Staff at EMBL
Dr. Peer Bork
Joint Head of Unit, Senior Scientist and Strategic Head of Bioinformatics, EMBL Heidelberg
Structural and Computational Biology
Bork Group
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
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Biography
PhD 1990, University of Leipzig.
Habilitation 1995, Humboldt University, Berlin.
At EMBL since 1991.
Joint Head of Unit since 2001.
ERC Advanced Investigator.
Publications
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Iskar, M., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., van Noort, V. & Bork, P. Mol Syst Biol. 2013 Apr 30;9:662. doi: 10.1038/msb.2013.20. PubMed
Country-specific antibiotic use practices impact the human gut resistome. Forslund, K., Sunagawa, S., Roat Kultima, J., Mende, D., Arumugam, M., Typas, A. & Bork, P. Genome Res. 2013 Apr 8. PubMed
Genomic variation landscape of the human gut microbiome. Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., Kota, K., Sunyaev, S.R., Weinstock, G.M. & Bork, P. Nature. 2013 Jan 3;493(7430):45-50. doi: 10.1038/nature11711. Epub 2012 Dec 5. PubMed
Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Ori, A., Banterle, N., Iskar, M., Andres-Pons, A., Escher, C., Khanh Bui, H., Sparks, L., Solis-Mezarino, V., Rinner, O., Bork, P., Lemke, E.A. & Beck, M. Mol Syst Biol. 2013 Mar 19;9:648. doi: 10.1038/msb.2013.4. PubMed
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. Kristensen, D.M., Waller, A.S., Yamada, T., Bork, P., Mushegian, A.R. & Koonin, E.V. J Bacteriol. 2013 Mar;195(5):941-50. doi: 10.1128/JB.01801-12. Epub 2012 Dec 7. PubMed
The microbiome explored: recent insights and future challenges. Blaser, M., Bork, P., Fraser, C., Knight, R. & Wang, J. Nat Rev Microbiol. 2013 Mar;11(3):213-7. doi: 10.1038/nrmicro2973. Epub 2013 Feb4. PubMed
Consistent mutational paths predict eukaryotic thermostability. van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D.R., Sinning, I., Hurt, E. & Bork, P. BMC Evol Biol. 2013 Jan 10;13:7. doi: 10.1186/1471-2148-13-7. PubMed
MOCAT: a metagenomics assembly and gene prediction toolkit. Kultima, J.R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D.R., Arumugam, M., Pan, Q., Liu, B., Qin, J., Wang, J. & Bork, P. PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17. PubMed
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L.J., von Mering, C. & Bork, P. Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. Epub 2011 Nov 16. PubMed
InterPro in 2011: new developments in the family and domain prediction database. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S., de Castro, E., Coggill, P., Corbett, M., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Fraser, M., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., McMenamin, C., Mi, H., Mutowo-Muellenet, P., Mulder, N., Natale, D., Orengo, C., Pesseat, S., Punta, M., Quinn, A.F., Rivoire, C., Sangrador-Vegas, A., Selengut, J.D., Sigrist, C.J., Scheremetjew, M., Tate, J., Thimmajanarthanan, M., Thomas, P.D., Wu, C.H., Yeats, C. & Yong, S.Y. Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. Epub 2011 Nov 16. PubMed
Transcription start site associated RNAs in bacteria. Yus, E., Guell, M., Vivancos, A.P., Chen, W.H., Lluch-Senar, M., Delgado, J., Gavin, A.C., Bork, P. & Serrano, L. Mol Syst Biol. 2012 May 22;8:585. doi: 10.1038/msb.2012.16. PubMed
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Yamada, T., Waller, A.S., Raes, J., Zelezniak, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., Weissenbach, J. & Bork, P. Mol Syst Biol. 2012 May 8;8:581. doi: 10.1038/msb.2012.13. PubMed
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. van Noort, V., Seebacher, J., Bader, S., Mohammed, S., Vonkova, I., Betts, M.J., Kuhner, S., Kumar, R., Maier, T., O'Flaherty, M., Rybin, V., Schmeisky, A., Yus, E., Stulke, J., Serrano, L., Russell, R.B., Heck, A.J., Bork, P. & Gavin, A.C. Mol Syst Biol. 2012 Feb 28;8:571. doi: 10.1038/msb.2012.4. PubMed
Deciphering a global network of functionally associated post-translational modifications. Minguez, P., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., van Noort, V. & Bork, P. Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31. PubMed
Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Iskar, M., Zeller, G., Zhao, X.M., van Noort, V. & Bork, P. Curr Opin Biotechnol. 2011 Dec 5. PubMed
Prediction of drug combinations by integrating molecular and pharmacological data. Zhao, X.M., Iskar, M., Zeller, G., Kuhn, M., Noort, V. & Bork, P. PLoS Comput Biol. 2011 Dec;7(12):e1002323. Epub 2011 Dec 29. PubMed
A holistic approach to marine eco-systems biology. Karsenti, E., Acinas, S.G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F., Claverie, J.M., Follows, M., Gorsky, G., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F., Ogata, H., Pesant, S., Reynaud, E.G., Sardet, C., Sieracki, M.E., Speich, S., Velayoudon, D., Weissenbach, J. & Wincker, P. PLoS Biol. 2011 Oct;9(10):e1001177. doi: 10.1371/journal.pbio.1001177. Epub 2011Oct 18. PubMed
Orthology prediction methods: a quality assessment using curated protein families. Trachana, K., Larsson, T.A., Powell, S., Chen, W.H., Doerks, T., Muller, J. & Bork, P. Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011Aug 19. PubMed
Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Amlacher, S., Sarges, P., Flemming, D., van Noort, V., Kunze, R., Devos, D.P., Arumugam, M., Bork, P. & Hurt, E. Cell. 2011 Jul 22;146(2):277-89. PubMed
iPath2.0: interactive pathway explorer. Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. & Bork, P. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W412-5. Epub 2011 May 5. PubMed
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Letunic, I. & Bork, P. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8. Epub 2011 Apr 5. PubMed
Enterotypes of the human gut microbiome. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Antolin, M., Artiguenave, F., Blottiere, H.M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K.U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., Merieux, A., Melo Minardi, R., M'rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S.D. & Bork, P. Nature. 2011 May 12;473(7346):174-80. Epub 2011 Apr 20. PubMed
