EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany


  • 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.


Total: 586 publication(s)


Eisenhaber B, Bork P, Eisenhaber F. (1998)

Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase

Protein Eng. 11(12):1155-1161. doi: 10.1093/protein/11.12.1155
Europe PMC | doi

Willeke F, Ridder R, Bork P, Klaes R, Mechtersheimer G, Schwarzbach M, Zimmer D, Kloor M, Lehnert T, Herfarth C, von Knebel Doeberitz M. (1998)

Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues

Mol. Carcinog. 23(4):195-200. doi: 10.1002/(sici)1098-2744(199812)23:4<195::aid-mc1>3.3.co;2-7
Europe PMC | doi

Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y. (1998)

Predicting function: from genes to genomes and back

J. Mol. Biol. 283(4):707-725. doi: 10.1006/jmbi.1998.2144
Europe PMC | doi

Dandekar T, Snel B, Huynen M, Bork P. (1998)

Conservation of gene order: a fingerprint of proteins that physically interact

Trends Biochem. Sci. 23(9):324-328. doi: 10.1016/s0968-0004(98)01274-2
Europe PMC | doi

Morett E, Bork P. (1998)

Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC

FEBS Lett. 433(1-2):108-112. doi: 10.1016/s0014-5793(98)00888-6
Europe PMC | doi

Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. (1998)

Homology-based fold predictions for Mycoplasma genitalium proteins

J. Mol. Biol. 280(3):323-326. doi: 10.1006/jmbi.1998.1884
Europe PMC | doi

Doerks T, Bairoch A, Bork P. (1998)

Protein annotation: detective work for function prediction

Trends Genet. 14(6):248-250. doi: 10.1016/s0168-9525(98)01486-3
Europe PMC | doi

Kharrat A, Millevoi S, Baraldi E, Ponting CP, Bork P, Pastore A. (1998)

Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries

Biochim. Biophys. Acta 1385(1):157-164. doi: 10.1016/s0167-4838(98)00041-7
Europe PMC | doi

Bansal A , Bork P, Stuckey P. (1998)


JMMSC 9(1):1-23.

Huynen MA, Bork P. (1998)

Measuring genome evolution

Paper presented at the Colloquium on Computational Biomolecular Science, IRVINE, CALIFORNIA, SEP 11-13, 1997.Proc. Natl. Acad. Sci. U.S.A. 95(11):5849-5856. doi: 10.1073/pnas.95.11.5849
Europe PMC | doi

Schultz J, Milpetz F, Bork P, Ponting CP. (1998)

SMART, a simple modular architecture research tool: identification of signaling domains

Paper presented at the Colloquium on Computational Biomolecular Science, IRVINE, CALIFORNIA, SEP 11-13, 1997.Proc. Natl. Acad. Sci. U.S.A. 95(11):5857-5864. doi: 10.1073/pnas.95.11.5857
Europe PMC | doi

Bork P, Koonin EV. (1998)

Predicting functions from protein sequences--where are the bottlenecks?

Nat. Genet. 18(4):313-318. doi: 10.1038/ng0498-313
Europe PMC | doi

Eisenhaber F, Bork P. (1998)

Wanted: subcellular localization of proteins based on sequence

Trends Cell Biol. 8(4):169-170. doi: 10.1016/s0962-8924(98)01226-4
Europe PMC | doi

Huynen M, Dandekar T, Bork P. (1998)

Differential genome analysis applied to the species-specific features of Helicobacter pylori

FEBS Lett. 426(1):1-5. doi: 10.1016/s0014-5793(98)00276-2
Europe PMC | doi

Beckmann G, Hanke J, Bork P, Reich JG. (1998)

Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins

J. Mol. Biol. 275(5):725-730. doi: 10.1006/jmbi.1997.1510
Europe PMC | doi

Bork P, Dandekar T, Eisenhaber F, Huynen M. (1998)

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases

J. Mol. Med. 76(2):77-79. doi: 10.1007/s001090050194
Europe PMC | doi

Bork P, Eisenberg D. (1998)

