EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

  • PhD 1990, University of Leipzig.
    Habilitation 1995, Humboldt University, Berlin.
    At EMBL since 1991, Head of Unit since 2001.
    Strategic Head of Bioinformatics at EMBL Heidelberg since 2011.
    Group leader in the Molecular Medicine Partnership Unit.
    ERC Advanced Investigator.

Publications

Total: 576 publication(s)

2010

Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P. (2010)

A network of conserved co-occurring motifs for the regulation of alternative splicing

Nucleic Acids Res. 38(22):7916-7926. doi: 10.1093/nar/gkq705
Europe PMC | doi

Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC. (2010)

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae

Mol. Syst. Biol. 6:430. doi: 10.1038/msb.2010.87
Europe PMC | doi

Dusko Ehrlich S, MetaHIT consortium. (2010)

[Metagenomics of the intestinal microbiota: potential applications]

Gastroenterol. Clin. Biol. 34 Suppl 1:S23-8. doi: 10.1016/s0399-8320(10)70017-8
Europe PMC | doi

Jensen LJ, Bork P. (2010)

Ontologies in quantitative biology: a basis for comparison, integration, and discovery

PLoS Biol. 8(5):e1000374. doi: 10.1371/journal.pbio.1000374
Europe PMC | doi

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. (2010)

A method and server for predicting damaging missense mutations

Nat. Methods 7(4):248-249. doi: 10.1038/nmeth0410-248
Europe PMC | doi

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, 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 JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, 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, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J. (2010)

A human gut microbial gene catalogue established by metagenomic sequencing

Nature 464(7285):59-65. doi: 10.1038/nature08821
Europe PMC | doi

Trachana K, Jensen LJ, Bork P. (2010)

Evolution and regulation of cellular periodic processes: a role for paralogues

EMBO Rep. 11(3):233-238. doi: 10.1038/embor.2010.9
Europe PMC | doi

Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D. (2010)

Ancient animal microRNAs and the evolution of tissue identity

Nature 463(7284):1084-1088. doi: 10.1038/nature08744
Europe PMC | doi

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. (2010)

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Genome Biol. 11(3):R24. doi: 10.1186/gb-2010-11-3-r24
Europe PMC | doi

Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P. (2010)

Drug-induced regulation of target expression

PLoS Comput. Biol. 6(9):289-301. doi: 10.1371/journal.pcbi.1000925
Europe PMC | doi

Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. (2010)

A side effect resource to capture phenotypic effects of drugs

Mol. Syst. Biol. 6:343. doi: 10.1038/msb.2009.98
Europe PMC | doi

Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. (2010)

STITCH 2: an interaction network database for small molecules and proteins

Nucleic Acids Res. 38(Database issue):D552-6. doi: 10.1093/nar/gkp937
Europe PMC | doi

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P. (2010)

AQUA: automated quality improvement for multiple sequence alignments

Bioinformatics 26(2):263-265. doi: 10.1093/bioinformatics/btp651
Europe PMC | doi

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. (2010)

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

Nucleic Acids Res. 38(Database issue):D190-5. doi: 10.1093/nar/gkp951
Europe PMC | doi

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA. (2010)

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

Science 327(5963):343-348. doi: 10.1126/science.1178028
Europe PMC | doi

Woerner SM, Yuan YP, Benner A, Korff S, von Knebel Doeberitz M, Bork P. (2010)

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology

Nucleic Acids Res. 38(Database issue):D682-9. doi: 10.1093/nar/gkp839
Europe PMC | doi


2009

Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L. (2009)

Transcriptome complexity in a genome-reduced bacterium

Science 326(5957):1268-1271. doi: 10.1126/science.1176951
Europe PMC | doi

Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC. (2009)

Proteome organization in a genome-reduced bacterium

Science 326(5957):1235-1240. doi: 10.1126/science.1176343
Europe PMC | doi

Yamada T, Bork P. (2009)

Evolution of biomolecular networks: lessons from metabolic and protein interactions

Nat. Rev. Mol. Cell Biol. 10(11):791-803. doi: 10.1038/nrm2787
Europe PMC | doi

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L. (2009)

Impact of genome reduction on bacterial metabolism and its regulation

Science 326(5957):1263-1268. doi: 10.1126/science.1177263
Europe PMC | doi

Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D. (2009)

ASTD: The Alternative Splicing and Transcript Diversity database

Genomics 93(3):213-220. doi: 10.1016/j.ygeno.2008.11.003
Europe PMC | doi

Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. (2009)

Quantifying environmental adaptation of metabolic pathways in metagenomics

Proc. Natl. Acad. Sci. U.S.A. 106(5):1374-1379. doi: 10.1073/pnas.0808022106
Europe PMC | doi

