EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

  • PhD 1990, University of Leipzig.
    Habilitation 1995, Humboldt University, Berlin.
    At EMBL since 1991, Head of Unit since 2001.
    Strategic Head of Bioinformatics at EMBL Heidelberg since 2011.
    ERC Advanced Investigator.

Publications

Total: 586 publication(s)

2006

Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ. (2006)

Similar gene expression profiles do not imply similar tissue functions

Trends Genet. 22(3):132-138. doi: 10.1016/j.tig.2006.01.006
Europe PMC | doi

Jensen LJ, Saric J, Bork P. (2006)

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

Nat. Rev. Genet. 7(2):119-129. doi: 10.1038/nrg1768
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

Foerstner KU, von Mering C, Hooper SD, Bork P. (2005)

Environments shape the nucleotide composition of genomes

EMBO Rep. 6(12):1208-1213. doi: 10.1038/sj.embor.7400538
Europe PMC | doi

Hooper SD, Bork P. (2005)

Medusa: a simple tool for interaction graph analysis

Bioinformatics 21(24):4432-4433. doi: 10.1093/bioinformatics/bti696
Europe PMC | doi

Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, Bork P, Wiese S, Gessler M, Kerkhoff E. (2005)

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

Gene Expr. Patterns 6(1):79-85. doi: 10.1016/j.modgep.2005.04.015
Europe PMC | doi

Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D. (2005)

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

Science 310(5752):1325-1326. doi: 10.1126/science.1119089
Europe PMC | doi

Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M. (2005)

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

J. Cell Biol. 171(4):627-640. doi: 10.1083/jcb.200507168
Europe PMC | doi

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

Suyama M, Lathe WC 3rd, Bork P. (2005)

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii

FEBS Lett. 579(24):5281-5286. doi: 10.1016/j.febslet.2005.08.051
Europe PMC | doi

Chimpanzee Sequencing and Analysis Consortium. (2005)

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

Nature 437(7055):69-87. doi: 10.1038/nature04072
Europe PMC | doi

Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U. (2005)

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

Microb. Cell Fact. 4:21. doi: 10.1186/1475-2859-4-21
Europe PMC | doi

Shah PK, Jensen LJ, Boué S, Bork P. (2005)

Extraction of transcript diversity from scientific literature

PLoS Comput. Biol. 1(1):e10. doi: 10.1371/journal.pcbi.0010010
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

Bork P, Serrano L. (2005)

Towards cellular systems in 4D

Cell 121(4):507-509. doi: 10.1016/j.cell.2005.05.001
Europe PMC | doi

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. (2005)

Systematic association of genes to phenotypes by genome and literature mining

PLoS Biol. 3(5):e134. doi: 10.1371/journal.pbio.0030134
Europe PMC | doi

Shah PK, Aloy P, Bork P, Russell RB. (2005)

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

Protein Sci. 14(5):1305-1314. doi: 10.1110/ps.041187405
Europe PMC | doi

Ciccarelli FD, Bork P. (2005)

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

Bioinformatics 21(8):1304-1307. doi: 10.1093/bioinformatics/bti221
Europe PMC | doi

de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S. (2005)

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

Bioinformatics 21(7):1164-1171. doi: 10.1093/bioinformatics/bti093
Europe PMC | doi

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. (2005)

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

Nature 434(7034):724-731. doi: 10.1038/nature03466
Europe PMC | doi

Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM. (2005)

Comparative metagenomics of microbial communities

Science 308(5721):554-557. doi: 10.1126/science.1107851
Europe PMC | doi

Ciccarelli FD, von Mering C, Suyama M, Harrington ED, Izaurralde E, Bork P. (2005)

Complex genomic rearrangements lead to novel primate gene function

Genome Res. 15(3):343-351. doi: 10.1101/gr.3266405
Europe PMC | doi

de Lichtenberg U, Jensen LJ, Brunak S, Bork P. (2005)

Dynamic complex formation during the yeast cell cycle

Science 307(5710):724-727. doi: 10.1126/science.1105103
Europe PMC | doi

Bork P. (2005)

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

Mol. Syst. Biol. 1:2005.0012. doi: 10.1038/msb4100016
Europe PMC | doi

Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G. (2005)

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

Genome Res. 15(1):98-110. doi: 10.1101/gr.3002305
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

Perez-Iratxeta C, Wjst M, Bork P, Andrade MA. (2005)

