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: 534 publication(s)

2008

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

Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P. (2008)

A molecular study of microbe transfer between distant environments

PLoS ONE 3(7):e2607. doi: 10.1371/journal.pone.0002607
Europe PMC | doi

Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P. (2008)

Circular reasoning rather than cyclic expression

Genome Biol. 9(6):403. doi: 10.1186/gb-2008-9-6-403
Europe PMC | doi

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. (2008)

eggNOG: automated construction and annotation of orthologous groups of genes

Nucleic Acids Res. 36(Database issue):D250-4. doi: 10.1093/nar/gkm796
Europe PMC | doi

Korff S, Woerner SM, Yuan YP, Bork P, von Knebel Doeberitz M, Gebert J. (2008)

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability

BMC Cancer 8:329. doi: 10.1186/1471-2407-8-329
Europe PMC | doi

Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. (2008)

STITCH: interaction networks of chemicals and proteins

Nucleic Acids Res. 36(Database issue):D684-8. doi: 10.1093/nar/gkm795
Europe PMC | doi

Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P. (2008)

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Mol. Syst. Biol. 4 doi: 10.1038/msb.2008.35
Europe PMC | doi

Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T. (2008)

NetworKIN: a resource for exploring cellular phosphorylation networks

Nucleic Acids Res. 36(Database issue):D695-9. doi: 10.1093/nar/gkm902
Europe PMC | doi

Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R. (2008)

Linear motif atlas for phosphorylation-dependent signaling

Sci Signal 1(35):ra2. doi: 10.1126/scisignal.1159433
Europe PMC | doi

Pallejà A, Harrington ED, Bork P. (2008)

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

BMC Genomics 9:335. doi: 10.1186/1471-2164-9-335
Europe PMC | doi

Perotti C, Liu R, Parusel CT, Böcher N, Schultz J, Bork P, Pfitzner E, Groner B, Shemanko CS. (2008)

Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation

Breast Cancer Res. 10(6):R94. doi: 10.1186/bcr2193
Europe PMC | doi

Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M. (2008)

Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution

Genome Biol. 9(12):R176. doi: 10.1186/gb-2008-9-12-r176
Europe PMC | doi

Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. (2008)

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families

Gene 407(1-2):199-215. doi: 10.1016/j.gene.2007.10.012
Europe PMC | doi

Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD. (2008)

Non-random retention of protein-coding overlapping genes in Metazoa

BMC Genomics 9:174. doi: 10.1186/1471-2164-9-174
Europe PMC | doi

Wiemann S, Mehrle A, Hahne F, Hermjakob H, Apweiler R, Arlt D, Bechtel S, Bielke W, Birmingham A, Smith Q, Bork P, Buchholz F, Cai X, Camon E, Carninci P, Chanda SK, Chen Z, Cusick M, Echeverri C, Eils J, Eils R, Frank R, Fraser A, Girod A, Haedrich B, Hannus M, Harris M, Hayashizaki Y, Hide W, Hofmann O, Huber P, Hyman A, Jensen L, Kallioniemi O, Khvorova A, Koski L, Kraybill B, LaBaer J, Landegren U, Lawerenz C, Lehrach H, Liu F-F, Majety M, Mathey-Prevot B, Medico E, Mills GB, Nomura N, The OBI Consortium, Perrimon N, Pizarro A, Poustka A, Quackenbush J, Rosenfelder H, Sahin O, Salehi-Ashtiani K, Sasse F, Sauermann M, Schimmer AD, Schmidt C, Selfors L, Shamu C, Sönnichsen B, Taylor C, Temple G, Vidal M, Weidlich M, Wrobel DJ, Zhang J. (2008)

MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects


Europe PMC


2007

Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM. (2007)

Genome-wide experimental determination of barriers to horizontal gene transfer

Science 318(5855):1449-1452. doi: 10.1126/science.1147112
Europe PMC | doi

Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E. (2007)

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing

Genes Dev. 21(20):2558-2570. doi: 10.1101/gad.443107
Europe PMC | doi

Raes J, Foerstner KU, Bork P. (2007)

Get the most out of your metagenome: computational analysis of environmental sequence data

Curr. Opin. Microbiol. 10(5):490-498. doi: 10.1016/j.mib.2007.09.001
Europe PMC | doi

de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ. (2007)

Evolution of cell cycle control: same molecular machines, different regulation

Cell Cycle 6(15):1819-1825.
Europe PMC

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

Pachkov M, Dandekar T, Korbel J, Bork P, Schuster S. (2007)

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism

Gene 396(2):215-225. doi: 10.1016/j.gene.2007.02.033
Europe PMC | doi

Perez-Iratxeta C, Bork P, Andrade-Navarro MA. (2007)

Update of the G2D tool for prioritization of gene candidates to inherited diseases

Nucleic Acids Res. 35(Web Server issue):W212-6. doi: 10.1093/nar/gkm223
Europe PMC | doi

Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE. (2007)

Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals

EMBO J. 26(11):2658-2669. doi: 10.1038/sj.emboj.7601699
Europe PMC | doi

Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T. (2007)

Systematic discovery of in vivo phosphorylation networks

Cell 129(7):1415-1426. doi: 10.1016/j.cell.2007.05.052
Europe PMC | doi

Raes J, Harrington ED, Singh AH, Bork P. (2007)

Protein function space: viewing the limits or limited by our view?

