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.
    Group leader in the Molecular Medicine Partnership Unit.
    ERC Advanced Investigator.

Publications

Total: 535 publication(s)

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.
Europe PMC

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.
Europe PMC

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.
Europe PMC

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.
Europe PMC

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

Doerks T, Huber S, Buchner E, Bork P. (2002)

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

Trends Biochem. Sci. 27(4):168-170. doi: 10.1016/s0968-0004(01)02042-4
Europe PMC | doi

Snel B, Bork P, Huynen MA. (2002)

The identification of functional modules from the genomic association of genes

Proc. Natl. Acad. Sci. U.S.A. 99(9):5890-5895. doi: 10.1073/pnas.092632599
Europe PMC | doi

Ciccarelli FD, Doerks T, Bork P. (2002)

AMOP, a protein module alternatively spliced in cancer cells

Trends Biochem. Sci. 27(3):113-115. doi: 10.1016/s0968-0004(01)02049-7
Europe PMC | doi

Korbel JO, Snel B, Huynen MA, Bork P. (2002)

SHOT: a web server for the construction of genome phylogenies

Trends Genet. 18(3):158-162. doi: 10.1016/s0168-9525(01)02597-5
Europe PMC | doi

Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P. (2002)

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

Trends Biochem. Sci. 27(2):59-62. doi: 10.1016/s0968-0004(01)02046-1
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

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

Bork P. (2002)

Comparative analysis of protein interaction networks

Paper presented at the European Conference on Computational Biology (ECCB 2002), SAARBRUCKEN, GERMANY, OCT 06-09, 2002.Bioinformatics 18 Suppl 2:S64.
Europe PMC

Brett D, Pospisil H, Valcárcel J, Reich J, Bork P. (2002)

Alternative splicing and genome complexity

Nat. Genet. 30(1):29-30. doi: 10.1038/ng803
Europe PMC | doi

Copley RR, Ponting CP, Schultz J, Bork P. (2002)

Sequence analysis of multidomain proteins: past perspectives and future directions

Adv. Protein Chem. 61:75-98. doi: 10.1016/s0065-3233(02)61002-2
Europe PMC | doi

Dandekar T, Snel B, Schmidt S, Lathe W, Suyama M, Huynen M, Bork P. (2002)

Comparative genome analysis of the mollicutes

Springer US.doi: 10.1007/0-306-47606-1_11
Europe PMC | doi

Doerks T, Copley RR, Schultz J, Ponting CP, Bork P. (2002)

Systematic identification of novel protein domain families associated with nuclear functions

Genome Res. 12(1):47-56. doi: 10.1101/gr.203201
Europe PMC | doi

Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ. (2002)

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

Nucleic Acids Res. 30(1):387-391. doi: 10.1093/nar/30.1.387
Europe PMC | doi

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. (2002)

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

Nature 415(6868):141-147. doi: 10.1038/415141a
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

Schmidt S, Bork P, Dandekar T. (2002)

A versatile structural domain analysis server using profile weight matrices

J Chem Inf Comput Sci 42(2):405-407. doi: 10.1021/ci010374r
Europe PMC | doi

Snel B, Bork P, Huynen MA. (2002)

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

Genome Res. 12(1):17-25. doi: 10.1101/gr.176501
Europe PMC | doi


2001

Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R. (2001)

The Spir actin organizers are involved in vesicle transport processes

Curr. Biol. 11(24):1963-1968. doi: 10.1016/s0960-9822(01)00602-9
Europe PMC | doi

Ponting CP, Mott R, Bork P, Copley RR. (2001)

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

Genome Res. 11(12):1996-2008. doi: 10.1101/gr.198701
Europe PMC | doi

Huynen MA, Snel B, Bork P, Gibson TJ. (2001)

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

Hum. Mol. Genet. 10(21):2463-2468. doi: 10.1093/hmg/10.21.2463
Europe PMC | doi

Perez-Iratxeta C, Bork P, Andrade MA. (2001)

XplorMed: a tool for exploring MEDLINE abstracts

Trends Biochem. Sci. 26(9):573-575. doi: 10.1016/s0968-0004(01)01926-0
Europe PMC | doi

Lathe WC 3rd, Bork P. (2001)

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

FEBS Lett. 502(3):113-116. doi: 10.1016/s0014-5793(01)02639-4
Europe PMC | doi

Linnebacher M, Gebert J, Rudy W, Woerner S, Yuan YP, Bork P, von Knebel Doeberitz M. (2001)

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

Int. J. Cancer 93(1):6-11. doi: 10.1002/ijc.1298
Europe PMC | doi

Woerner SM, Gebert J, Yuan YP, Sutter C, Ridder R, Bork P, von Knebel Doeberitz M. (2001)

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

Int. J. Cancer 93(1):12-19. doi: 10.1002/ijc.1299
Europe PMC | doi

Huynen MA, Snel B, Bork P. (2001)

Inversions and the dynamics of eukaryotic gene order

Trends Genet. 17(6):304-306. doi: 10.1016/s0168-9525(01)02302-2
Europe PMC | doi

Andrade MA, Petosa C, O'Donoghue SI, Müller CW, Bork P. (2001)