The ecoresponsive genome of Daphnia pulex. Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H., Tokishita, S., Aerts, A., Arnold, G.J., Basu, M.K., Bauer, D.J., Caceres, C.E., Carmel, L., Casola, C., Choi, J.H., Detter, J.C., Dong, Q., Dusheyko, S., Eads, B.D., Frohlich, T., Geiler-Samerotte, K.A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E.V., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J.R., Muller, J., Pangilinan, J., Patwardhan, R.P., Pitluck, S., Pritham, E.J., Rechtsteiner, A., Rho, M., Rogozin, I.B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y.I., Yamagata, H., Yamada, T., Ye, Y., Shaw, J.R., Andrews, J., Crease, T.J., Tang, H., Lucas, S.M., Robertson, H.M., Bork, P., Koonin, E.V., Zdobnov, E.M., Grigoriev, I.V., Lynch, M. & Boore, J.L. Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761. PubMed
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, L.J. & von Mering, C. Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. Epub 2010 Nov 2. PubMed
Network neighbors of drug targets contribute to drug side-effect similarity. Brouwers, L., Iskar, M., Zeller, G., van Noort, V. & Bork, P. PLoS One. 2011;6(7):e22187. Epub 2011 Jul 13. PubMed
SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Harrington, E.D., Arumugam, M., Raes, J., Bork, P. & Relman, D.A. Bioinformatics. 2010 Dec 1;26(23):2979-80. Epub 2010 Oct 21. PubMed
SmashCommunity: a metagenomic annotation and analysis tool. Arumugam, M., Harrington, E.D., Foerstner, K.U., Raes, J. & Bork, P. Bioinformatics. 2010 Dec 1;26(23):2977-8. Epub 2010 Oct 19. PubMed
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Gallego, O., Betts, M.J., Gvozdenovic-Jeremic, J., Maeda, K., Matetzki, C., Aguilar-Gurrieri, C., Beltran-Alvarez, P., Bonn, S., Fernandez-Tornero, C., Jensen, L.J., Kuhn, M., Trott, J., Rybin, V., Muller, C.W., Bork, P., Kaksonen, M., Russell, R.B. & Gavin, A.C. Mol Syst Biol. 2010 Nov 30;6:430. doi: 10.1038/msb.2010.87. PubMed
A human gut microbial gene catalogue established by metagenomic sequencing. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D.R., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., Xie, Y., Tap, J., Lepage, P., Bertalan, M., Batto, J.M., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H.B., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H., Yu, C., Li, S., Jian, M., Zhou, Y., Li, Y., Zhang, X., Li, S., Qin, N., Yang, H., Wang, J., Brunak, S., Dore, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Bork, P., Ehrlich, S.D. & Wang, J. Nature. 2010 Mar 4;464(7285):59-65. PubMed
High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Granovskaia, M.V., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L.M. Genome Biol. 2010 Mar 1;11(3):R24. PubMed
Evolution and regulation of cellular periodic processes: a role for paralogues. Trachana, K., Jensen, L.J. & Bork, P. EMBO Rep. 2010 Mar;11(3):233-8. Epub 2010 Feb 19. PubMed
Ancient animal microRNAs and the evolution of tissue identity. Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G.J., Bork, P. & Arendt, D. Nature. 2010 Feb 25;463(7284):1084-8. Epub 2010 Jan 31. PubMed
AQUA: automated quality improvement for multiple sequence alignments. Muller, J., Creevey, C.J., Thompson, J.D., Arendt, D. & Bork, P. Bioinformatics. 2010 Jan 15;26(2):263-5. Epub 2009 Nov 19. PubMed
Drug-induced regulation of target expression. Iskar, M., Campillos, M., Kuhn, M., Jensen, L.J., van Noort, V. & Bork, P. PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000925. PubMed
Impact of genome reduction on bacterial metabolism and its regulation. Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.H., Wodke, J.A., Guell, M., Martinez, S., Bourgeois, R., Kuhner, S., Raineri, E., Letunic, I., Kalinina, O.V., Rode, M., Herrmann, R., Gutierrez-Gallego, R., Russell, R.B., Gavin, A.C., Bork, P. & Serrano, L. Science. 2009 Nov 27;326(5957):1263-8. PubMed
Transcriptome complexity in a genome-reduced bacterium. Guell, M., van Noort, V., Yus, E., Chen, W.H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuhner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.C., Bork, P. & Serrano, L. Science. 2009 Nov 27;326(5957):1268-71. PubMed
Evolution of biomolecular networks: lessons from metabolic and protein interactions. Yamada, T. & Bork, P. Nat Rev Mol Cell Biol. 2009 Nov;10(11):791-803. PubMed
ASTD: The Alternative Splicing and Transcript Diversity database. Koscielny, G., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Riethoven, J.J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M., Harrington, E., Boue, S., Eyras, E., Plass, M., Lopez, F., Ritchie, W., Moucadel, V., Ara, T., Pospisil, H., Herrmann, A., G Reich, J., Guigo, R., Bork, P., Doeberitz, M.K., Vilo, J., Hide, W., Apweiler, R., Thanaraj, T.A. & Gautheret, D. Genomics. 2009 Mar;93(3):213-20. Epub 2008 Dec 24. PubMed
Sequence-based feature prediction and annotation of proteins. Juncker, A.S., Jensen, L.J., Pierleoni, A., Bernsel, A., Tress, M.L., Bork, P., von Heijne, G., Valencia, A., Ouzounis, C.A., Casadio, R. & Brunak, S. Genome Biol. 2009 Feb 2;10(2):206. PubMed
SMART 6: recent updates and new developments. Letunic, I., Doerks, T. & Bork, P. Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. Epub 2008 Oct 31. PubMed
InterPro: the integrative protein signature database. Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. & Yeats, C. Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. Epub 2008 Oct 21. PubMed
Proteome organization in a genome-reduced bacterium.
Kühner S., van Noort V., Betts M.J., Leo-Macias A., Batisse C., Rode M., Yamada T., Maier T., Bader S., Beltran-Alvarez P., Castaño-Diez D., Chen W.H., Devos D., Güell Cargol M., Norambuena T., Racke I., Rybin V., Schmidt A., Yus E., Aebersold R., Herrmann R., Böttcher B., Frangakis A.S., Russell R.B., Serrano L., Bork, P. and Gavin, A.C.