G2D: a tool for mining genes associated with disease

BMC Genet. 6:45. doi: 10.1186/1471-2156-6-45
Europe PMC | doi

Tenhaken R, Doerks T, Bork P. (2005)

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

BMC Bioinformatics 6:169. doi: 10.1186/1471-2105-6-169
Europe PMC | doi

von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. (2005)

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

Nucleic Acids Res. 33(Database issue):D433-7. doi: 10.1093/nar/gki005
Europe PMC | doi

Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P. (2005)

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

Nucleic Acids Res. 33(3):946-954. doi: 10.1093/nar/gki236
Europe PMC | doi


2004

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

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

Krause R, von Mering C, Bork P, Dandekar T. (2004)

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

Bioessays 26(12):1333-1343. doi: 10.1002/bies.20141
Europe PMC | doi

Kim H, Klein R, Majewski J, Ott J. (2004)

Estimating rates of alternative splicing in mammals and invertebrates

Nat. Genet. 36(9):915-6; author reply 916-7. doi: 10.1038/ng0904-915
Europe PMC | doi

Liska AJ, Popov AV, Sunyaev S, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A. (2004)

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

Proteomics 4(9):2707-2721. doi: 10.1002/pmic.200300813
Europe PMC | doi

Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA. (2004)

Gene annotation from scientific literature using mappings between keyword systems

Bioinformatics 20(13):2084-2091. doi: 10.1093/bioinformatics/bth207
Europe PMC | doi

Suyama M, Torrents D, Bork P. (2004)

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

Bioinformatics 20(12):1968-1970. doi: 10.1093/bioinformatics/bth172
Europe PMC | doi

Jensen LJ, Lagarde J, von Mering C, Bork P. (2004)

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

Nucleic Acids Res. 32(Web Server issue):W445-8. doi: 10.1093/nar/gkh407
Europe PMC | doi

Korbel JO, Jensen LJ, von Mering C, Bork P. (2004)

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

Nat. Biotechnol. 22(7):911-917. doi: 10.1038/nbt988
Europe PMC | doi

Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. (2004)

Protein interaction networks from yeast to human

Curr. Opin. Struct. Biol. 14(3):292-299. doi: 10.1016/j.sbi.2004.05.003
Europe PMC | doi

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. (2004)

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

Nature 428(6982):493-521. doi: 10.1038/nature02426
Europe PMC | doi

Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB. (2004)

Structure-based assembly of protein complexes in yeast

Science 303(5666):2026-2029. doi: 10.1126/science.1092645
Europe PMC | doi

Doerks T, Andrade MA, Lathe W 3rd, von Mering C, Bork P. (2004)

Global analysis of bacterial transcription factors to predict cellular target processes

Trends Genet. 20(3):126-131. doi: 10.1016/j.tig.2004.01.006
Europe PMC | doi

Forler D, Rabut G, Ciccarelli FD, Herold A, Köcher T, Niggeweg R, Bork P, Ellenberg J, Izaurralde E. (2004)

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

Mol. Cell. Biol. 24(3):1155-1167. doi: 10.1128/mcb.24.3.1155-1167.2004
Europe PMC | doi

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. (2004)

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

Nat. Biotechnol. 22(2):177-183. doi: 10.1038/nbt926
Europe PMC | doi

Bork P, Orengo CA. (2004)

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

Curr. Opin. Struct. Biol. 14(3):261-263.
Europe PMC

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. (2004)

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

Bioinformatics 20(2):268-270. doi: 10.1093/bioinformatics/btg398
Europe PMC | doi

Doerks T, von Mering C, Bork P. (2004)

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

Nucleic Acids Res. 32(21):6321-6326. doi: 10.1093/nar/gkh973
Europe PMC | doi

Jensen LJ, Bork P. (2004)

Quality analysis and integration of large-scale molecular data sets

Drug Discov. Today 3(2):51-56.
Europe PMC

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

Saric J, Jensen LJ, Bork P, Ouzounova R, Rojas I. (2004)

Extracting Regulatory Gene Expression Networks From Pubmed

In: Proceedings of the 42nd Meeting of the Association for Computational Linguistics (ACL'04). pp 192-199.