Sequences and topology - Deriving biological knowledge from genomic sequences

Curr. Opin. Struct. Biol. 8(3):331-332. doi: 10.1016/S0959-440X(98)80066-3
Europe PMC | doi

Brown NP, Sander C, Bork P. (1998)

Frame: detection of genomic sequencing errors

Bioinformatics 14(4):367-371. doi: 10.1093/bioinformatics/14.4.367
Europe PMC | doi

Dandekar T, Beyer K, Bork P, Kenealy MR, Pantopoulos K, Hentze M, Sonntag-Buck V, Flouriot G, Gannon F, Schreiber S. (1998)

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches

Paper presented at the German Conference on Bioinformatics (GCB 97), KLOSTER IRSEE, GERMANY, SEP, 1997.Bioinformatics 14(3):271-278. doi: 10.1093/bioinformatics/14.3.271
Europe PMC | doi

Schuster S, Fell DA, Pfeiffer T, Dandekar T, Bork, P. (1998)

Elementary modes analysis illustrated with human red cell metabolism

In: Larsson, C., Pahlman, I.-L. & Gustafsson, L. (eds.), BioThermoKinectis in the Post Genomic Era. pp 332-339.

Schwirzke M, Gnirke A, Bork P, Tarin D, Weidle UH. (1998)

Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis

Anticancer Res. 18(3A):1409-1421.
Europe PMC

Yuan YP, Eulenstein O, Vingron M, Bork P. (1998)

Towards detection of orthologues in sequence databases

Paper presented at the German Conference on Bioinformatics (GCB 97), KLOSTER IRSEE, GERMANY, SEP, 1997.Bioinformatics 14(3):285-289. doi: 10.1093/bioinformatics/14.3.285
Europe PMC | doi


Hegyi H, Lai JM, Bork P. (1997)

The Sequence Alerting Server--a new WEB server

Comput. Appl. Biosci. 13(6):619-620.
Europe PMC

Morozov V, Mushegian AR, Koonin EV, Bork P. (1997)

A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases

Trends Biochem. Sci. 22(11):417-418. doi: 10.1016/s0968-0004(97)01128-6
Europe PMC | doi

Green EA, Pietrokovski S, Henikoff S, Bork P, Attwood T, Hood L, Bairoch A. (1997)

Genome maps 8. Building gene families. Wall chart

Science 278(5338):615-630. doi: 10.1126/science.278.5338.615
Europe PMC | doi

Henikoff S, Greene EA, Pietrokovski S, Bork P, Attwood TK, Hood L. (1997)

Gene families: the taxonomy of protein paralogs and chimeras

Science 278(5338):609-614. doi: 10.1126/science.278.5338.609
Europe PMC | doi

Huynen MA, Diaz-Lazcoz Y, Bork P. (1997)

Differential genome display

Trends Genet. 13(10):389-390. doi: 10.1016/s0168-9525(97)01255-9
Europe PMC | doi

Bork P, Schultz J, Ponting CP. (1997)

Cytoplasmic signalling domains: the next generation

Trends Biochem. Sci. 22(8):296-298. doi: 10.1016/s0968-0004(97)01084-0
Europe PMC | doi

Görlich D, Dabrowski M, Bischoff FR, Kutay U, Bork P, Hartmann E, Prehn S, Izaurralde E. (1997)

A novel class of RanGTP binding proteins

J. Cell Biol. 138(1):65-80. doi: 10.1083/jcb.138.1.65
Europe PMC | doi

Hegyi H, Bork P. (1997)

On the classification and evolution of protein modules

J. Protein Chem. 16(5):545-551. doi: 10.1023/a:1026382032119
Europe PMC | doi

Ponting CP, Cai YD, Bork P. (1997)

The breast cancer gene product TSG101: a regulator of ubiquitination?

