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)

2002

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. doi: 10.1093/bioinformatics/18.suppl_2.S64
Europe PMC | doi

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

Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P. (2000)

Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins

EMBO Rep. 1(1):53-58. doi: 10.1093/embo-reports/kvd009
Europe PMC | doi

Andrade MA, Bork P. (2000)

Automated extraction of information in molecular biology

FEBS Lett. 476(1-2):12-17. doi: 10.1016/s0014-5793(00)01661-6
Europe PMC | doi

Dimopoulos G, Casavant TL, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares MB, Kafatos FC. (2000)

Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines

Proc. Natl. Acad. Sci. U.S.A. 97(12):6619-6624. doi: 10.1073/pnas.97.12.6619
Europe PMC | doi

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

Exploitation of gene context

Curr. Opin. Struct. Biol. 10(3):366-370. doi: 10.1016/s0959-440x(00)00098-1
Europe PMC | doi

Schultz J, Doerks T, Ponting CP, Copley RR, Bork P. (2000)

More than 1,000 putative new human signalling proteins revealed by EST data mining

Nat. Genet. 25(2):201-204. doi: 10.1038/76069
Europe PMC | doi

Andrade MA, Ponting CP, Gibson TJ, Bork P. (2000)

Homology-based method for identification of protein repeats using statistical significance estimates

J. Mol. Biol. 298(3):521-537. doi: 10.1006/jmbi.2000.3684
Europe PMC | doi

Brett D, Hanke J, Lehmann G, Haase S, Delbrück S, Krueger S, Reich J, Bork P. (2000)

EST comparison indicates 38% of human mRNAs contain possible alternative splice forms

FEBS Lett. 474(1):83-86. doi: 10.1016/s0014-5793(00)01581-7
Europe PMC | doi

Sunyaev S, Ramensky V, Bork P. (2000)

Towards a structural basis of human non-synonymous single nucleotide polymorphisms

Trends Genet. 16(5):198-200. doi: 10.1016/s0168-9525(00)01988-0
Europe PMC | doi

Bork P. (2000)

Powers and pitfalls in sequence analysis: the 70% hurdle

Genome Res. 10(4):398-400. doi: 10.1101/gr.10.4.398
Europe PMC | doi

Stutz F, Bachi A, Doerks T, Braun IC, Séraphin B, Wilm M, Bork P, Izaurralde E. (2000)

REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export

RNA 6(4):638-650. doi: 10.1017/s1355838200000078
Europe PMC | doi

Otto IM, Raabe T, Rennefahrt UE, Bork P, Rapp UR, Kerkhoff E. (2000)

The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization

Curr. Biol. 10(6):345-348. doi: 10.1016/s0960-9822(00)00388-2
Europe PMC | doi

Isaksson A, Landegren U, Syvänen AC, Bork P, Stein C, Ortigao F, Brookes AJ. (2000)

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem

Eur. J. Hum. Genet. 8(2):154-156. doi: 10.1038/sj.ejhg.5200424
Europe PMC | doi

Bork P. (2000)

Analysis of Amino Acid Sequences

Academic Press.
Europe PMC

Bork P (ed). (2000)

Advances in Protein Chemistry

Advances in Protein Chemistry and Structural Biology.
Europe PMC

Bork P, Eisenberg D. (2000)

Genome and proteome informatics - Editorial overview

Curr. Opin. Struct. Biol. 10(3):341-342. doi: 10.1016/S0959-440X(00)00093-2
Europe PMC | doi

Bork P, Snel B, Lehmann G, Suyama M, Dandekar T, Lathe W III, Huynen M. (2000)

Comparative genome analysis: exploiting the context of genes to infer evolution and predict function

In: Sankoff D, Nadeau JF (eds), Comparative Genomics. Springer Netherlands. pp 281-294.doi: 10.1007/978-94-011-4309-7_25
Europe PMC | doi

Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F. (2000)

HGBASE: a database of SNPs and other variations in and around human genes

Nucleic Acids Res. 28(1):356-360. doi: 10.1093/nar/28.1.356
Europe PMC | doi

Ponting CP, Schultz J, Copley RR, Andrade MA, Bork P. (2000)