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, 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 AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)

InterPro: the integrative protein signature database

Nucleic Acids Res. 37(Database issue):D211-5. doi: 10.1093/nar/gkn785
Europe PMC | doi

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. (2009)

STRING 8--a global view on proteins and their functional interactions in 630 organisms

Nucleic Acids Res. 37(Database issue):D412-6. doi: 10.1093/nar/gkn760
Europe PMC | doi

Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. (2009)

Sequence-based feature prediction and annotation of proteins

Genome Biol. 10(2):206. doi: 10.1186/gb-2009-10-2-206
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2009)

SMART 6: recent updates and new developments

Nucleic Acids Res. 37(Database issue):D229-32. doi: 10.1093/nar/gkn808
Europe PMC | doi

Singh AH, Doerks T, Letunic I, Raes J, Bork P. (2009)

Discovering functional novelty in metagenomes: examples from light-mediated processes

J. Bacteriol. 191(1):32-41. doi: 10.1128/jb.01084-08
Europe PMC | doi


2008

Jensen LJ, Bork P. (2008)

Biochemistry. Not comparable, but complementary

Science 322(5898):56-57. doi: 10.1126/science.1164801
Europe PMC | doi

Harrington ED, Bork P. (2008)

Sircah: a tool for the detection and visualization of alternative transcripts

Bioinformatics 24(17):1959-1960. doi: 10.1093/bioinformatics/btn361
Europe PMC | doi

Raes J, Bork P. (2008)

Molecular eco-systems biology: towards an understanding of community function

Nat. Rev. Microbiol. 6(9):693-699. doi: 10.1038/nrmicro1935
Europe PMC | doi

Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. (2008)

Drug target identification using side-effect similarity

Science 321(5886):263-266. doi: 10.1126/science.1158140
Europe PMC | doi

Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M. (2008)

KEGG Atlas mapping for global analysis of metabolic pathways

Nucleic Acids Res. 36(Web Server issue):W423-6. doi: 10.1093/nar/gkn282
Europe PMC | doi

Pincus D, Letunic I, Bork P, Lim WA. (2008)

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

Proc. Natl. Acad. Sci. U.S.A. 105(28):9680-9684. doi: 10.1073/pnas.0803161105
Europe PMC | doi

Harrington ED, Jensen LJ, Bork P. (2008)

Predicting biological networks from genomic data

Paper presented at the Conference on Targeting and Tinkering with Interaction Networks, Barcelona, SPAIN, APR 14-16, 2008.FEBS Lett. 582(8):1251-1258. doi: 10.1016/j.febslet.2008.02.033
Europe PMC | doi

Kuhn M, Campillos M, González P, Jensen LJ, Bork P. (2008)

Large-scale prediction of drug-target relationships

Paper presented at the Conference on Targeting and Tinkering with Interaction Networks, Barcelona, SPAIN, APR 14-16, 2008.FEBS Lett. 582(8):1283-1290. doi: 10.1016/j.febslet.2008.02.024
Europe PMC | doi

Tribolium Genome Sequencing Consortium, Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G. (2008)

The genome of the model beetle and pest Tribolium castaneum

Nature 452(7190):949-955. doi: 10.1038/nature06784
Europe PMC | doi

Eisenhaber F, Bork P. (2008)

Sequence and Structure of Proteins

In: H.-J. Rehm, G. Reed, Recombinant Proteins, Monoclonal Antibodies, and Therapeutic Genes, vol 5a. Biotechnology, Biotechnology, 2nd edition edn. Wiley-VCH Verlag GmbH, Weinheim. pp 43-86.doi: DOI: 10.1002/9783527620869
doi

Letunic I, Yamada T, Kanehisa M, Bork P. (2008)

iPath: interactive exploration of biochemical pathways and networks

Trends Biochem. Sci. 33(3):101-103. doi: 10.1016/j.tibs.2008.01.001
Europe PMC | doi

King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D. (2008)

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

Nature 451(7180):783-788. doi: 10.1038/nature06617
Europe PMC | doi

Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P. (2008)

A computational screen for type I polyketide synthases in metagenomics shotgun data

PLoS ONE 3(10):e3515. doi: 10.1371/journal.pone.0003515
Europe PMC | doi

Foerstner KU, Doerks T, Muller J, Raes J, Bork P. (2008)

A nitrile hydratase in the eukaryote Monosiga brevicollis

PLoS ONE 3(12):e3976. doi: 10.1371/journal.pone.0003976
Europe PMC | doi

Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R. (2008)

SuperTarget and Matador: resources for exploring drug-target relationships

Nucleic Acids Res. 36(Database issue):D919-22. doi: 10.1093/nar/gkm862
Europe PMC | doi