J. Mol. Med. 75(7):467-469.
Europe PMC

Ponting C, Schultz J, Bork P. (1997)

SPRY domains in ryanodine receptors (Ca(2+)-release channels)

Trends Biochem. Sci. 22(6):193-194. doi: 10.1016/s0968-0004(97)01049-9
Europe PMC | doi

Mushegian AR, Bassett DE Jr, Boguski MS, Bork P, Koonin EV. (1997)

Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs

Proc. Natl. Acad. Sci. U.S.A. 94(11):5831-5836. doi: 10.1073/pnas.94.11.5831
Europe PMC | doi

Bork P. (1997)

Bioinformatics and molecular medicine--introduction and call for papers

J. Mol. Med. 75(1):3-4.
Europe PMC

Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV. (1997)

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins

FASEB J. 11(1):68-76.
Europe PMC

Schultz J, Ponting CP, Hofmann K, Bork P. (1997)

SAM as a protein interaction domain involved in developmental regulation

Protein Sci. 6(1):249-253. doi: 10.1002/pro.5560060128
Europe PMC | doi

Yuan YP, Schultz J, Mlodzik M, Bork P. (1997)

Secreted fringe-like signaling molecules may be glycosyltransferases

Cell 88(1):9-11. doi: 10.1016/s0092-8674(00)81852-8
Europe PMC | doi


Gibson TJ, Koonin EV, Musco G, Pastore A, Bork P. (1996)

Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction

Trends Neurosci. 19(11):465-468. doi: 10.1016/s0166-2236(96)20054-2
Europe PMC | doi

Nagle DL, Karim MA, Woolf EA, Holmgren L, Bork P, Misumi DJ, McGrail SH, Dussault BJ Jr, Perou CM, Boissy RE, Duyk GM, Spritz RA, Moore KJ. (1996)

Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome

Nat. Genet. 14(3):307-311. doi: 10.1038/ng1196-307
Europe PMC | doi

Bork P, Bairoch A. (1996)

Go hunting in sequence databases but watch out for the traps

Trends Genet. 12(10):425-427. doi: 10.1016/0168-9525(96)60040-7
Europe PMC | doi

Henrissat B, Bork P. (1996)

On the classification of modular proteins

Protein Eng. 9(9):725-726. doi: 10.1093/protein/9.9.725
Europe PMC | doi

Koonin EV, Mushegian AR, Bork P. (1996)

Non-orthologous gene displacement

Trends Genet. 12(9):334-336. doi: 10.1016/0168-9525(96)20010-1
Europe PMC | doi

Okumura M, Matthews RJ, Robb B, Litman GW, Bork P, Thomas ML. (1996)

Comparison of CD45 extracellular domain sequences from divergent vertebrate species suggests the conservation of three fibronectin type III domains

J. Immunol. 157(4):1569-1575.
Europe PMC

Bork P, Brown NP, Hegyi H, Schultz J. (1996)

The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues

Protein Sci. 5(7):1421-1425. doi: 10.1002/pro.5560050720
Europe PMC | doi

Koonin EV, Altschul SF, Bork P. (1996)

BRCA1 protein products ... Functional motifs..

Nat. Genet. 13(3):266-268. doi: 10.1038/ng0796-266
Europe PMC | doi

Ponting CP, Bork P. (1996)

Pleckstrin's repeat performance: a novel domain in G-protein signaling?

Trends Biochem. Sci. 21(7):245-246. doi: 10.1016/0968-0004(96)30027-3
Europe PMC | doi

Bork P, Koonin EV. (1996)

Protein sequence motifs

Curr. Opin. Struct. Biol. 6(3):366-376. doi: 10.1016/s0959-440x(96)80057-1
Europe PMC | doi

Bork P, Blomberg N, Nilges M. (1996)

Internal repeats in the BRCA2 protein sequence

Nat. Genet. 13(1):22-23. doi: 10.1038/ng0596-22
Europe PMC | doi

Bork P, Downing AK, Kieffer B, Campbell ID. (1996)

Structure and distribution of modules in extracellular proteins

Q. Rev. Biophys. 29(2):119-167. doi: 10.1017/s0033583500005783
Europe PMC | doi

Koonin EV, Bork P. (1996)

Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes

Trends Biochem. Sci. 21(4):128-129. doi: 10.1016/0968-0004(96)30007-8
Europe PMC | doi

Bork P. (1996)

Sperm-egg binding protein or proto-oncogene?