Science, 2009, 326, 1235-1240
Full text
Molecular eco-systems biology: towards an understanding of community function. Raes, J. & Bork, P. Nat Rev Microbiol. 2008 Sep;6(9):693-9. Epub 2008 Jun 30. PubMed
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Pincus, D., Letunic, I., Bork, P. & Lim, W.A. Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9680-4. Epub 2008 Jul 3. PubMed
KEGG Atlas mapping for global analysis of metabolic pathways. Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S. & Kanehisa, M. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W423-6. Epub 2008 May13. PubMed
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. King, N., Westbrook, M.J., Young, S.L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., Marr, M., Pincus, D., Putnam, N., Rokas, A., Wright, K.J., Zuzow, R., Dirks, W., Good, M., Goodstein, D., Lemons, D., Li, W., Lyons, J.B., Morris, A., Nichols, S., Richter, D.J., Salamov, A., Sequencing, J.G., Bork, P., Lim, W.A., Manning, G., Miller, W.T., McGinnis, W., Shapiro, H., Tjian, R., Grigoriev, I.V. & Rokhsar, D. Nature. 2008 Feb 14;451(7180):783-8. PubMed
iPath: interactive exploration of biochemical pathways and networks. Letunic, I., Yamada, T., Kanehisa, M. & Bork, P. Trends Biochem Sci. 2008 Feb 12;. PubMed
Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Shah, P.K., Tripathi, L.P., Jensen, L.J., Gahnim, M., Mason, C., Furlong, E.E., Rodrigues, V., White, K.P., Bork, P. & Sowdhamini, R. Gene. 2008 Jan 15;407(1-2):199-215. Epub 2007 Oct 15. PubMed
NetworKIN: a resource for exploring cellular phosphorylation networks. Linding, R., Jensen, L.J., Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., Yaffe, M.B. & Pawson, T. Nucleic Acids Res. 2008 Jan;36(Database issue):D695-9. Epub 2007 Nov 2. PubMed
STITCH: interaction networks of chemicals and proteins. Kuhn, M., von Mering, C., Campillos, M., Jensen, L.J. & Bork, P. Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8. Epub 2007 Dec 15. PubMed
eggNOG: automated construction and annotation of orthologous groups of genes. Jensen, L.J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. & Bork, P. Nucleic Acids Res. 2008 Jan;36(Database issue):D250-4. Epub 2007 Oct 16. PubMed
SuperTarget and Matador: resources for exploring drug-target relationships. Gunther, S., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., Ahmed, J., Urdiales, E.G., Gewiess, A., Jensen, L.J., Schneider, R., Skoblo, R., Russell, R.B., Bourne, P.E., Bork, P. & Preissner, R. Nucleic Acids Res. 2008 Jan;36(Database issue):D919-22. Epub 2007 Oct 16. PubMed
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution. Quijano, C., Tomancak, P., Lopez-Marti, J., Suyama, M., Bork, P., Milan, M., Torrents, D. & Manzanares, M. Genome Biol. 2008;9(12):R176. Epub 2008 Dec 16. PubMed
Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? Palleja, A., Harrington, E.D. & Bork, P. BMC Genomics. 2008 Jul 15;9:335. PubMed
Circular reasoning rather than cyclic expression. Jensen, L.J., de Lichtenberg, U., Jensen, T.S., Brunak, S. & Bork, P. Genome Biol. 2008;9(6):403. Epub 2008 Jun 23. PubMed
A nitrile hydratase in the eukaryote Monosiga brevicollis. Foerstner, K.U., Doerks, T., Muller, J., Raes, J. & Bork, P. PLoS One. 2008;3(12):e3976. Epub 2008 Dec 19. PubMed
Genome-wide experimental determination of barriers to horizontal gene transfer. Sorek, R., Zhu, Y., Creevey, C.J., Francino, M.P., Bork, P. & Rubin, E.M. Science. 2007 Nov 30;318(5855):1449-52. Epub 2007 Oct 18. PubMed
4DXpress: a database for cross-species expression pattern comparisons. Haudry, Y., Berube, H., Letunic, I., Weeber, P.D., Gagneur, J., Girardot, C., Kapushesky, M., Arendt, D., Bork, P., Brazma, A., Furlong, E., Wittbrodt, J. & Henrich, T. Nucleic Acids Res. 2007 Oct 4;. PubMed
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Eulalio, A., Rehwinkel, J., Stricker, M., Huntzinger, E., Yang, S.F., Doerks, T., Dorner, S., Bork, P., Boutros, M. & Izaurralde, E. Genes Dev. 2007 Oct 15;21(20):2558-70. Epub 2007 Sep 27. PubMed
Get the most out of your metagenome: computational analysis of environmental sequence data. Raes, J., Foerstner, K.U. & Bork, P. Curr Opin Microbiol. 2007 Oct;10(5):490-8. Epub 2007 Oct 23. PubMed
Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J. & Bork, P. Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13913-8. Epub 2007 Aug 23. PubMed
Evolution of cell cycle control: same molecular machines, different regulation. de Lichtenberg, U., Jensen, T.S., Brunak, S., Bork, P. & Jensen, L.J. Cell Cycle. 2007 Aug 1;6(15):1819-25. Epub 2007 Jun 4. PubMed
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Pachkov, M., Dandekar, T., Korbel, J., Bork, P. & Schuster, S. Gene. 2007 Jul 15;396(2):215-25. Epub 2007 Mar 24. PubMed
Systematic discovery of in vivo phosphorylation networks. Linding, R., Jensen, L.J., Ostheimer, G.J., van Vugt, M.A., Jorgensen, C., Miron, I.M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J.G., Samson, L.D., Woodgett, J.R., Russell, R.B., Bork, P., Yaffe, M.B. & Pawson, T. Cell. 2007 Jun 29;129(7):1415-26. Epub 2007 Jun 14. PubMed
Protein function space: viewing the limits or limited by our view? Raes, J., Harrington, E.D., Singh, A.H. & Bork, P. Curr Opin Struct Biol. 2007 Jun;17(3):362-9. Epub 2007 Jun 15. PubMed
Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes. Boettner, M., Steffens, C., von Mering, C., Bork, P., Stahl, U. & Lang, C. J Biotechnol. 2007 May 31;130(1):1-10. Epub 2007 Feb 28. PubMed
Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals. Danckwardt, S., Kaufmann, I., Gentzel, M., Foerstner, K.U., Gantzert, A.S., Gehring, N.H., Neu-Yilik, G., Bork, P., Keller, W., Wilm, M., Hentze, M.W. & Kulozik, A.E. EMBO J. 2007 Apr 26;. PubMed
Quantitative phylogenetic assessment of microbial communities in diverse environments. von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward, N. & Bork, P. Science. 2007 Feb 23;315(5815):1126-30. Epub 2007 Feb 1. PubMed
Quantification of insect genome divergence. Zdobnov, E.M. & Bork, P. Trends Genet. 2007 Jan;23(1):16-20. Epub 2006 Nov 9. PubMed
STRING 7--recent developments in the integration and prediction of protein interactions. von Mering, C., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B. & Bork, P. Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62. Epub 2006 Nov 10. PubMed
