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Staff at EMBL

CP-60003241

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

E-mail: send a mail

Biography

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

Publications

Total: 455 publication(s)

2014

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. (2014)
Potential of fecal microbiota for early-stage detection of colorectal cancer.
Mol. Syst. Biol. 10(11):766. doi:10.15252/msb.20145645
Europe PMC | doi

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. (2014)
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res. doi:10.1093/nar/gku1243
Europe PMC | doi

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P. (2014)
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.
Nucleic Acids Res. doi:10.1093/nar/gku1147
Europe PMC | doi

Betts MJ, Lu Q, Jiang Y, Drusko A, Wichmann O, Utz M, Valtierra-Gutiérrez IA, Schlesner M, Jaeger N, Jones DT, Pfister S, Lichter P, Eils R, Siebert R, Bork P, Apic G, Gavin AC, Russell RB. (2014)
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.
Nucleic Acids Res.
Europe PMC

Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P. (2014)
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.
PLoS ONE 9(11) doi:10.1371/journal.pone.0111122
Europe PMC | doi

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. (2014)
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res. doi:10.1093/nar/gku1081
Europe PMC | doi

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. (2014)
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Nucleic Acids Res. doi:10.1093/nar/gku1003
Europe PMC | doi

Durdu S, Iskar M, Revenu C, Schieber N, Kunze A, Bork P, Schwab Y, Gilmour D. (2014)
Luminal signalling links cell communication to tissue architecture during organogenesis.
Nature 515(7525):120-124. doi:10.1038/nature13852
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2014)
SMART: recent updates, new developments and status in 2015.
Nucleic Acids Res. doi:10.1093/nar/gku949
Europe PMC | doi

Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. (2014)
LotuS: an efficient and user-friendly OTU processing pipeline.
Microbiome 2:30. doi:10.1186/2049-2618-2-30
Europe PMC | doi

Woerner SM, Tosti E, Yuan YP, Kloor M, Bork P, Edelmann W, Gebert J. (2014)
Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors
Mol. Carcinog. doi:10.1002/mc.22213
Europe PMC | doi

Chen WH, Zhao XM, van Noort V, Bork P. (2014)
Comments on "human dominant disease genes are enriched in paralogs originating from whole genome duplication"
PLoS Comput. Biol. 10(7) doi:10.1371/journal.pcbi.1003758
Europe PMC | doi

Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD, Bork P, Wang J. (2014)
An integrated catalog of reference genes in the human gut microbiome
Nat. Biotechnol. 32(8):834-841. doi:10.1038/nbt.2942
Europe PMC | doi

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P. (2014)
Classification and quantification of bacteriophage taxa in human gut metagenomes
ISME J 8(7):1551-1552. doi:10.1038/ismej.2014.66
Europe PMC | doi

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P. (2014)
Classification and quantification of bacteriophage taxa in human gut metagenomes
ISME J 8(7):1391-1402. doi:10.1038/ismej.2014.30
Europe PMC | doi

Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD. (2014)
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Nat. Biotechnol. 32(8):822-828. doi:10.1038/nbt.2939
Europe PMC | doi

van Noort VV, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P. (2014)
Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene expression profiling
Cancer Res. doi:10.1158/0008-5472.CAN-13-3540
Europe PMC | doi

Costea PI, Zeller G, Sunagawa S, Bork P. (2014)
A fair comparison
Nat. Methods 11(4):359. doi:10.1038/nmeth.2897
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 JJ, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Weissenbach J, Ehrlich SD, Bork P. (2014)
Enterotypes of the human gut microbiome (vol 473, pg 174, 2011)
NATURE 506(7489) doi:10.1038/nature13075
doi

Gallina AM, Bork P, Bordo D. (2014)
Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs
J. Mol. Recognit. 27(2):65-72. doi:10.1002/jmr.2332
Europe PMC | doi

Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin AC. (2014)
A quantitative liposome microarray to systematically characterize protein-lipid interactions
Nat. Methods 11(1):47-50. doi:10.1038/nmeth.2734
Europe PMC | doi

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. (2014)
eggNOG v4.0: nested orthology inference across 3686 organisms
Nucleic Acids Res. 42(Database issue):D231-9. doi:10.1093/nar/gkt1253
Europe PMC | doi

Forslund K, Sunagawa S, Coelho LP, Bork P. (2014)
Metagenomic insights into the human gut resistome and the forces that shape it
Bioessays 36(3):316-329. doi:10.1002/bies.201300143
Europe PMC | doi

Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P. (2014)
STITCH 4: integration of protein-chemical interactions with user data
Nucleic Acids Res. 42(Database issue):D401-7. doi:10.1093/nar/gkt1207
Europe PMC | doi


2013

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. (2013)
Metagenomic species profiling using universal phylogenetic marker genes
Nat. Methods 10(12):1196-1199. doi:10.1038/nmeth.2693
Europe PMC | doi

Mende DR, Sunagawa S, Zeller G, Bork P. (2013)
Accurate and universal delineation of prokaryotic species
Nat. Methods 10(9):881-884. doi:10.1038/nmeth.2575
Europe PMC | doi

Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H. (2013)
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
ISME J 7(9):1678-1695. doi:10.1038/ismej.2013.59
Europe PMC | doi

Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG. (2013)
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
Environ. Microbiol. 16(9):2659-2671. doi:10.1111/1462-2920.12250
Europe PMC | doi

Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O. (2013)
Richness of human gut microbiome correlates with metabolic markers
Nature 500(7464):541-546. doi:10.1038/nature12506
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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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


2009

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

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

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

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

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