Evolution of domain families

Adv. Protein Chem. 54:185-244. doi: 10.1016/s0065-3233(00)54007-8
Europe PMC | doi

Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. (2000)

SMART: a web-based tool for the study of genetically mobile domains

Nucleic Acids Res. 28(1):231-234. doi: 10.1093/nar/28.1.231
Europe PMC | doi

Snel B, Bork P, Huynen M. (2000)

Genome evolution. Gene fusion versus gene fission

Trends Genet. 16(1):9-11. doi: 10.1016/s0168-9525(99)01924-1
Europe PMC | doi

Sunyaev S, Hanke J, Brett D, Aydin A, Zastrow I, Lathe W, Bork P, Reich J. (2000)

Individual variation in protein-coding sequences of human genome

Adv. Protein Chem. 54:409-437. doi: 10.1016/s0065-3233(00)54012-1
Europe PMC | doi


1999

Liu Z, Macias MJ, Bottomley MJ, Stier G, Linge JP, Nilges M, Bork P, Sattler M. (1999)

The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins

Structure 7(12):1557-1566. doi: 10.1016/s0969-2126(00)88346-x
Europe PMC | doi

Bork P, Huynen MA. (1999)

A point of entry into genomics

Nat. Genet. 23(3):273. doi: 10.1038/15453
Europe PMC | doi

Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P. (1999)

Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes

J. Mol. Med. 77(11):754-760. doi: 10.1007/s001099900059
Europe PMC | doi

Barnes MR, Russell RB, Copley RR, Ponting CP, Bork P, Cumberledge S, Reichsman F, Moore HM. (1999)

A lipid-binding domain in Wnt: a case of mistaken identity?

Curr. Biol. 9(19):R717-9. doi: 10.1016/s0960-9822(99)80465-5
Europe PMC | doi

Copley RR, Ponting CP, Bork P. (1999)

Phospholipases A2 and Wnts are unlikely to share a common ancestor

Curr. Biol. 9(19):R718-9. doi: 10.1016/s0960-9822(99)80466-7
Europe PMC | doi

Dandekar T, Schuster S, Snel B, Huynen M, Bork P. (1999)

Pathway alignment: application to the comparative analysis of glycolytic enzymes

Biochem. J. 343 Pt 1:115-124. doi: 10.1042/0264-6021:3430115
Europe PMC | doi

Hanke J, Brett D, Zastrow I, Aydin A, Delbrück S, Lehmann G, Luft F, Reich J, Bork P. (1999)

Alternative splicing of human genes: more the rule than the exception?

Trends Genet. 15(10):389-390. doi: 10.1016/s0168-9525(99)01830-2
Europe PMC | doi

Smalla M, Schmieder P, Kelly M, Ter Laak A, Krause G, Ball L, Wahl M, Bork P, Oschkinat H. (1999)

Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites

Protein Sci. 8(10):1954-1961. doi: 10.1110/ps.8.10.1954
Europe PMC | doi

Eisenhaber B, Bork P, Eisenhaber F. (1999)

Prediction of potential GPI-modification sites in proprotein sequences

J. Mol. Biol. 292(3):741-758. doi: 10.1006/jmbi.1999.3069
Europe PMC | doi

Hanke J, Lehmann G, Bork P, Reich JG. (1999)

Associative database of protein sequences

Bioinformatics 15(9):741-748. doi: 10.1093/bioinformatics/15.9.741
Europe PMC | doi

Müller SA, Sasaki T, Bork P, Wolpensinger B, Schulthess T, Timpl R, Engel A, Engel J. (1999)

Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures

J. Mol. Biol. 291(4):801-813. doi: 10.1006/jmbi.1999.2996
Europe PMC | doi

Ponting CP, Hofmann K, Bork P. (1999)

A latrophilin/CL-1-like GPS domain in polycystin-1

Curr. Biol. 9(16):R585-8. doi: 10.1016/s0960-9822(99)80379-0
Europe PMC | doi

Bork P, Dandekar T, Snel B, Huynen MA. (1999)

Genome comparisons to monitor molecular evolution

In: Göbel UB, Ruf BR (eds), Microbial Evolution and Infection: 50. Congress of DGHM and 25. Annual Meeting of DGI. Einhorn-presse Verlag, Reinbek.