New developments in the InterPro database. Mulder, N.J., Apweiler, R., Attwood, T.K., 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, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. & Yeats, C. Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8. PubMed
Prediction of effective genome size in metagenomic samples. Raes, J., Korbel, J.O., Lercher, M.J., von Mering, C. & Bork, P. Genome Biol. 2007;8(1):R10. PubMed
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Hooper, S.D., Boue, S., Krause, R., Jensen, L.J., Mason, C.E., Ghanim, M., White, K.P., Furlong, E.E. & Bork, P. Mol Syst Biol. 2007;3:72. Epub 2007 Jan 16. PubMed
Insights into social insects from the genome of the honeybee Apis mellifera. Sequencing Consortium, T.H. (Bork, P.) Nature. 2006 Nov 23;444(7118):512. PubMed
Assessing systems properties of yeast mitochondria through an interaction map of the organelle. Perocchi, F., Jensen, L.J., Gagneur, J., Ahting, U., von Mering, C., Bork, P., Prokisch, H. & Steinmetz, L.M. PLoS Genet. 2006 Oct 20;2(10):e170. PubMed
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Letunic, I. & Bork, P. Bioinformatics. 2006 Oct 18;. PubMed
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome. Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D. & Arnone, M.I. Dev Biol. 2006 Sep 5;. PubMed
Computational characterization of multiple Gag-like human proteins. Campillos, M., Doerks, T., Shah, P.K. & Bork, P. Trends Genet. 2006 Sep 15;. PubMed
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Suyama, M., Torrents, D. & Bork, P. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12. PubMed
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Behm-Ansmant, I., Rehwinkel, J., Doerks, T., Stark, A., Bork, P. & Izaurralde, E. Genes Dev. 2006 Jun 30;. PubMed
LSAT: learning about alternative transcripts in MEDLINE. Shah, P.K. & Bork, P. Bioinformatics. 2006 Apr 1;22(7):857-65. Epub 2006 Jan 12. PubMed
Proteome survey reveals modularity of the yeast cell machinery. Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dumpelfeld, B., Edelmann, A., Heurtier, M.A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A.M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J.M., Kuster, B., Bork, P., Russell, R.B. & Superti-Furga, G. Nature. 2006 Mar 30;440(7084):631-6. Epub 2006 Jan 22. PubMed
Toward automatic reconstruction of a highly resolved tree of life. Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C.J., Snel, B. & Bork, P. Science. 2006 Mar 3;311(5765):1283-7. PubMed
Comparative analysis of environmental sequences: potential and challenges. Förstner, K.U., von Mering, C. & Bork, P. Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):519-23. PubMed
Extraction of regulatory gene/protein networks from Medline. Saric, J., Jensen, L.J., Ouzounova, R., Rojas, I. & Bork, P. Bioinformatics. 2006 Mar 15;22(6):645-50. Epub 2005 Jul 26. PubMed
Identification and analysis of evolutionarily cohesive functional modules in protein networks. Campillos, M., von Mering, C., Jensen, L.J. & Bork, P. Genome Res. 2006 Mar;16(3):374-82. Epub 2006 Jan 31. PubMed
Literature mining for the biologist: from information retrieval to biological discovery. Jensen, L.J., Saric, J. & Bork, P. Nat Rev Genet. 2006 Feb;7(2):119-29. PubMed
SMART 5: domains in the context of genomes and networks. Letunic, I., Copley, R.R., Pils, B., Pinkert, S., Schultz, J. & Bork, P. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D257-60. PubMed
Co-evolution of transcriptional and posttranslational cell-cycle regulation Jensen, LJ; Jensen, TS; de Lichtenberg, U; Brunak, S; Bork, P. Nature 2006 443(7111) 594-597
Medusa: a simple tool for interaction graph analysis. Hooper, S.D. & Bork, P. Bioinformatics. 2005 Dec 15;21(24):4432-3. Epub 2005 Sep 27. PubMed
Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases. Mees, A., Rock, R., Ciccarelli, F.D., Leberfinger, C.B., Borawski, J.M., Bork, P., Wiese, S., Gessler, M. & Kerkhoff, E. Gene Expr Patterns. 2005 Dec;6(1):79-85. Epub 2005 Aug 15. PubMed
Environments shape the nucleotide composition of genomes. Foerstner, K.U., von Mering, C., Hooper, S.D. & Bork, P. EMBO Rep 2005 Dec;6(12):1208-13. PubMed
Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. 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. Science 2005 Nov 25;310(5752):1325-6. PubMed
Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system. Taxis, C., Keller, P., Kavagiou, Z., Jensen, L.J., Colombelli, J., Bork, P., Stelzer, E.H.K. & Knop, M. J Cell Biol 2005 Nov 21;171(4):627-40. Epub 2005 Nov 14. PubMed
Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii. Suyama, M., Lathe WC, 3rd & Bork, P. FEBS Lett 2005 Oct 10;579(24):5281-6. PubMed
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. Rehwinkel, J., Letunic, I., Raes, J., Bork, P. & Izaurralde, E. RNA 2005 Oct;11(10):1530-44. PubMed
G2D: a tool for mining genes associated with disease. Perez-Iratxeta, C., Wjst, M., Bork, P. & Andrade, M.A. BMC Genet 2005 Aug 22;6:45. PubMed
Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. Bussow, K., Scheich, C., Sievert, V., Harttig, U., Schultz, J., Simon, B., Bork, P., Lehrach, H. & Heinemann, U. Microb Cell Fact 2005 Jul 5;4:21. PubMed
DCD - a novel plant specific domain in proteins involved in development and programmed cell death. Tenhaken, R., Doerks, T. & Bork, P. BMC Bioinformatics 2005 Jul 11;6:169. PubMed
Consistency of genome-based methods in measuring Metazoan evolution. Zdobnov, E.M., von Mering, C., Letunic, I. & Bork, P. FEBS Lett 2005 Jun 13;579(15):3355-61. Epub 2005 Apr 18. PubMed
Extraction of transcript diversity from scientific literature. Shah, P.K., Jensen, L.J., Boue, S. & Bork, P. PLoS Comput Biol. 2005 Jun;1(1):e10. Epub 2005 Jun 24. PubMed
Towards cellular systems in 4D. Bork, P. & Serrano, L. Cell 2005 May 20;121(4):507-9. PubMed
Structural similarity to bridge sequence space: finding new families on the bridges. Shah, P.K., Aloy, P., Bork, P. & Russell, R.B. Protein Sci 2005 May;14(5):1305-14. PubMed
