

doi:10.1038/nmeth.2897.

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.

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.

Biggest challenges in bioinformatics

Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM, HUB Participants

EMBO reports, 2013

doi:10.1038/embor.2013.34.

Insights into bilaterian evolution from three spiralian genomes

Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS

Nature, 2013

doi:10.1038/nature11696.

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.

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.

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.

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.

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.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH

Science (New York, N.Y.), 2010

doi:10.1126/science.1196914.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T

Journal of biomedical semantics, 2010

doi:10.1186/2041-1480-1-8.

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.

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.

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.

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.

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.

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.

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.

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.

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:.

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.

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.

Next station in microarray data analysis: GEPAS

Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J

Nucleic acids research, 2006

doi:10.1093/nar/gkl197.

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.

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.

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.

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.

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.

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.

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.

The way we write

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

EMBO reports, 2003

doi:10.1038/sj.embor.embor833.

Evaluation of annotation strategies using an entire genome sequence

Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA

Bioinformatics (Oxford, England), 2003

doi:10.1093/bioinformatics/btg077.

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.

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.

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.

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.

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.

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.

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.

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:.

What's in a genome?

Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E

Nature, 1992

doi:10.1038/358287a0.

No matching publications found

Edit