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: 524 publication(s)

2013

Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J. (2013)

Experimental characterization of the human non-sequence-specific nucleic acid interactome

Genome Biol. 14(7):R81. doi: 10.1186/gb-2013-14-7-r81
Europe PMC | doi

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. (2013)

Country-specific antibiotic use practices impact the human gut resistome

Genome Res. 23(7):1163-1169. doi: 10.1101/gr.155465.113
Europe PMC | doi

Blaser M, Bork P, Fraser C, Knight R, Wang J. (2013)

The microbiome explored: recent insights and future challenges

Nat. Rev. Microbiol. 11(3):213-217. doi: 10.1038/nrmicro2973
Europe PMC | doi

Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV. (2013)

Orthologous gene clusters and taxon signature genes for viruses of prokaryotes

J. Bacteriol. 195(5):941-950. doi: 10.1128/jb.01801-12
Europe PMC | doi

Beltrao P, Bork P, Krogan NJ, van Noort V. (2013)

Evolution and functional cross-talk of protein post-translational modifications

Mol. Syst. Biol. 9(1):714. doi: 10.1002/msb.201304521
Europe PMC | doi

Chen WH, Zhao XM, van Noort V, Bork P. (2013)

Human monogenic disease genes have frequently functionally redundant paralogs

PLoS Comput. Biol. 9(5):e1003073. doi: 10.1371/journal.pcbi.1003073
Europe PMC | doi

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. (2013)

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Nucleic Acids Res. 41(Database issue):D808-15. doi: 10.1093/nar/gks1094
Europe PMC | doi

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P. (2013)

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

Mol. Syst. Biol. 9:662. doi: 10.1038/msb.2013.20
Europe PMC | doi

Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P. (2013)

Systematic identification of proteins that elicit drug side effects

Mol. Syst. Biol. 9:663. doi: 10.1038/msb.2013.10
Europe PMC | doi

Minguez P, Letunic I, Parca L, Bork P. (2013)

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Nucleic Acids Res. 41(Database issue):D306-11. doi: 10.1093/nar/gks1230
Europe PMC | doi

Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M. (2013)

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines

Mol. Syst. Biol. 9:648. doi: 10.1038/msb.2013.4
Europe PMC | doi

Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J. (2013)

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data

Bioinformatics 29(1):132-134. doi: 10.1093/bioinformatics/bts656
Europe PMC | doi

Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. (2013)

Genomic variation landscape of the human gut microbiome

Nature 493(7430):45-50. doi: 10.1038/nature11711
Europe PMC | doi

van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. (2013)

Consistent mutational paths predict eukaryotic thermostability

BMC Evol. Biol. 13:7. doi: 10.1186/1471-2148-13-7
Europe PMC | doi


2012

Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay JÉ, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedrós-Alió C, Bertilsson S. (2012)

Role for urea in nitrification by polar marine Archaea

Proc. Natl. Acad. Sci. U.S.A. 109(44):17989-17994. doi: 10.1073/pnas.1201914109
Europe PMC | doi

Iskar M, Zeller G, Zhao XM, van Noort V, Bork P. (2012)

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

Curr. Opin. Biotechnol. 23(4):609-616. doi: 10.1016/j.copbio.2011.11.010
Europe PMC | doi

Chen WH, Trachana K, Lercher MJ, Bork P. (2012)

Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age

Mol. Biol. Evol. 29(7):1703-1706. doi: 10.1093/molbev/mss014
Europe PMC | doi

Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. (2012)

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

ISME J 6(7):1415-1426. doi: 10.1038/ismej.2011.212
Europe PMC | doi

Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JW, Jauch A, Bartram CR, Reinhardt D, Koch KA, Bandapalli OR, Kulozik AE. (2012)

A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL

Br. J. Haematol. 157(2):180-187. doi: 10.1111/j.1365-2141.2012.09028.x
Europe PMC | doi

Chen WH, Minguez P, Lercher MJ, Bork P. (2012)

OGEE: an online gene essentiality database

Nucleic Acids Res. 40(Database issue):D901-6. doi: 10.1093/nar/gkr986
Europe PMC | doi

Chen YP, Bork P. (2012)

The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). Introduction

BMC Genomics 13 Suppl 1:I1. doi: 10.1186/1471-2164-13-s1-i1
Europe PMC | doi

Doerks T, van Noort V, Minguez P, Bork P. (2012)

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins

PLoS ONE 7(4):e34302. doi: 10.1371/journal.pone.0034302
Europe PMC | doi

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, 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 AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY. (2012)

InterPro in 2011: new developments in the family and domain prediction database

Nucleic Acids Res. 40(10):4725. doi: 10.1093/nar/gkr948
Europe PMC | doi

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. (2012)

