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Staff at EMBL

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Publications

Total: 45 publication(s)

2014

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. (2014)
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res. doi:10.1093/nar/gku1243
Europe PMC | doi

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. (2014)
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res. doi:10.1093/nar/gku1081
Europe PMC | doi


2012

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. (2012)
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Nucleic Acids Res. 40(Database issue):D284-9. doi:10.1093/nar/gkr1060
Europe PMC | doi

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. (2012)
InterPro in 2011: new developments in the family and domain prediction database
Nucleic Acids Res. 40(10):4725. doi:10.1093/nar/gkr948
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2012)
SMART 7: recent updates to the protein domain annotation resource
Nucleic Acids Res. 40(Database issue):D302-5. doi:10.1093/nar/gkr931
Europe PMC | doi


2011

Letunic I, Bork P. (2011)
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
Nucleic Acids Res. 39(Web Server issue):W475-8. doi:10.1093/nar/gkr201
Europe PMC | doi

Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. (2011)
iPath2.0: interactive pathway explorer
Nucleic Acids Res. 39(Web Server issue):W412-5. doi:10.1093/nar/gkr313
Europe PMC | doi

Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. (2011)
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data
Mol. Syst. Biol. 7:473. doi:10.1038/msb.2011.6
Europe PMC | doi


2010

Procter JB, Thompson J, Letunic I, Creevey C, Jossinet F, Barton GJ. (2010)
Visualization of multiple alignments, phylogenies and gene family evolution
Nat. Methods 7(3 Suppl):S16-25. doi:10.1038/nmeth.1434
Europe PMC | doi

Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. (2010)
A side effect resource to capture phenotypic effects of drugs
Mol. Syst. Biol. 6:343. doi:10.1038/msb.2009.98
Europe PMC | doi

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. (2010)
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
Nucleic Acids Res. 38(Database issue):D190-5. doi:10.1093/nar/gkp951
Europe PMC | doi


2009

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. (2009)
Impact of genome reduction on bacterial metabolism and its regulation
Science 326(5957):1263-1268. doi:10.1126/science.1177263
Europe PMC | doi

Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. (2009)
Quantifying environmental adaptation of metabolic pathways in metagenomics
Proc. Natl. Acad. Sci. U.S.A. 106(5):1374-1379. doi:10.1073/pnas.0808022106
Europe PMC | doi

Singh AH, Doerks T, Letunic I, Raes J, Bork P. (2009)
Discovering functional novelty in metagenomes: examples from light-mediated processes
J. Bacteriol. 191(1):32-41. doi:10.1128/jb.01084-08
Europe PMC | doi

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. (2009)
InterPro: the integrative protein signature database
Nucleic Acids Res. 37(Database issue):D211-5. doi:10.1093/nar/gkn785
Europe PMC | doi

Whitaker JW, Letunic I, McConkey GA, Westhead DR. (2009)
metaTIGER: a metabolic evolution resource
Nucleic Acids Res. 37(Database issue):D531-8. doi:10.1093/nar/gkn826
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2009)
SMART 6: recent updates and new developments
Nucleic Acids Res. 37(Database issue):D229-32. doi:10.1093/nar/gkn808
Europe PMC | doi


2008

Pincus D, Letunic I, Bork P, Lim WA. (2008)
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages
Proc. Natl. Acad. Sci. U.S.A. 105(28):9680-9684. doi:10.1073/pnas.0803161105
Europe PMC | doi

Letunic I, Yamada T, Kanehisa M, Bork P. (2008)
iPath: interactive exploration of biochemical pathways and networks
Trends Biochem. Sci. 33(3):101-103. doi:10.1016/j.tibs.2008.01.001
Europe PMC | doi

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. (2008)
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
Nature 451(7180):783-788. doi:10.1038/nature06617
Europe PMC | doi

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. (2008)
4DXpress: a database for cross-species expression pattern comparisons
Nucleic Acids Res. 36(Database issue):D847-53. doi:10.1093/nar/gkm797
Europe PMC | doi


2007

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. (2007)
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
Proc. Natl. Acad. Sci. U.S.A. 104(35):13913-13918. doi:10.1073/pnas.0702636104
Europe PMC | doi

Letunic I, Bork P. (2007)
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
Bioinformatics 23(1):127-128. doi:10.1093/bioinformatics/btl529
Europe PMC | doi