Bork P, Doerks T, Springer TA, Snel B. (1999)

Domains in plexins: links to integrins and transcription factors

Trends Biochem. Sci. 24(7):261-263. doi: 10.1016/s0968-0004(99)01416-4
Europe PMC | doi

Huynen MA, Dandekar T, Bork P. (1999)

Variation and evolution of the citric-acid cycle: a genomic perspective

Trends Microbiol. 7(7):281-291. doi: 10.1016/s0966-842x(99)01539-5
Europe PMC | doi

Copley RR, Schultz J, Ponting CP, Bork P. (1999)

Protein families in multicellular organisms

Curr. Opin. Struct. Biol. 9(3):408-415. doi: 10.1016/s0959-440x(99)80055-4
Europe PMC | doi

Morett E, Bork P. (1999)

A novel transactivation domain in parkin

Trends Biochem. Sci. 24(6):229-231. doi: 10.1016/s0968-0004(99)01381-x
Europe PMC | doi

Ponting CP, Aravind L, Schultz J, Bork P, Koonin EV. (1999)

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer

J. Mol. Biol. 289(4):729-745. doi: 10.1006/jmbi.1999.2827
Europe PMC | doi

Ponting CP, Bork P, Schultz J, Aravind L. (1999)

No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho

Trends Biochem. Sci. 24(5):177-178. doi: 10.1016/s0968-0004(99)01379-1
Europe PMC | doi

Nagle DL, McGrail SH, Vitale J, Woolf EA, Dussault BJ Jr, DiRocco L, Holmgren L, Montagno J, Bork P, Huszar D, Fairchild-Huntress V, Ge P, Keilty J, Ebeling C, Baldini L, Gilchrist J, Burn P, Carlson GA, Moore KJ. (1999)

The mahogany protein is a receptor involved in suppression of obesity

Nature 398(6723):148-152. doi: 10.1038/18210
Europe PMC | doi

Bansal AK, Bork P. (1999)

Applying logic programming ro derive novel functional information of genomes.

Paper presented at the First International Workshop on Practical Aspects of Declarative Languages, PADL'99, San Antonio, Texas, USA, January 1999.In: Gupta G (ed), Lecture notes in computer science 1551: Practical aspects of declarative languages. Springer Verlag. pp 275-289.

Bork P. (1999)

Bioinformatik... (editorial)

Biospektrum 3:172.

Eisenhaber F, Bork P. (1999)

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries

Paper presented at the 1st International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 98), NOVOSIBIRSK, RUSSIA, AUG 24-31, 1998.Bioinformatics 15(7-8):528-535. doi: 10.1093/bioinformatics/15.7.528
Europe PMC | doi

Gibson T, Bork P. (1999)

Sequence analysis, dotplot, aligning sequences, indels and gap-penalty

In: Creighton T (ed.), Encyclopedia of Molecular Biology. Wiley & Sons Inc., New York. pp 86-90; 765-766; 961-962; 1252; 2220-2324.

Huynen M, Snel B, Bork P. (1999)

Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes

Science 286(5444):1443.
Europe PMC

Ponting CP, Schultz J, Milpetz F, Bork P. (1999)

SMART: identification and annotation of domains from signalling and extracellular protein sequences

Nucleic Acids Res. 27(1):229-232. doi: 10.1093/nar/27.1.229
Europe PMC | doi

Snel B, Bork P, Huynen MA. (1999)

Genome phylogeny based on gene content

Nat. Genet. 21(1):108-110. doi: 10.1038/5052
Europe PMC | doi


1998

Cai Y, Bork P. (1998)

Homology-based gene prediction using neural nets

Anal. Biochem. 265(2):269-274. doi: 10.1006/abio.1998.2876
Europe PMC | doi