STITCH 3: zooming in on protein-chemical interactions

Nucleic Acids Res. 40(Database issue):D876-80. doi: 10.1093/nar/gkr1011
Europe PMC | doi

Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P. (2012)

MOCAT: a metagenomics assembly and gene prediction toolkit

PLoS ONE 7(10):e47656. doi: 10.1371/journal.pone.0047656
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2012)

SMART 7: recent updates to the protein domain annotation resource

Nucleic Acids Res. 40(Database issue):D302-5. doi: 10.1093/nar/gkr931
Europe PMC | doi

Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. (2012)

Assessment of metagenomic assembly using simulated next generation sequencing data

PLoS ONE 7(2):e31386. doi: 10.1371/journal.pone.0031386
Europe PMC | doi

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. (2012)

Deciphering a global network of functionally associated post-translational modifications

Mol. Syst. Biol. 8:599. doi: 10.1038/msb.2012.31
Europe PMC | doi

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. (2012)

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Nucleic Acids Res. 40(Database issue):D284-9. doi: 10.1093/nar/gkr1060
Europe PMC | doi

van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC. (2012)

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium

Mol. Syst. Biol. 8:571. doi: 10.1038/msb.2012.4
Europe PMC | doi

Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P. (2012)

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

Mol. Syst. Biol. 8:581. doi: 10.1038/msb.2012.13
Europe PMC | doi

Yus E, Güell M, Vivancos AP, Chen WH, Lluch-Senar M, Delgado J, Gavin AC, Bork P, Serrano L. (2012)

Transcription start site associated RNAs in bacteria

Mol. Syst. Biol. 8:585. doi: 10.1038/msb.2012.16
Europe PMC | doi


2011

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. (2011)

Identifying single copy orthologs in Metazoa

PLoS Comput. Biol. 7(12):e1002269. doi: 10.1371/journal.pcbi.1002269
Europe PMC | doi

Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P. (2011)

Prediction of drug combinations by integrating molecular and pharmacological data

PLoS Comput. Biol. 7(12):e1002323. doi: 10.1371/journal.pcbi.1002323
Europe PMC | doi

Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P, Tara Oceans Consortium. (2011)

A holistic approach to marine eco-systems biology

PLoS Biol. 9(10):e1001177. doi: 10.1371/journal.pbio.1001177
Europe PMC | doi

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P. (2011)

Orthology prediction methods: a quality assessment using curated protein families

Bioessays 33(10):769-780. doi: 10.1002/bies.201100062
Europe PMC | doi

Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E. (2011)

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile

Cell 146(2):277-289. doi: 10.1016/j.cell.2011.06.039
Europe PMC | doi

Letunic I, Bork P. (2011)

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Nucleic Acids Res. 39(Web Server issue):W475-8. doi: 10.1093/nar/gkr201
Europe PMC | doi

Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. (2011)

iPath2.0: interactive pathway explorer

Nucleic Acids Res. 39(Web Server issue):W412-5. doi: 10.1093/nar/gkr313
Europe PMC | doi

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, 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 HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, 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, Mérieux 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 SD, Bork P. (2011)

Enterotypes of the human gut microbiome

Nature 473(7346):174-180. doi: 10.1038/nature09944
Europe PMC | doi

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. (2011)

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Nat. Biotechnol. 29(5):415-420. doi: 10.1038/nbt.1823
Europe PMC | doi

Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. (2011)

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

Mol. Syst. Biol. 7:473. doi: 10.1038/msb.2011.6
Europe PMC | doi

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, 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 YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL. (2011)

The ecoresponsive genome of Daphnia pulex

Science 331(6017):555-561. doi: 10.1126/science.1197761
Europe PMC | doi

Brouwers L, Iskar M, Zeller G, van Noort V, Bork P. (2011)

Network neighbors of drug targets contribute to drug side-effect similarity

PLoS ONE 6(7):e22187. doi: 10.1371/journal.pone.0022187
Europe PMC | doi

Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P. (2011)

Universally distributed single-copy genes indicate a constant rate of horizontal transfer

PLoS ONE 6(8):e22099. doi: 10.1371/journal.pone.0022099
Europe PMC | doi

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. (2011)

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Nucleic Acids Res. 39(Database issue):D561-8. doi: 10.1093/nar/gkq973
Europe PMC | doi


2010

Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P. (2010)

SmashCommunity: a metagenomic annotation and analysis tool

Bioinformatics 26(23):2977-2978. doi: 10.1093/bioinformatics/btq536
Europe PMC | doi

Harrington ED, Arumugam M, Raes J, Bork P, Relman DA. (2010)

SmashCell: a software framework for the analysis of single-cell amplified genome sequences

Bioinformatics 26(23):2979-2980. doi: 10.1093/bioinformatics/btq564
Europe PMC | doi

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