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. (2007)
New developments in the InterPro database
Nucleic Acids Res. 35(Database issue):D224-8. doi:10.1093/nar/gkl841
Europe PMC | doi


2006

Honeybee Genome Sequencing Consortium. (2006)
Insights into social insects from the genome of the honeybee Apis mellifera
Nature 443(7114):931-949. doi:10.1038/nature05260
Europe PMC | doi

Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P. (2006)
SMART 5: domains in the context of genomes and networks
Nucleic Acids Res. 34(Database issue):D257-60. doi:10.1093/nar/gkj079
Europe PMC | doi


2005

Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E. (2005)
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
RNA 11(10):1530-1544. doi:10.1261/rna.2160905
Europe PMC | doi

Zdobnov EM, von Mering C, Letunic I, Bork P. (2005)
Consistency of genome-based methods in measuring Metazoan evolution
FEBS Lett. 579(15):3355-3361. doi:10.1016/j.febslet.2005.04.006
Europe PMC | doi

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. (2005)
InterPro, progress and status in 2005
Nucleic Acids Res. 33(Database issue):D201-5. doi:10.1093/nar/gki106
Europe PMC | doi


2004

Koehl A, Schmidt N, Rieger A, Pilgram SM, Letunic I, Bork P, Soto F, Friauf E, Nothwang HG. (2004)
Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression
Eur. J. Neurosci. 20(12):3244-3258. doi:10.1111/j.1460-9568.2004.03791.x
Europe PMC | doi

International Chicken Genome Sequencing Consortium. (2004)
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Nature 432(7018):695-716. doi:10.1038/nature03154
Europe PMC | doi

Scheich C, Leitner D, Sievert V, Leidert M, Schlegel B, Simon B, Letunic I, Büssow K, Diehl A. (2004)
Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis
BMC Struct. Biol. 4:4. doi:10.1186/1472-6807-4-4
Europe PMC | doi

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P. (2004)
SMART 4.0: towards genomic data integration
Nucleic Acids Res. 32(Database issue):D142-4. doi:10.1093/nar/gkh088
Europe PMC | doi


2003

Boue S, Letunic I, Bork P. (2003)
Alternative splicing and evolution
Bioessays 25(11):1031-1034. doi:10.1002/bies.10371
Europe PMC | doi

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. (2003)
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
Nucleic Acids Res. 31(13):3625-3630. doi:10.1093/nar/gkg545
Europe PMC | doi

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. (2003)
The InterPro Database, 2003 brings increased coverage and new features
Nucleic Acids Res. 31(1):315-318. doi:10.1093/nar/gkg046
Europe PMC | doi


2002

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. (2002)
Initial sequencing and comparative analysis of the mouse genome
Nature 420(6915):520-562. doi:10.1038/nature01262
Europe PMC | doi

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. (2002)
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
Science 298(5591):149-159. doi:10.1126/science.1077061
Europe PMC | doi

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. (2002)
Immunity-related genes and gene families in Anopheles gambiae
Science 298(5591):159-165. doi:10.1126/science.1077136
Europe PMC | doi

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. (2002)
The genome sequence of the malaria mosquito Anopheles gambiae
Science 298(5591):129-149. doi:10.1126/science.1076181
Europe PMC | doi

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. (2002)
InterPro: an integrated documentation resource for protein families, domains and functional sites
Brief. Bioinformatics 3(3):225-235. doi:10.1093/bib/3.3.225
Europe PMC | doi

Letunic I, Copley RR, Bork P. (2002)
Common exon duplication in animals and its role in alternative splicing
Hum. Mol. Genet. 11(13):1561-1567. doi:10.1093/hmg/11.13.1561
Europe PMC | doi

Copley RR, Letunic I, Bork P. (2002)
Genome and protein evolution in eukaryotes
Curr Opin Chem Biol 6(1):39-45. doi:10.1016/s1367-5931(01)00278-2
Europe PMC | doi

Copley RR, Doerks T, Letunic I, Bork P. (2002)
Protein domain analysis in the era of complete genomes
FEBS Lett. 513(1):129-134. doi:10.1016/s0014-5793(01)03289-6
Europe PMC | doi

Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. (2002)
Recent improvements to the SMART domain-based sequence annotation resource
Nucleic Acids Res. 30(1):242-244. doi:10.1093/nar/30.1.242
Europe PMC | doi