Comparison of ARM and HEAT protein repeats

J. Mol. Biol. 309(1):1-18. doi: 10.1006/jmbi.2001.4624
Europe PMC | doi

Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG. (2001)

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

Anal. Chem. 73(9):1917-1926. doi: 10.1021/ac0013709
Europe PMC | doi

Doerks T, Copley R, Bork P. (2001)

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

Trends Biochem. Sci. 26(3):145-146. doi: 10.1016/s0968-0004(00)01769-2
Europe PMC | doi

Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, Bork P. (2001)

Prediction of deleterious human alleles

Hum. Mol. Genet. 10(6):591-597. doi: 10.1093/hmg/10.6.591
Europe PMC | doi

Bork P, Copley R. (2001)

Genome speak

Nature 409(6822):815. doi: 10.1038/35057269
Europe PMC | doi

Bork P, Copley R. (2001)

The draft sequences. Filling in the gaps

Nature 409(6822):818-820. doi: 10.1038/35057274
Europe PMC | doi

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. (2001)

Initial sequencing and analysis of the human genome

Nature 409(6822):860-921. doi: 10.1038/35057062
Europe PMC | doi

Schultz J, Jones T, Bork P, Sheer D, Blencke S, Steyrer S, Wellbrock U, Bevec D, Ullrich A, Wallasch C. (2001)

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

Genomics 71(3):368-370. doi: 10.1006/geno.2000.6447
Europe PMC | doi

Sunyaev S, Lathe W 3rd, Bork P. (2001)

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

Curr. Opin. Struct. Biol. 11(1):125-130. doi: 10.1016/s0959-440x(00)00175-5
Europe PMC | doi

Becker S, Gehrsitz A, Bork P, Buchner S, Buchner E. (2001)

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

Gene 262(1-2):15-22. doi: 10.1016/s0378-1119(00)00548-5
Europe PMC | doi

Eisenhaber B, Bork P, Eisenhaber F. (2001)

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

Protein Eng. 14(1):17-25. doi: 10.1093/protein/14.1.17
Europe PMC | doi

Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB, Koonin EV. (2001)

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

Genome Biol. 2(12):RESEARCH0051.
Europe PMC

Suyama M, Bork P. (2001)

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

Trends Genet. 17(1):10-13. doi: 10.1016/s0168-9525(00)02159-4
Europe PMC | doi


2000

Herold A, Suyama M, Rodrigues JP, Braun IC, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E. (2000)

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

Mol. Cell. Biol. 20(23):8996-9008. doi: 10.1128/mcb.20.23.8996-9008.2000
Europe PMC | doi

Copley RR, Bork P. (2000)

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

J. Mol. Biol. 303(4):627-641. doi: 10.1006/jmbi.2000.4152
Europe PMC | doi

Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlü N, Bork P, Hyman AA. (2000)

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

Nature 408(6810):331-336. doi: 10.1038/35042526
Europe PMC | doi

Doerks T, Strauss M, Brendel M, Bork P. (2000)

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

Trends Biochem. Sci. 25(10):483-485. doi: 10.1016/s0968-0004(00)01664-9
Europe PMC | doi

Lathe WC 3rd, Snel B, Bork P. (2000)

Gene context conservation of a higher order than operons

Trends Biochem. Sci. 25(10):474-479. doi: 10.1016/s0968-0004(00)01663-7
Europe PMC | doi

Brett D, Lehmann G, Hanke J, Gross S, Reich J, Bork P. (2000)

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

Trends Genet. 16(9):416-418. doi: 10.1016/s0168-9525(00)02089-8
Europe PMC | doi

Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P. (2000)

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

Nucleic Acids Res. 28(17):3278-3288. doi: 10.1093/nar/28.17.3278
Europe PMC | doi

Snel B, Lehmann G, Bork P, Huynen MA. (2000)

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

Nucleic Acids Res. 28(18):3442-3444. doi: 10.1093/nar/28.18.3442
Europe PMC | doi

Huynen M, Snel B, Lathe W 3rd, Bork P. (2000)

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

Genome Res. 10(8):1204-1210. doi: 10.1101/gr.10.8.1204
Europe PMC | doi

Sunyaev SR, Lathe WC 3rd, Ramensky VE, Bork P. (2000)

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

Trends Genet. 16(8):335-337. doi: 10.1016/s0168-9525(00)02058-8
Europe PMC | doi

Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B. (2000)

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

Trends Biochem. Sci. 25(7):317-318. doi: 10.1016/s0968-0004(00)01599-1
Europe PMC | doi

Eisenhaber B, Bork P, Yuan Y, Löffler G, Eisenhaber F. (2000)

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

Trends Biochem. Sci. 25(7):340-341. doi: 10.1016/s0968-0004(00)01601-7
Europe PMC | doi

Sánchez-Pulido L, Yuan YP, Andrade MA, Bork P. (2000)

NAIL-Network Analysis Interface for Linking HMMER results

Bioinformatics 16(7):656-657. doi: 10.1093/bioinformatics/16.7.656
Europe PMC | doi