Curr. Opin. Struct. Biol. 17(3):362-369. doi: 10.1016/j.sbi.2007.05.010
Europe PMC | doi

Boettner M, Steffens C, von Mering C, Bork P, Stahl U, Lang C. (2007)

Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes

J. Biotechnol. 130(1):1-10. doi: 10.1016/j.jbiotec.2007.02.019
Europe PMC | doi

von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. (2007)

Quantitative phylogenetic assessment of microbial communities in diverse environments

Science 315(5815):1126-1130. doi: 10.1126/science.1133420
Europe PMC | doi

Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. (2007)

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Mol. Syst. Biol. 3:72. doi: 10.1038/msb4100112
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

Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. (2007)

Prediction of effective genome size in metagenomic samples

Genome Biol. 8(1):R10. doi: 10.1186/gb-2007-8-1-r10
Europe PMC | doi

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. (2007)

STRING 7--recent developments in the integration and prediction of protein interactions

Nucleic Acids Res. 35(Database issue):D358-62. doi: 10.1093/nar/gkl825
Europe PMC | doi

Zdobnov EM, Bork P. (2007)

Quantification of insect genome divergence

Trends Genet. 23(1):16-20. doi: 10.1016/j.tig.2006.10.004
Europe PMC | doi


2006

Raible F, Tessmar-Raible K, Arboleda E, Kaller T, Bork P, Arendt D, Arnone MI. (2006)

Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome

Dev. Biol. 300(1):461-475. doi: 10.1016/j.ydbio.2006.08.070
Europe PMC | doi

Campillos M, Doerks T, Shah PK, Bork P. (2006)

Computational characterization of multiple Gag-like human proteins

Trends Genet. 22(11):585-589. doi: 10.1016/j.tig.2006.09.006
Europe PMC | doi

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

Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P. (2006)

Co-evolution of transcriptional and post-translational cell-cycle regulation

Nature 443(7111):594-597. doi: 10.1038/nature05186
Europe PMC | doi

Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM. (2006)

Assessing systems properties of yeast mitochondria through an interaction map of the organelle

PLoS Genet. 2(10):e170. doi: 10.1371/journal.pgen.0020170
Europe PMC | doi

Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E. (2006)

mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes

Genes Dev. 20(14):1885-1898. doi: 10.1101/gad.1424106
Europe PMC | doi

Suyama M, Torrents D, Bork P. (2006)

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Nucleic Acids Res. 34(Web Server issue):W609-12. doi: 10.1093/nar/gkl315
Europe PMC | doi

Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE. (2006)

A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development

Dev. Cell 10(6):797-807. doi: 10.1016/j.devcel.2006.04.009
Europe PMC | doi

Suyama M, Harrington E, Bork P, Torrents D. (2006)

Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes

PLoS Comput. Biol. 2(6):e76. doi: 10.1371/journal.pcbi.0020076
Europe PMC | doi

Shah PK, Bork P. (2006)

LSAT: learning about alternative transcripts in MEDLINE

Bioinformatics 22(7):857-865. doi: 10.1093/bioinformatics/btk044
Europe PMC | doi

Campillos M, von Mering C, Jensen LJ, Bork P. (2006)

Identification and analysis of evolutionarily cohesive functional modules in protein networks

Genome Res. 16(3):374-382. doi: 10.1101/gr.4336406
Europe PMC | doi

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. (2006)

Toward automatic reconstruction of a highly resolved tree of life

Science 311(5765):1283-1287. doi: 10.1126/science.1123061
Europe PMC | doi

Foerstner KU, von Mering C, Bork P. (2006)

Comparative analysis of environmental sequences: potential and challenges

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 361(1467):519-523. doi: 10.1098/rstb.2005.1809
Europe PMC | doi

Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. (2006)

Proteome survey reveals modularity of the yeast cell machinery

Nature 440(7084):631-636. doi: 10.1038/nature04532
Europe PMC | doi

Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P. (2006)

Extraction of regulatory gene/protein networks from Medline

Bioinformatics 22(6):645-650. doi: 10.1093/bioinformatics/bti597
Europe PMC | doi

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