2003

Ciccarelli FD, Izaurralde E, Bork P. (2003)

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

BMC Bioinformatics 4:64. doi: 10.1186/1471-2105-4-64
Europe PMC | doi

Sunyaev S, Kondrashov FA, Bork P, Ramensky V. (2003)

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

Hum. Mol. Genet. 12(24):3325-3330. doi: 10.1093/hmg/ddg359
Europe PMC | doi

Torrents D, Suyama M, Zdobnov E, Bork P. (2003)

A genome-wide survey of human pseudogenes

Genome Res. 13(12):2559-2567. doi: 10.1101/gr.1455503
Europe PMC | doi

von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P. (2003)

Genome evolution reveals biochemical networks and functional modules

Proc. Natl. Acad. Sci. U.S.A. 100(26):15428-15433. doi: 10.1073/pnas.2136809100
Europe PMC | doi

Boue S, Letunic I, Bork P. (2003)

Alternative splicing and evolution

Bioessays 25(11):1031-1034. doi: 10.1002/bies.10371
Europe PMC | doi

Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. (2003)

Protein disorder prediction: implications for structural proteomics

Structure 11(11):1453-1459. doi: 10.1016/j.str.2003.10.002
Europe PMC | doi

Krause R, von Mering C, Bork P. (2003)

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

Paper presented at the International Conference in Bioinformatics, ATLANTA, GEORGIA, NOV 13-16, 2003.Bioinformatics 19(15):1901-1908. doi: 10.1093/bioinformatics/btg344
Europe PMC | doi

Gatfield D, Unterholzner L, Ciccarelli FD, Bork P, Izaurralde E. (2003)

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

EMBO J. 22(15):3960-3970. doi: 10.1093/emboj/cdg371
Europe PMC | doi

Ciccarelli FD, Bork P, Kerkhoff E. (2003)

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

Trends Biochem. Sci. 28(7):349-352. doi: 10.1016/s0968-0004(03)00116-6
Europe PMC | doi

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. (2003)

The DNA sequence of human chromosome 7

Nature 424(6945):157-164. doi: 10.1038/nature01782
Europe PMC | doi

Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P. (2003)

Systematic discovery of analogous enzymes in thiamin biosynthesis

Nat. Biotechnol. 21(7):790-795. doi: 10.1038/nbt834
Europe PMC | doi

Perez-Iratxeta C, Pérez AJ, Bork P, Andrade MA. (2003)

Update on XplorMed: A web server for exploring scientific literature

Nucleic Acids Res. 31(13):3866-3868. doi: 10.1093/nar/gkg538
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

Schmidt S, Sunyaev S, Bork P, Dandekar T. (2003)

Metabolites: a helping hand for pathway evolution?

Trends Biochem. Sci. 28(6):336-341. doi: 10.1016/s0968-0004(03)00114-2
Europe PMC | doi

Netzel R, Perez-Iratxeta C, Bork P, Andrade MA. (2003)

The way we write

EMBO Rep. 4(5):446-451. doi: 10.1038/sj.embor.embor833
Europe PMC | doi

Shah PK, Perez-Iratxeta C, Bork P, Andrade MA. (2003)

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

BMC Bioinformatics 4:20. doi: 10.1186/1471-2105-4-20
Europe PMC | doi

Ciccarelli FD, Proukakis C, Patel H, Cross H, Azam S, Patton MA, Bork P, Crosby AH. (2003)

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

Genomics 81(4):437-441. doi: 10.1016/s0888-7543(03)00011-9
Europe PMC | doi

Huynen MA, Snel B, von Mering C, Bork P. (2003)

Function prediction and protein networks

Curr. Opin. Cell Biol. 15(2):191-198. doi: 10.1016/s0955-0674(03)00009-7
Europe PMC | doi

Woerner SM, Benner A, Sutter C, Schiller M, Yuan YP, Keller G, Bork P, Doeberitz Mv, Gebert JF. (2003)

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

Oncogene 22(15):2226-2235. doi: 10.1038/sj.onc.1206421
Europe PMC | doi

Kanehisa M, Bork P. (2003)

Bioinformatics in the post-sequence era

Nat. Genet. 33 Suppl:305-310. doi: 10.1038/ng1109
Europe PMC | doi

Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S. (2003)

Increase of functional diversity by alternative splicing

Trends Genet. 19(3):124-128. doi: 10.1016/s0168-9525(03)00023-4
Europe PMC | doi

Morett E, Saab G, Merino E, Bork P, Rajan E, Olvera L, Olvera M. (2003)

High Rate of Gene Displacement in Vitamin Biosynthesis Pathways

In: Andrade MA (ed), Bioinformatics and Genomes. Horizon Scientific Press. pp 69-79.