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Hillier, L.W., Graves, T.A., Fulton, R.S., Fulton, L.A., Pepin, K.H., Minx, P., Wagner-McPherson, C., Layman, D., Wylie, K., Sekhon, M., Becker, M.C., Fewell, G.A., Delehaunty, K.D., Miner, T.L., Nash, W.E., 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, E.A., 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, S.S., Strong, C.M., Grewal, N., Goyea, E., Hou, S., Levy, A., Martinka, S., Mead, K., McLellan, M.D., Meyer, R., Randall-Maher, J., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Shah, N., Swearengen-Shahid, S., Snider, J., Strong, J.T., Thompson, J., Yoakum, M., Leonard, S., Pearman, C., Trani, L., Radionenko, M., Waligorski, J.E., Wang, C., Rock, S.M., Tin-Wollam, A.M., Maupin, R., Latreille, P., Wendl, M.C., Yang, S.P., Pohl, C., Wallis, J.W., Spieth, J., Bieri, T.A., Berkowicz, N., Nelson, J.O., Osborne, J., Ding, L., Meyer, R., Sabo, A., Shotland, Y., Sinha, P., Wohldmann, P.E., Cook, L.L., Hickenbotham, M.T., Eldred, J., Williams, D., Jones, T.A., She, X., Ciccarelli, F.D., Izaurralde, E., Taylor, J., Schmutz, J., Myers, R.M., Cox, D.R., Huang, X., McPherson, J.D., Mardis, E.R., Clifton, S.W., Warren, W.C., Chinwalla, A.T., Eddy, S.R., Marra, M.A., Ovcharenko, I., Furey, T.S., Miller, W., Eichler, E.E., Bork, P., Suyama, M., Torrents, D., Waterston, R.H. & Wilson, R.K. Nature 2005 Apr 7;434(7034):724-31. PubMed
Systematic association of genes to phenotypes by genome and literature mining. Korbel, J.O., Doerks, T., Jensen, L.J., Perez-Iratxeta, C., Kaczanowski, S., Hooper, S.D., Andrade, M.A. & Bork, P. PLoS Biol 2005 Apr 5;3(5):e134. PubMed
Comparative metagenomics of microbial communities. Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P. & Rubin, E.M. Science 2005 Apr 22;308(5721):554-7. PubMed
The WHy domain mediates the response to desiccation in plants and bacteria. Ciccarelli, F.D. & Bork, P. Bioinformatics 2005 Apr 15;21(8):1304-7. Epub 2004 Dec 14. PubMed
Complex genomic rearrangements lead to novel primate gene function. Ciccarelli, F.D., von Mering, C., Suyama, M., Harrington, E.D., Izaurralde, E. & Bork, P. Genome Res 2005 Mar;15(3):343-51. Epub 2005 Feb 14. PubMed
Dynamic complex formation during the yeast cell cycle. de Lichtenberg, U., Jensen, L.J., Brunak, S. & Bork, P. Science 2005 Feb 4;307(5710):724-7. PubMed
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. & Bork, P. Nucleic Acids Res 2005 Jan 1;33 Database Issue:D433-7. PubMed
InterPro, progress and status in 2005. Mulder, N.J., Apweiler, R., Attwood, T.K., 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, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., Vaughan, R. & Wu, C.H. Nucleic Acids Res 2005 Jan 1;33(Database issue):D201-5. PubMed
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Bourque, G., Zdobnov, E.M., Bork, P., Pevzner, P.A. & Tesler, G. Genome Res 2005 Jan;15(1):98-110. Epub 2004 Dec 08. PubMed
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. Zdobnov, E.M., Campillos, M., Harrington, E.D., Torrents, D. & Bork, P. Nucleic Acids Res 2005 Feb 16;33(3):946-54. Print 2005. PubMed
Is there biological research beyond Systems Biology? A comparative analysis of terms. Bork, P. Molecular Systems Biology 2005
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Hillier, L.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A., Delany, M.E., Dodgson, J.B., Chinwalla, A.T., Cliften, P.F., Clifton, S.W., Delehaunty, K.D., Fronick, C., Fulton, R.S., Graves, T.A., Kremitzki, C., Layman, D., Magrini, V., McPherson, J.D., Miner, T.L., Minx, P., Nash, W.E., Nhan, M.N., Nelson, J.O., Oddy, L.G., Pohl, C.S., Randall-Maher, J., Smith, S.M., Wallis, J.W., Yang, S.P., Romanov, M.N., Rondelli, C.M., Paton, B., Smith, J., Morrice, D., Daniels, L., Tempest, H.G., Robertson, L., Masabanda, J.S., Griffin, D.K., Vignal, A., Fillon, V., Jacobbson, L., Kerje, S., Andersson, L., Crooijmans, R.P., Aerts, J., van der Poel, J.J., Ellegren, H., Caldwell, R.B., Hubbard, S.J., Grafham, D.V., Kierzek, A.M., McLaren, S.R., Overton, I.M., Arakawa, H., Beattie, K.J., Bezzubov, Y., Boardman, P.E., Bonfield, J.K., Croning, M.D., Davies, R.M., Francis, M.D., Humphray, S.J., Scott, C.E., Taylor, R.G., Tickle, C., Brown, W.R., Rogers, J., Buerstedde, J.M., Wilson, S.A., Stubbs, L., Ovcharenko, I., Gordon, L., Lucas, S., Miller, M.M., Inoko, H., Shiina, T., Kaufman, J., Salomonsen, J., Skjoedt, K., Wong, G.K., Wang, J., Liu, B., Wang, J., Yu, J., Yang, H., Nefedov, M., Koriabine, M., Dejong, P.J., Goodstadt, L., Webber, C., Dickens, N.J., Letunic, I., Suyama, M., Torrents, D., von Mering, C., Zdobnov, E.M., Makova, K., Nekrutenko, A., Elnitski, L., Eswara, P., King, D.C., Yang, S., Tyekucheva, S., Radakrishnan, A., Harris, R.S., Chiaromonte, F., Taylor, J., He, J., Rijnkels, M., Griffiths-Jones, S., Ureta-Vidal, A., Hoffman, M.M., Severin, J., Searle, S.M., Law, A.S., Speed, D., Waddington, D., Cheng, Z., Tuzun, E., Eichler, E., Bao, Z., Flicek, P., Shteynberg, D.D., Brent, M.R., Bye, J.M., Huckle, E.J., Chatterji, S., Dewey, C., Pachter, L., Kouranov, A., Mourelatos, Z., Hatzigeorgiou, A.G., Paterson, A.H., Ivarie, R., Brandstrom, M., Axelsson, E., Backstrom, N., Berlin, S., Webster, M.T., Pourquie, O., Reymond, A., Ucla, C., Antonarakis, S.E., Long, M., Emerson, J.J., Betran, E., Dupanloup, I., Kaessmann, H., Hinrichs, A.S., Bejerano, G., Furey, T.S., Harte, R.A., Raney, B., Siepel, A., Kent, W.J., Haussler, D., Eyras, E., Castelo, R., Abril, J.F., Castellano, S., Camara, F., Parra, G., Guigo, R., Bourque, G., Tesler, G., Pevzner, P.A., Smit, A., Fulton, L.A., Mardis, E.R. & Wilson, R.K. Nature 2004 Dec 9;432(7018):695-716. PubMed
Shared components of protein complexes--versatile building blocks or biochemical artefacts? Krause, R., von Mering, C., Bork, P. & Dandekar, T. Bioessays 2004 Dec;26(12):1333-43. PubMed
Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression. Koehl, A., Schmidt, N., Rieger, A., Pilgram, S.M., Letunic, I., Bork, P., Soto, F., Friauf, E. & Nothwang, H.G. Eur J Neurosci 2004 Dec;20(12):3244-58. PubMed
Comparison of computational methods for the identification of cell cycle regulated genes. de Lichtenberg, U., Jensen, L.J., Fausboll, A., Jensen, T.S., Bork, P. & Brunak, S. Bioinformatics 2004 Oct 28. PubMed
Gene annotation from scientific literature using mappings between keyword systems. Perez, A.J., Perez-Iratxeta, C., Bork, P., Thode, G. & Andrade, M.A. Bioinformatics 2004 Sep 1;20(13):2084-91. Epub 2004 Apr 01. PubMed
Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome. Liska, A.J., Popov, A.V., Sunyaev, S., Coughlin, P., Habermann, B., Shevchenko, A., Bork, P., Karsenti, E. & Shevchenko, A. Proteomics 2004 Sep;4(9):2707-21. PubMed
ArrayProspector: a web resource of functional associations inferred from microarray expression data. Jensen, L.J., Lagarde, J., von Mering, C. & Bork, P. Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W445-8. PubMed