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. (2008)

4DXpress: a database for cross-species expression pattern comparisons

Nucleic Acids Res. 36(Database issue):D847-53. doi: 10.1093/nar/gkm797
Europe PMC | doi

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

A molecular study of microbe transfer between distant environments

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

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

Circular reasoning rather than cyclic expression

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

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

eggNOG: automated construction and annotation of orthologous groups of genes

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

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

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

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

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

STITCH: interaction networks of chemicals and proteins

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

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

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

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

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

NetworKIN: a resource for exploring cellular phosphorylation networks

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

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

Linear motif atlas for phosphorylation-dependent signaling

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

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

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

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

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

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

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

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

Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution

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

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

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

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

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

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

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

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

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


Europe PMC


2007

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

Genome-wide experimental determination of barriers to horizontal gene transfer

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

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

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

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

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

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

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

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

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

Cell Cycle 6(15):1819-1825. doi: 10.4161/cc.6.15.4537
Europe PMC | doi

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. (2007)

Quantitative assessment of protein function prediction from metagenomics shotgun sequences

Proc. Natl. Acad. Sci. U.S.A. 104(35):13913-13918. doi: 10.1073/pnas.0702636104
Europe PMC | doi

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

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

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

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

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

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

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

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

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

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

Systematic discovery of in vivo phosphorylation networks

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

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

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

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

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

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

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

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

Quantitative phylogenetic assessment of microbial communities in diverse environments

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

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

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Mol. Syst. Biol. 3:72. doi: 10.1038/msb4100112
Europe PMC | doi

Letunic I, Bork P. (2007)

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Bioinformatics 23(1):127-128. doi: 10.1093/bioinformatics/btl529
Europe PMC | doi

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2007)

New developments in the InterPro database

Nucleic Acids Res. 35(Database issue):D224-8. doi: 10.1093/nar/gkl841
Europe PMC | doi

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

Prediction of effective genome size in metagenomic samples

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

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

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

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

Zdobnov EM, Bork P. (2007)

Quantification of insect genome divergence

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


2006

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

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

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

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

Computational characterization of multiple Gag-like human proteins

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

Honeybee Genome Sequencing Consortium. (2006)

Insights into social insects from the genome of the honeybee Apis mellifera

Nature 443(7114):931-949. doi: 10.1038/nature05260
Europe PMC | doi

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Shah PK, Bork P. (2006)

LSAT: learning about alternative transcripts in MEDLINE

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

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

Identification and analysis of evolutionarily cohesive functional modules in protein networks

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

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

Toward automatic reconstruction of a highly resolved tree of life

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

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

Comparative analysis of environmental sequences: potential and challenges

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

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

Proteome survey reveals modularity of the yeast cell machinery

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

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

Extraction of regulatory gene/protein networks from Medline

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

Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ. (2006)

Similar gene expression profiles do not imply similar tissue functions

Trends Genet. 22(3):132-138. doi: 10.1016/j.tig.2006.01.006
Europe PMC | doi

Jensen LJ, Saric J, Bork P. (2006)

Literature mining for the biologist: from information retrieval to biological discovery

Nat. Rev. Genet. 7(2):119-129. doi: 10.1038/nrg1768
Europe PMC | doi

Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P. (2006)

SMART 5: domains in the context of genomes and networks

Nucleic Acids Res. 34(Database issue):D257-60. doi: 10.1093/nar/gkj079
Europe PMC | doi


2005

Foerstner KU, von Mering C, Hooper SD, Bork P. (2005)

Environments shape the nucleotide composition of genomes

EMBO Rep. 6(12):1208-1213. doi: 10.1038/sj.embor.7400538
Europe PMC | doi

Hooper SD, Bork P. (2005)

Medusa: a simple tool for interaction graph analysis

Bioinformatics 21(24):4432-4433. doi: 10.1093/bioinformatics/bti696
Europe PMC | doi

Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, Bork P, Wiese S, Gessler M, Kerkhoff E. (2005)

Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases

Gene Expr. Patterns 6(1):79-85. doi: 10.1016/j.modgep.2005.04.015
Europe PMC | doi

Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D. (2005)

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

Science 310(5752):1325-1326. doi: 10.1126/science.1119089
Europe PMC | doi

Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M. (2005)

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system

J. Cell Biol. 171(4):627-640. doi: 10.1083/jcb.200507168
Europe PMC | doi

Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E. (2005)

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets

RNA 11(10):1530-1544. doi: 10.1261/rna.2160905
Europe PMC | doi

Suyama M, Lathe WC 3rd, Bork P. (2005)

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii

FEBS Lett. 579(24):5281-5286. doi: 10.1016/j.febslet.2005.08.051
Europe PMC | doi