Science 271(5254):1431-2; author reply 1434-5. doi: 10.1126/science.271.5254.1431
Europe PMC | doi

Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV. (1996)

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

Curr. Biol. 6(3):279-291. doi: 10.1016/s0960-9822(02)00478-5
Europe PMC | doi

Bork P, Gibson TJ. (1996)

Applying motif and profile searches

Meth. Enzymol. 266:162-184. doi: 10.1016/s0076-6879(96)66013-3
Europe PMC | doi

Hanke J, Beckmann G, Bork P, Reich JG. (1996)

Self-organizing hierarchic networks for pattern recognition in protein sequence

Protein Sci. 5(1):72-82. doi: 10.1002/pro.5560050109
Europe PMC | doi

Löhning C, Pohlschmidt M, Glücksmann-Kuis MA, Duyk G, Bork P, Schneider MO, Reeders ST, Frischauf AM. (1996)

Structural motifs of the PKD1 protein

Nephrol. Dial. Transplant. 11 Suppl 6:2-4.
Europe PMC

Yajnik V, Blaikie P, Bork P, Margolis B. (1996)

Identification of residues within the SHC phosphotyrosine binding/phosphotyrosine interaction domain crucial for phosphopeptide interaction

J. Biol. Chem. 271(4):1813-1816. doi: 10.1074/jbc.271.4.1813
Europe PMC | doi


Ouzounis C, Bork P, Casari G, Sander C. (1995)

New protein functions in yeast chromosome VIII

Protein Sci. 4(11):2424-2428. doi: 10.1002/pro.5560041121
Europe PMC | doi

Andrade MA, Bork P. (1995)

HEAT repeats in the Huntington's disease protein

Nat. Genet. 11(2):115-116. doi: 10.1038/ng1095-115
Europe PMC | doi

Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C. (1995)

Challenging times for bioinformatics

Nature 376(6542):647-648. doi: 10.1038/376647a0
Europe PMC | doi

Sudol M, Chen HI, Bougeret C, Einbond A, Bork P. (1995)

Characterization of a novel protein-binding module--the WW domain

FEBS Lett. 369(1):67-71. doi: 10.1016/0014-5793(95)00550-s
Europe PMC | doi

Bork P, Holm L, Koonin EV, Sander C. (1995)

The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction

Proteins 22(3):259-266. doi: 10.1002/prot.340220306
Europe PMC | doi

Bork P, Patthy L. (1995)

The SEA module: a new extracellular domain associated with O-glycosylation

Protein Sci. 4(7):1421-1425. doi: 10.1002/pro.5560040716
Europe PMC | doi

Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. (1995)

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology

Mol. Microbiol. 16(5):955-967. doi: 10.1111/j.1365-2958.1995.tb02321.x
Europe PMC | doi

Sudol M, Bork P, Einbond A, Kastury K, Druck T, Negrini M, Huebner K, Lehman D. (1995)

Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain

J. Biol. Chem. 270(24):14733-14741. doi: 10.1074/jbc.270.24.14733
Europe PMC | doi

Bork P, Margolis B. (1995)

A phosphotyrosine interaction domain

Cell 80(5):693-694. doi: 10.1016/0092-8674(95)90347-x
Europe PMC | doi

Bork P, Ouzounis C, McEntyre J. (1995)

Ready for a motif submission? A proposed checklist

Trends Biochem. Sci. 20(3):104. doi: 10.1016/s0968-0004(00)88974-4
Europe PMC | doi

Bork P, Gellerich J, Groth H, Hooft R, Martin F. (1995)

Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search

Protein Sci. 4(2):268-274. doi: 10.1002/pro.5560040213
Europe PMC | doi


Bork P, Koonin EV. (1994)

A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity

Proteins 20(4):347-355. doi: 10.1002/prot.340200407
Europe PMC | doi


Meitinger T, Meindl A, Bork P, Rost B, Sander C, Haasemann M, Murken J. (1993)

Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure

Nat. Genet. 5(4):376-380. doi: 10.1038/ng1293-376
Europe PMC | doi

Kolstø AB, Bork P, Kvaløy K, Lindback T, Grønstadt A, Kristensen T, Sander C. (1993)

Prokaryotic members of a new family of putative helicases with similarity to transcription activator SNF2

J. Mol. Biol. 230(2):684-688. doi: 10.1006/jmbi.1993.1185
Europe PMC | doi


Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. (1992)

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III

Protein Sci. 1(12):1677-1690. doi: 10.1002/pro.5560011216
Europe PMC | doi

Narahara A, Naterstad K, Kristensen T, Lopez R, Bork P, Kolstø AB. (1992)

Cloning of a gene from Bacillus cereus with homology to the mreB gene from Escherichia coli

Gene 122(1):181-185. doi: 10.1016/0378-1119(92)90047-s
Europe PMC | doi

Bork P, Doolittle RF. (1992)

Proposed acquisition of an animal protein domain by bacteria

Proc. Natl. Acad. Sci. U.S.A. 89(19):8990-8994. doi: 10.1073/pnas.89.19.8990
Europe PMC | doi

Bork P, Sander C, Valencia A. (1992)

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins

Proc. Natl. Acad. Sci. U.S.A. 89(16):7290-7294. doi: 10.1073/pnas.89.16.7290
Europe PMC | doi

Bork P. (1992)

The modular architecture of vertebrate collagens

FEBS Lett. 307(1):49-54. doi: 10.1016/0014-5793(92)80900-2
Europe PMC | doi

Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. (1992)

What's in a genome?

Nature 358(6384) doi: 10.1038/358287a0
Europe PMC | doi

Bork P, Sander C. (1992)

A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor

FEBS Lett. 300(3):237-240. doi: 10.1016/0014-5793(92)80853-9
Europe PMC | doi

Bork P, Sander C, Valencia A, Bukau B. (1992)

A module of the DnaJ heat shock proteins found in malaria parasites

Trends Biochem. Sci. 17(4) doi: 10.1016/0968-0004(92)90319-5
Europe PMC | doi


Bork P, Rohde K. (1991)

More von Willebrand factor type A domains? Sequence similarities with malaria thrombospondin-related anonymous protein, dihydropyridine-sensitive calcium channel and inter-alpha-trypsin inhibitor

Biochem. J. 279 ( Pt 3):908-910. doi: 10.1042/bj2790908
Europe PMC | doi

Bork P, Preissner R. (1991)

On alpha-helices terminated by glycine. 2. Recognition by sequence patterns

Biochem. Biophys. Res. Commun. 180(2):666-672. doi: 10.1016/s0006-291x(05)81117-9
Europe PMC | doi

Preissner R, Bork P. (1991)

On alpha-helices terminated by glycine. 1. Identification of common structural features

Biochem. Biophys. Res. Commun. 180(2):660-665. doi: 10.1016/s0006-291x(05)81116-7
Europe PMC | doi

Bork P. (1991)

Shuffled domains in extracellular proteins

FEBS Lett. 286(1-2):47-54. doi: 10.1016/0014-5793(91)80937-x
Europe PMC | doi

Bork P. (1991)

Complement components C1r/C1s, bone morphogenic protein 1 and Xenopus laevis developmentally regulated protein UVS.2 share common repeats

FEBS Lett. 282(1):9-12. doi: 10.1016/0014-5793(91)80433-4
Europe PMC | doi


Bork P, Rohde K. (1990)

Sequence similarities between tryptophan synthase beta subunit and other pyridoxal-phosphate-dependent enzymes

Biochem. Biophys. Res. Commun. 171(3):1319-1325. doi: 10.1016/0006-291x(90)90830-g
Europe PMC | doi

Bork P, Grunwald C. (1990)

Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach

Eur. J. Biochem. 191(2):347-358. doi: 10.1111/j.1432-1033.1990.tb19129.x
Europe PMC | doi


Bork P. (1989)

Recognition of functional regions in primary structures using a set of property patterns

FEBS Lett. 257(1):191-195. doi: 10.1016/0014-5793(89)81818-6
Europe PMC | doi