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Korbel, J.O., Jensen, L.J., von Mering, C. & Bork, P. Nat Biotechnol 2004 Jul;22(7):911-7. PubMed
Protein interaction networks from yeast to human. Bork, P., Jensen, L.J., von Mering, C., Ramani, A.K., Lee, I. & Marcotte, E.M. Curr Opin Struct Biol 2004 Jun;14(3):292-9. PubMed
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Suyama, M., Torrents, D. & Bork, P. Bioinformatics 2004 Apr 1. PubMed
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs, R.A., Weinstock, G.M., Metzker, M.L., Muzny, D.M., Sodergren, E.J., Scherer, S., Scott, G., Steffen, D., Worley, K.C., Burch, P.E., Okwuonu, G., Hines, S., Lewis, L., DeRamo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R., Celera, Holt, R.A., Adams, M.D., Amanatides, P.G., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, C.A., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, C.L., Nguyen, T., Pfannkoch, C.M., Sitter, C., Sutton, G.G., Venter, J.C., Woodage, T., Smith, D., Lee, H.M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, R.B., Dunn, D.M., Green, E.D., Blakesley, R.W., Bouffard, G.G., De Jong, P.J., 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, C.M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W.C., Havlak, P.H., Chen, R., Durbin, K.J., Egan, A., Ren, Y., Song, X.Z., Li, B., Liu, Y., Qin, X., Cawley, S., Worley, K.C., Cooney, A.J., D'Souza, L.M., Martin, K., Wu, J.Q., Gonzalez-Garay, M.L., Jackson, A.R., Kalafus, K.J., McLeod, M.P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D.A., Zhang, Z., Bailey, J.A., Eichler, E.E., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B.J., Young, J.M., Huang, H., Wang, H., Xing, H., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Mar Alba, M., Abril, J.F., Guigo, R., Smit, A., Dubchak, I., Rubin, E.M., Couronne, O., Poliakov, A., Hubner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y.A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H.J., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, M.I., Kwitek, A.E., Lazar, J., Pasko, D., Tonellato, P.J., Twigger, S., Ponting, C.P., Duarte, J.M., Rice, S., Goodstadt, L., Beatson, S.A., Emes, R.D., Winter, E.E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R.C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T.D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S.M., Cooper, G.M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E.A., Venter, J.C., Payseur, B.A., Bourque, G., Lopez-Otin, C., Puente, X.S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V.B., Caspi, A., Tesler, G., Pevzner, P.A., Haussler, D., Roskin, K.M., Baertsch, R., Clawson, H., Furey, T.S., Hinrichs, A.S., Karolchik, D., Kent, W.J., Rosenbloom, K.R., Trumbower, H., Weirauch, M., Cooper, D.N., Stenson, P.D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R.R., Taylor, M.S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S. & Collins, F. Nature 2004 Apr 1;428(6982):493-521. PubMed
Structure-based assembly of protein complexes in yeast. Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A.C., Bork, P., Superti-Furga, G., Serrano, L. & Russell, R.B. Science 2004 Mar 26;303(5666):2026-9. PubMed
Global analysis of bacterial transcription factors to predict cellular target processes. Doerks, T., Andrade, M.A., Lathe W, 3rd, von Mering, C. & Bork, P. Trends Genet 2004 Mar;20(3):126-31. PubMed
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. 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, S.G., 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. Nat Biotechnol 2004 Feb;22(2):177-83. PubMed
RanBP2/Nup358 Provides a Major Binding Site for NXF1-p15 Dimers at the Nuclear Pore Complex and Functions in Nuclear mRNA Export. Forler, D., Rabut, G., Ciccarelli, F.D., Herold, A., Kocher, T., Niggeweg, R., Bork, P., Ellenberg, J. & Izaurralde, E. Mol Cell Biol 2004 Feb;24(3):1155-67. PubMed
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.H., Gohla, R., Gossling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J.O., Lengauer, T., Liebich, I., Van Der Linden, M., Luz, H., Meissner, K., Von Mering, C., Mevissen, H.T., Mewes, H.W., Michael, H., Mokrejs, M., Muller, T., Pospisil, H., Rarey, M., Reich, J.G., 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. Bioinformatics 2004 Jan 22;20(2):268-270. PubMed
SMART 4.0: towards genomic data integration. Letunic, I., Copley, R.R., Schmidt, S., Ciccarelli, F.D., Doerks, T., Schultz, J., Ponting, C.P. & Bork, P. Nucleic Acids Res 2004 Jan 1;32(1):D142-4. PubMed
Extracting regulatory gene expression networks from pubmed. Sarik, J., Lensen, L.J., Ouzounova, R., Rojas, I. & Bork, P. Proceedings of the 42nd annuual meeting of the association of computational linguistics 2004;192-199.
Quality analysis and integration of large scale molecular data sets. Jensen, L.J. & Bork, P. Drug Discovery Today (TARGETS) 2004;3:51-56.
Estimating rates of alternative splicing in mammals and invertebrates. Harrington, E.D., Boue, S., Valcarcel, J., Reich, J.G., & Bork, P. Nature Genet 2004;36:916-917.
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Doerks, T., von Mering, C. & Bork, P. Nucleic Acids Res ;32(21):6321-6. Print 2004. PubMed
Sequences and structures in context. Bork, P. & Orengo, C. Curr. Opin. Struct. Biol. 2004 14 261-263
Genome evolution reveals biochemical networks and functional modules. von Mering, C., Zdobnov, E.M., Tsoka, S., Ciccarelli, F.D., Pereira-Leal, J.B., Ouzounis, C.A. & Bork, P. Proc Natl Acad Sci U S A 2003 Dec 23;100(26):15428-33. PubMed
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. Ciccarelli, F.D., Izaurralde, E. & Bork, P. BMC Bioinformatics 2003 Dec 19;4(1):64. PubMed
Impact of selection, mutation rate and genetic drift on human genetic variation. Sunyaev, S., Kondrashov, F.A., Bork, P. & Ramensky, V. Hum Mol Genet 2003 Dec 15;12(24):3325-30. PubMed
A genome-wide survey of human pseudogenes. Torrents, D., Suyama, M., Zdobnov, E. & Bork, P. Genome Res 2003 Dec;13(12):2559-67. PubMed
Alternative splicing and evolution. Boue, S., Letunic, I. & Bork, P. Bioessays 2003 Nov;25(11):1031-4. PubMed
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. Krause, R., von Mering, C. & Bork, P. Bioinformatics 2003 Oct 12;19(15):1901-8. PubMed
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. Gatfield, D., Unterholzner, L., Ciccarelli, F.D., Bork, P. & Izaurralde, E. EMBO J 2003 Aug 1;22(15):3960-70. PubMed