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

Perez-Iratxeta C, Astola N, Ciccarelli FD, Sha PK, Bork P, Andrade MA. (2003)

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

Appl. Bioinformatics 2(3):189-191.
Europe PMC

Shevchenko A, Sunyaev S, Liska A, Bork P, Shevchenko A. (2003)

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

Methods Mol. Biol. 211:221-234.
Europe PMC

Torrents D, Suyama M, Bork P. (2003)

Pseudogenes and Genomes

In: Andrade MA (ed), Bioinformatics and Genomes. Horizon Scientific Press. pp 197-209.

von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. (2003)

STRING: a database of predicted functional associations between proteins

Nucleic Acids Res. 31(1):258-261. doi: 10.1093/nar/gkg034
Europe PMC | doi

Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK. (2003)

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

Paper presented at the 67th Cold Spring Harbor Symposium on Quantitative Biology, Cold Spring Harbor, NY, 2003.Cold Spring Harb. Symp. Quant. Biol. 68:13-22. doi: 10.1101/sqb.2003.68.13
Europe PMC | doi


2002

Kloor M, Bork P, Duwe A, Klaes R, von Knebel Doeberitz M, Ridder R. (2002)

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

Biochim. Biophys. Acta 1579(2-3):219-224. doi: 10.1016/s0167-4781(02)00543-2
Europe PMC | doi

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

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

Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F. (2002)

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

Proc. Natl. Acad. Sci. U.S.A. 99(22):14422-14427. doi: 10.1073/pnas.212527599
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

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

Ramensky V, Bork P, Sunyaev S. (2002)

Human non-synonymous SNPs: server and survey

Nucleic Acids Res. 30(17):3894-3900. doi: 10.1093/nar/gkf493
Europe PMC | doi

Andrade MA, Ciccarelli FD, Perez-Iratxeta C, Bork P. (2002)

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

Genome Biol. 3(9):RESEARCH0047. doi: 10.1186/gb-2002-3-9-research0047
Europe PMC | doi

Bordo D, Bork P. (2002)

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

EMBO Rep. 3(8):741-746. doi: 10.1093/embo-reports/kvf150
Europe PMC | doi

Mott R, Schultz J, Bork P, Ponting CP. (2002)

Predicting protein cellular localization using a domain projection method

Genome Res. 12(8):1168-1174. doi: 10.1101/gr.96802
Europe PMC | doi

Patel H, Cross H, Proukakis C, Hershberger R, Bork P, Ciccarelli FD, Patton MA, McKusick VA, Crosby AH. (2002)

SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia

Nat. Genet. 31(4):347-348. doi: 10.1038/ng937
Europe PMC | doi

Aloy P, Ciccarelli FD, Leutwein C, Gavin AC, Superti-Furga G, Bork P, Bottcher B, Russell RB. (2002)

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

EMBO Rep. 3(7):628-635. doi: 10.1093/embo-reports/kvf135
Europe PMC | doi

Perez-Iratxeta C, Bork P, Andrade MA. (2002)

Association of genes to genetically inherited diseases using data mining

Nat. Genet. 31(3):316-319. doi: 10.1038/ng895
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

Perez-Iratxeta C, Bork P, Andrade MA. (2002)

Exploring MEDLINE abstracts with XplorMed

Drugs Today 38(6):381-389. doi: 10.1358/dot.2002.38.6.678344
Europe PMC | doi

Perez-Iratxeta C, Keer HS, Bork P, Andrade MA. (2002)

Computing fuzzy associations for the analysis of biological literature

BioTechniques 32(6):1380-2, 1384-5. doi: 10.2144/02326bc03
Europe PMC | doi

Thomasova D, Ton LQ, Copley RR, Zdobnov EM, Wang X, Hong YS, Sim C, Bork P, Kafatos FC, Collins FH. (2002)

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

Proc. Natl. Acad. Sci. U.S.A. 99(12):8179-8184. doi: 10.1073/pnas.082235599
Europe PMC | doi

Von Mering C, Bork P. (2002)

Proteinkomplexe und Netzwerke: Neue Herausforderungen für die Proteomik

GenomXPress 2/02:2-4.

von Mering C, Bork P. (2002)

Teamed up for transcription

Nature 417(6891):797-798. doi: 10.1038/417797a
Europe PMC | doi

von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. (2002)

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

Nature 417(6887):399-403. doi: 10.1038/nature750
Europe PMC | doi