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.

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

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

BMJ open, 2018

doi:10.1136/bmjopen-2018-021682.

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

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

Nucleic acids research, 2014

doi:10.1093/nar/gku1243.

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.

SMART 7: recent updates to the protein domain annotation resource

Letunic I, Doerks T, Bork P

Nucleic acids research, 2012

doi:10.1093/nar/gkr931.

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

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

Nucleic acids research, 2012

doi:10.1093/nar/gkr1060.

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

Letunic I, Bork P

Nucleic acids research, 2011

doi:10.1093/nar/gkr201.

iPath2.0: interactive pathway explorer

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

Nucleic acids research, 2011

doi:10.1093/nar/gkr313.

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

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

Molecular systems biology, 2011

doi:10.1038/msb.2011.6.

Visualization of multiple alignments, phylogenies and gene family evolution

Procter JB, Thompson J, Letunic I, Creevey C, Jossinet F, Barton GJ

Nature methods, 2010

doi:10.1038/nmeth.1434.

A side effect resource to capture phenotypic effects of drugs.

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

Molecular systems biology, 2010

doi:10.1038/msb.2009.98.

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

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

Nucleic acids research, 2010

doi:10.1093/nar/gkp951.

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.

Quantifying environmental adaptation of metabolic pathways in metagenomics

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

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

doi:10.1073/pnas.0808022106.

InterPro: the integrative protein signature database

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

Nucleic acids research, 2009

doi:10.1093/nar/gkn785.

SMART 6: recent updates and new developments

Letunic I, Doerks T, Bork P

Nucleic acids research, 2009

doi:10.1093/nar/gkn808.

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

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

Journal of bacteriology, 2009

doi:10.1128/jb.01084-08.

metaTIGER: a metabolic evolution resource

Whitaker JW, Letunic I, McConkey GA, Westhead DR

Nucleic acids research, 2009

doi:10.1093/nar/gkn826.

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

Pincus D, Letunic I, Bork P, Lim WA

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

doi:10.1073/pnas.0803161105.

iPath: interactive exploration of biochemical pathways and networks

Letunic I, Yamada T, Kanehisa M, Bork P

Trends in biochemical sciences, 2008

doi:10.1016/j.tibs.2008.01.001.

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

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

Nature, 2008

doi:10.1038/nature06617.

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

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

Nucleic acids research, 2008

doi:10.1093/nar/gkm797.

Quantitative assessment of protein function prediction from metagenomics shotgun sequences

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

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

doi:10.1073/pnas.0702636104.

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

Letunic I, Bork P

Bioinformatics (Oxford, England), 2007

doi:10.1093/bioinformatics/btl529.

New developments in the InterPro database

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

Nucleic acids research, 2007

doi:10.1093/nar/gkl841.

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

Honeybee Genome Sequencing Consortium

Nature, 2006

doi:10.1038/nature05260.

SMART 5: domains in the context of genomes and networks

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

Nucleic acids research, 2006

doi:10.1093/nar/gkj079.

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

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

RNA (New York, N.Y.), 2005

doi:10.1261/rna.2160905.

Consistency of genome-based methods in measuring Metazoan evolution

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

FEBS letters, 2005

doi:10.1016/j.febslet.2005.04.006.

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.

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

International Chicken Genome Sequencing Consortium

Nature, 2004

doi:10.1038/nature03154.

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

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

The European journal of neuroscience, 2004

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

Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

Scheich C, Leitner D, Sievert V, Leidert M, Schlegel B, Simon B, Letunic I, Büssow K, Diehl A

BMC structural biology, 2004

doi:10.1186/1472-6807-4-4.

SMART 4.0: towards genomic data integration

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

Nucleic acids research, 2004

doi:10.1093/nar/gkh088.

Alternative splicing and evolution

Boue S, Letunic I, Bork P

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

doi:10.1002/bies.10371.

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

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

Nucleic acids research, 2003

doi:10.1093/nar/gkg545.

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.

Common exon duplication in animals and its role in alternative splicing

Letunic I, Copley RR, Bork P

Human molecular genetics, 2002

doi:10.1093/hmg/11.13.1561.

Protein domain analysis in the era of complete genomes

Copley RR, Doerks T, Letunic I, Bork P

FEBS letters, 2002

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

Genome and protein evolution in eukaryotes

Copley RR, Letunic I, Bork P

Current opinion in chemical biology, 2002

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

Recent improvements to the SMART domain-based sequence annotation resource

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

Nucleic acids research, 2002

doi:10.1093/nar/30.1.242.