The DNA sequence of human chromosome 7. Hillier, L.W., Fulton, R.S., Fulton, L.A., Graves, T.A., Pepin, K.H., Wagner-McPherson, C., Layman, D., Maas, J., Jaeger, S., Walker, R., Wylie, K., Sekhon, M., Becker, M.C., O'Laughlin, M.D., Schaller, M.E., Fewell, G.A., Delehaunty, K.D., Miner, T.L., Nash, W.E., 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, C.M., Hou, S., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Leonard, S., Rohlfing, T., Rock, S.M., Tin-Wollam, A.M., Abbott, A., Minx, P., Maupin, R., Strowmatt, C., Latreille, P., Miller, N., Johnson, D., Murray, J., Woessner, J.P., Wendl, M.C., Yang, S.P., Schultz, B.R., Wallis, J.W., Spieth, J., Bieri, T.A., Nelson, J.O., Berkowicz, N., Wohldmann, P.E., Cook, L.L., Hickenbotham, M.T., Eldred, J., Williams, D., Bedell, J.A., Mardis, E.R., Clifton, S.W., Chissoe, S.L., Marra, M.A., 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, W.J., Furey, T.S., Baertsch, R.A., Brent, M.R., Keibler, E., Flicek, P., Bork, P., Suyama, M., Bailey, J.A., Portnoy, M.E., Torrents, D., Chinwalla, A.T., Gish, W.R., Eddy, S.R., McPherson, J.D., Olson, M.V., Eichler, E.E., Green, E.D., Waterston, R.H. & Wilson, R.K. Nature 2003 Jul 10;424(6945):157-64. PubMed
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Puntervoll, P., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M., Ausiello, G., Brannetti, B., Costantini, A., Ferre, 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., Kuster, B., Helmer-Citterich, M., Hunter, W.N., Aasland, R. & Gibson, T.J. Nucleic Acids Res 2003 Jul 1;31(13):3625-30. PubMed
Update on XplorMed: A web server for exploring scientific literature. Perez-Iratxeta, C., Perez, A.J., Bork, P. & Andrade, M.A. Nucleic Acids Res 2003 Jul 1;31(13):3866-8. PubMed
Systematic discovery of analogous enzymes in thiamin biosynthesis. Morett, E., Korbel, J.O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B. & Bork, P. Nat Biotechnol 2003 Jul;21(7):790-5. PubMed
The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold. Ciccarelli, F.D., Bork, P. & Kerkhoff, E. Trends Biochem Sci 2003 Jul;28(7):349-52. PubMed
Metabolites: a helping hand for pathway evolution? Schmidt, S., Sunyaev, S., Bork, P. & Dandekar, T. Trends Biochem Sci 2003 Jun;28(6):336-41. PubMed
Information extraction from full text scientific articles: where are the keywords? Shah, P.K., Perez-Iratxeta, C., Bork, P. & Andrade, M.A. BMC Bioinformatics 2003 May 29;4(1):20. PubMed
The way we write. Netzel, R., Perez-Iratxeta, C., Bork, P. & Andrade, M.A. EMBO Rep 2003 May;4(5):446-51. PubMed
Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes. Woerner, S.M., Benner, A., Sutter, C., Schiller, M., Yuan, Y.P., Keller, G., Bork, P., Doeberitz, M.K. & Gebert, J.F. Oncogene 2003 Apr 17;22(15):2226-35. PubMed
Function prediction and protein networks. Huynen, M.A., Snel, B., Mering, C. & Bork, P. Curr Opin Cell Biol 2003 Apr;15(2):191-8. PubMed
The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia. Ciccarelli, F.D., Proukakis, C., Patel, H., Cross, H., Azam, S., Patton, M.A., Bork, P. & Crosby, A.H. Genomics 2003 Apr;81(4):437-41. PubMed
Increase of functional diversity by alternative splicing. Kriventseva, E.V., Koch, I., Apweiler, R., Vingron, M., Bork, P., Gelfand, M.S. & Sunyaev, S. Trends Genet 2003 Mar;19(3):124-8. PubMed
Bioinformatics in the post-sequence era. Kanehisa, M. & Bork, P. Nat Genet 2003 Mar;33 Suppl:305-10. PubMed
STRING: a database of predicted functional associations between proteins. von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P. & Snel, B. Nucleic Acids Res 2003 Jan 1;31(1):258-61. PubMed
The InterPro Database, 2003 brings increased coverage and new features. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R.R., 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, S.E., Pagni, M., Peyruc, D., Ponting, C.P., Selengut, J.D., Servant, F., Sigrist, C.J., Vaughan, R. & Zdobnov, E.M. Nucleic Acids Res 2003 Jan 1;31(1):315-8. PubMed
The human genome: genes, pseudogenes, and variation on chromosome 7. Waterston, R.H., Hillier, L.W., Fulton, L.A., Fulton, R.S., Graves, T.A., Pepin, K.H., Bork, P., Suyama, M., Torrents, D., Chinwalla, A.T., Mardis, E.R., McPherson, J.D. & Wilson, R.K. Cold Spring Harb Symp Quant Biol 2003;68:13-22. PubMed
Detection and characterization of pseudogenes. Torrents, D., Suyama, M. & Bork, P. In "Bioinformatics and Genomes." M. Andrade (Ed). Horizon Sci. Press, 197-209
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes. Shevchenko, A., Sunyaev, S., Liska, A., Bork, P. & Shevchenko, A. Methods Mol Biol 2003;211:221-34. PubMed
High rate of gene displacement in vitamine biosynthetic pathways. Morett, E., Saab-Rincon, G., Merino, E., Bork, P., Rajan, E., Olvera, L. & Olvera, M. In "Bioinformatics and Genomes." M. Andrade (Ed.). Horizon Sci. Press, 69-79
Initial sequencing and comparative analysis of the mouse genome. Waterston, R.H., Lindblad-Toh, K., Birney, E., et al. Nature 2002 Dec 5;420(6915):520-62. PubMed
Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes. Kloor, M., Bork, P., Duwe, A., Klaes, R., von Knebel Doeberitz, M. & Ridder, R. Biochim Biophys Acta 2002 Dec 12;1579(2-3):219-24. PubMed
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D., Holt, R.A., Subramanian, G.M., Mueller, H.M., Dimopoulos, G., Law, J.H., Wells, M.A., Birney, E., Charlab, R., Halpern, A.L., Kokoza, E., Kraft, C.L., Lai, Z., Lewis, S., Louis, C., Barillas-Mury, C., Nusskern, D., Rubin, G.M., Salzberg, S.L., Sutton, G.G., Topalis, P., Wides, R., Wincker, P., Yandell, M., Collins, F.H., Ribeiro, J., Gelbart, W.M., Kafatos, F.C. & Bork, P. Science 2002 Oct 4;298(5591):149-59. PubMed
The genome sequence of the malaria mosquito Anopheles gambiae. Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M., Wides, R., Salzberg, S.L., Loftus, B., Yandell, M., Majoros, W.H., Rusch, D.B., Lai, Z., Kraft, C.L., Abril, J.F., Anthouard, V., Arensburger, P., Atkinson, P.W., Baden, H., de Berardinis, V., Baldwin, D., Benes, V., Biedler, J., Blass, C., Bolanos, R., Boscus, D., Barnstead, M., Cai, S., Center, A., Chatuverdi, K., Christophides, G.K., Chrystal, M.A., Clamp, M., Cravchik, A., Curwen, V., Dana, A., Delcher, A., Dew, I., Evans, C.A., Flanigan, M., Grundschober-Freimoser, A., Friedli, L., Gu, Z., Guan, P., Guigo, R., Hillenmeyer, M.E., Hladun, S.L., Hogan, J.R., Hong, Y.S., Hoover, J., Jaillon, O., Ke, Z., Kodira, C., Kokoza, E., Koutsos, A., Letunic, I., Levitsky, A., Liang, Y., Lin, J.J., Lobo, N.F., Lopez, J.R., Malek, J.A., McIntosh, T.C., Meister, S., Miller, J., Mobarry, C., Mongin, E., Murphy, S.D., O'Brochta, D.A., Pfannkoch, C., Qi, R., Regier, M.A., Remington, K., Shao, H., Sharakhova, M.V., Sitter, C.D., Shetty, J., Smith, T.J., Strong, R., Sun, J., Thomasova, D., Ton, L.Q., Topalis, P., Tu, Z., Unger, M.F., Walenz, B., Wang, A., Wang, J., Wang, M., Wang, X., Woodford, K.J., Wortman, J.R., Wu, M., Yao, A., Zdobnov, E.M., Zhang, H., Zhao, Q., Zhao, S., Zhu, S.C., Zhimulev, I., Coluzzi, M., della Torre, A., Roth, C.W., Louis, C., Kalush, F., Mural, R.J., Myers, E.W., Adams, M.D., Smith, H.O., Broder, S., Gardner, M.J., Fraser, C.M., Birney, E., Bork, P., Brey, P.T., Venter, J.C., Weissenbach, J., Kafatos, F.C., Collins, F.H. & Hoffman, S.L. Science 2002 Oct 4;298(5591):129-49. PubMed
Immunity-related genes and gene families in Anopheles gambiae. Christophides, G.K., Zdobnov, E., Barillas-Mury, C., Birney, E., Blandin, S., Blass, C., Brey, P.T., Collins, F.H., Danielli, A., Dimopoulos, G., Hetru, C., Hoa, N.T., Hoffmann, J.A., Kanzok, S.M., Letunic, I., Levashina, E.A., Loukeris, T.G., Lycett, G., Meister, S., Michel, K., Moita, L.F., Muller, H.M., Osta, M.A., Paskewitz, S.M., Reichhart, J.M., Rzhetsky, A., Troxler, L., Vernick, K.D., Vlachou, D., Volz, J., von Mering, C., Xu, J., Zheng, L., Bork, P. & Kafatos, F.C. Science 2002 Oct 4;298(5591):159-65. PubMed
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Schell, M.A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M.C., Desiere, F., Bork, P., Delley, M., Pridmore, R.D. & Arigoni, F. Proc Natl Acad Sci U S A 2002 Oct 29;99(22):14422-7. PubMed
Comparative analysis of protein interaction networks. Bork, P. Bioinformatics 2002 Oct;18 Suppl 2:S64. PubMed
Human non-synonymous SNPs: server and survey. Ramensky, V., Bork, P. & Sunyaev, S. Nucleic Acids Res 2002 Sep 1;30(17):3894-900. PubMed
InterPro: an integrated documentation resource for protein families, domains and functional sites. Mulder, N.J., Apweiler, R., Attwood, T.K., 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, C.P., Servant, F. & Sigrist, C.J. Brief Bioinform 2002 Sep;3(3):225-35. PubMed
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria. Andrade, M.A., Ciccarelli, F.D., Perez-Iratxeta, C. & Bork, P. Genome Biol 2002 Aug 15;3(9):RESEARCH0047. PubMed
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia. Patel, H., Cross, H., Proukakis, C., Hershberger, R., Bork, P., Ciccarelli, F.D., Patton, M.A., McKusick, V.A. & Crosby, A.H. Nat Genet 2002 Aug;31(4):347-8. PubMed
Predicting protein cellular localization using a domain projection method. Mott, R., Schultz, J., Bork, P. & Ponting, C.P. Genome Res 2002 Aug;12(8):1168-74. PubMed
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations. Bordo, D. & Bork, P. EMBO Rep 2002 Aug;3(8):741-6. PubMed
Association of genes to genetically inherited diseases using data mining. Perez-Iratxeta, C., Bork, P. & Andrade, M.A. Nat Genet 2002 Jul;31(3):316-9. PubMed
A complex prediction: three-dimensional model of the yeast exosome. Aloy, P., Ciccarelli, F.D., Leutwein, C., Gavin, A.C., Superti-Furga, G., Bork, P., Böttcher, B. & Russell, R.B. EMBO Rep 2002 Jul;3(7):628-35. PubMed
Teamed up for transcription. von Mering, C. & Bork, P. Nature 2002 Jun 20;417(6891):797-8. PubMed
Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae. Thomasova, D., Ton, L.Q., Copley, R.R., Zdobnov, E.M., Wang, X., Hong, Y.S., Sim, C., Bork, P., Kafatos, F.C. & Collins, F.H. Proc Natl Acad Sci U S A 2002 Jun 11;99(12):8179-84. PubMed
Computing fuzzy associations for the analysis of biological literature. Perez-Iratxeta, C., Keer, H.S., Bork, P. & Andrade, M.A. Biotechniques 2002 Jun;32(6):1380-2, 1384-5. PubMed
Exploring MEDLINE abstracts with XplorMed. Perez-Iratxeta, C., Bork, P. & Andrade, M.A. Drugs Today (Barc) 2002 Jun;38(6):381-9. PubMed
Comparative assessment of large-scale data sets of protein-protein interactions. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. & Bork, P. Nature 2002 May 23;417(6887):399-403. PubMed
The identification of functional modules from the genomic association of genes. Snel, B., Bork, P. & Huynen, M.A. Proc Natl Acad Sci U S A 2002 Apr 30;99(9):5890-5. PubMed
BSD: a novel domain in transcription factors and synapse-associated proteins. Doerks, T., Huber, S., Buchner, E. & Bork, P. Trends Biochem Sci 2002 Apr;27(4):168-70. PubMed
A versatile structural domain analysis server using profile weight matrices. Schmidt, S., Bork, P. & Dandekar, T. J Chem Inf Comput Sci 2002 Mar-Apr;42(2):405-7. PubMed
SHOT: a web server for the construction of genome phylogenies. Korbel, J.O., Snel, B., Huynen, M.A. & Bork, P. Trends Genet 2002 Mar;18(3):158-62. PubMed
AMOP, a protein module alternatively spliced in cancer cells. Ciccarelli, F.D., Doerks, T. & Bork, P. Trends Biochem Sci 2002 Mar;27(3):113-5. PubMed
Protein domain analysis in the era of complete genomes. Copley, R.R., Doerks, T., Letunic, I. & Bork, P. FEBS Lett 2002 Feb 20;513(1):129-34. PubMed
Genome and protein evolution in eukaryotes. Copley, R.R., Letunic, I. & Bork, P. Curr Opin Chem Biol 2002 Feb;6(1):39-45. PubMed
CASH a beta-helix domain widespread among carbohydrate-binding proteins. Ciccarelli, F.D., Copley, R.R., Doerks, T., Russell, R.B. & Bork, P. Trends Biochem Sci 2002 Feb;27(2):59-62. PubMed
Functional organization of the yeast proteome by systematic analysis of protein complexes. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, 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, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. & Superti-Furga, G. Nature 2002 Jan 10;415(6868):141-7. PubMed
Recent improvements to the SMART domain-based sequence annotation resource. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P. & Bork, P. Nucleic Acids Res 2002 Jan 1;30(1):242-4. PubMed
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Fredman, D., Siegfried, M., Yuan, Y.P., Bork, P., Lehvaslaiho, H. & Brookes, A.J. Nucleic Acids Res 2002 Jan 1;30(1):387-91. PubMed
Genomes in flux: the evolution of archaeal and proteobacterial gene content. Snel, B., Bork, P. & Huynen, M.A. Genome Res 2002 Jan;12(1):17-25. PubMed
Systematic identification of novel protein domain families associated with nuclear functions. Doerks, T., Copley, R.R., Schultz, J., Ponting, C.P. & Bork, P. Genome Res 2002 Jan;12(1):47-56. PubMed
Alternative splicing and genome complexity. Brett, D., Pospisil, H., Valcarcel, J., Reich, J. & Bork, P. Nat Genet 2002 Jan;30(1):29-30. PubMed