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Peer Bork
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- affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
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2020 – today
- 2023
- [j118]Ana Hernández-Plaza
, Damian Szklarczyk
, Jorge Botas
, Carlos P. Cantalapiedra
, Joaquín Giner-Lamia
, Daniel R. Mende
, Rebecca Kirsch, Thomas Rattei
, Ivica Letunic
, Lars Juhl Jensen
, Peer Bork
, Christian von Mering
, Jaime Huerta-Cepas
:
eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res. 51(D1): 389-394 (2023) - [j117]Typhaine Paysan-Lafosse
, Matthias Blum
, Sara Chuguransky
, Tiago Grego
, Beatriz Lázaro Pinto
, Gustavo A. Salazar
, Maxwell L. Bileschi
, Peer Bork
, Alan J. Bridge
, Lucy J. Colwell
, Julian Gough
, Daniel H. Haft
, Ivica Letunic
, Aron Marchler-Bauer
, Huaiyu Mi
, Darren A. Natale
, Christine A. Orengo
, Arun Prasad Pandurangan
, Catherine Rivoire
, Christian J. A. Sigrist
, Ian Sillitoe
, Narmada Thanki
, Paul D. Thomas
, Silvio C. E. Tosatto
, Cathy H. Wu
, Alex Bateman
:
InterPro in 2022. Nucleic Acids Res. 51(D1): 418-427 (2023) - [j116]Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli
, Katerina C. Nastou
, Farrokh Mehryary
, Radja Hachilif, Annika L. Gable, Tao Fang
, Nadezhda T. Doncheva
, Sampo Pyysalo, Peer Bork, Lars Juhl Jensen, Christian von Mering
:
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51(D1): 638-646 (2023) - [j115]Anthony Fullam
, Ivica Letunic
, Thomas S. B. Schmidt
, Quinten R. Ducarmon
, Nicolai Karcher
, Supriya Khedkar
, Michael Kuhn
, Martin Larralde
, Oleksandr M. Maistrenko
, Lukas Malfertheiner
, Alessio Milanese
, João F. Matias Rodrigues, Claudia Sanchis-López
, Christian Schudoma
, Damian Szklarczyk
, Shinichi Sunagawa
, Georg Zeller
, Jaime Huerta-Cepas
, Christian von Mering
, Peer Bork
, Daniel R. Mende
:
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res. 51(D1): 760-766 (2023) - [c13]Nils Hoffmann
, Irena Maus
, Sebastian Beier
, Peter Belmann, Jan Krüger
, Andreas Tauch, Alexander Goesmann
, Roland Eils, Peer Bork
, Oliver Kohlbacher
, Ursula Kummer, Rolf Backofen
, Ivo Buchhalter
, Alexander Sczyrba
:
Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. CoRDI 2023 - 2022
- [j114]Thea Van Rossum
, Paul I. Costea, Lucas Paoli
, Renato Alves, Roman Thielemann
, Shinichi Sunagawa
, Peer Bork:
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes. Bioinform. 38(4): 1162-1164 (2022) - [j113]Caroline Vernette
, Julien Lecubin
, Pablo Sánchez
, Silvia G. Acinas
, Marcel Babin
, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane
, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp
, Daniele Iudicone, Olivier Jaillon
, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stephane Pesant, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa
, Patrick Wincker, Tom O. Delmont
, Eric Pelletier
, Magali Lescot
:
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic Acids Res. 50(W1): 516-526 (2022) - 2021
- [j112]Matthias Blum
, Hsin-Yu Chang
, Sara Chuguransky
, Tiago Grego
, Swaathi Kandasamy
, Alex L. Mitchell
, Gift Nuka, Typhaine Paysan-Lafosse
, Matloob Qureshi
, Shriya Raj
, Lorna J. Richardson
, Gustavo A. Salazar
, Lowri Williams
, Peer Bork, Alan J. Bridge
, Julian Gough, Daniel H. Haft, Ivica Letunic
, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale
, Marco Necci, Christine A. Orengo, Arun Prasad Pandurangan
, Catherine Rivoire
, Christian J. A. Sigrist, Ian Sillitoe
, Narmada Thanki, Paul D. Thomas
, Silvio C. E. Tosatto
, Cathy H. Wu
, Alex Bateman
, Robert D. Finn
:
The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 49(Database-Issue): D344-D354 (2021) - [j111]Ivica Letunic
, Supriya Khedkar
, Peer Bork:
SMART: recent updates, new developments and status in 2020. Nucleic Acids Res. 49(Database-Issue): D458-D460 (2021) - [j110]Damian Szklarczyk, Annika L. Gable
, Katerina C. Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T. Doncheva
, Marc Legeay
, Tao Fang, Peer Bork, Lars Juhl Jensen
, Christian von Mering
:
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49(Database-Issue): D605-D612 (2021) - [j109]Sanathoi Gurumayum
, Puzi Jiang, Xiaowen Hao, Tulio de Lima Campos
, Neil D. Young
, Pasi K. Korhonen, Robin B. Gasser
, Peer Bork, Xing-Ming Zhao
, Lijie He, Wei-Hua Chen
:
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Res. 49(Database-Issue): D998-D1003 (2021) - [j108]Ivica Letunic, Peer Bork:
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49(Webserver-Issue): 293-296 (2021) - 2020
- [j107]Yuanyue Li
, Michael Kuhn, Anne-Claude Gavin
, Peer Bork:
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. Bioinform. 36(4): 1213-1218 (2020) - [j106]Daniel R. Mende
, Ivica Letunic, Oleksandr M. Maistrenko
, Thomas S. B. Schmidt
, Alessio Milanese
, Lucas Paoli
, Ana Hernández-Plaza, Askarbek N. Orakov, Sofia K. Forslund
, Shinichi Sunagawa
, Georg Zeller
, Jaime Huerta-Cepas
, Luís Pedro Coelho
, Peer Bork:
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Res. 48(Database-Issue): D621-D625 (2020)
2010 – 2019
- 2019
- [j105]Jaime Huerta-Cepas
, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K. Forslund
, Helen Cook
, Daniel R. Mende
, Ivica Letunic, Thomas Rattei
, Lars Juhl Jensen
, Christian von Mering
, Peer Bork:
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47(Database-Issue): D309-D314 (2019) - [j104]Alex L. Mitchell
, Teresa K. Attwood
, Patricia C. Babbitt, Matthias Blum
, Peer Bork, Alan J. Bridge
, Shoshana D. Brown, Hsin-Yu Chang
, Sara El-Gebali
, Matthew Fraser, Julian Gough, David Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez
, Aurelien Luciani
, Fábio Madeira
, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale
, Marco Necci
, Gift Nuka, Christine A. Orengo, Arun Prasad Pandurangan
, Typhaine Paysan-Lafosse
, Sebastien Pesseat, Simon C. Potter
, Matloob Qureshi
, Neil D. Rawlings
, Nicole Redaschi
, Lorna J. Richardson
, Catherine Rivoire
, Gustavo A. Salazar
, Amaia Sangrador-Vegas, Christian J. A. Sigrist
, Ian Sillitoe, Granger G. Sutton, Narmada Thanki, Paul D. Thomas
, Silvio C. E. Tosatto
, Siew-Yit Yong, Robert D. Finn
:
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47(Database-Issue): D351-D360 (2019) - [j103]Damian Szklarczyk, Annika L. Gable
, David Lyon
, Alexander Junge
, Stefan Wyder, Jaime Huerta-Cepas
, Milan Simonovic, Nadezhda T. Doncheva
, John H. Morris
, Peer Bork
, Lars Juhl Jensen
, Christian von Mering
:
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47(Database-Issue): D607-D613 (2019) - [j102]Ivica Letunic, Peer Bork:
Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47(Webserver-Issue): W256-W259 (2019) - 2018
- [j101]Ivica Letunic
, Peer Bork:
20 years of the SMART protein domain annotation resource. Nucleic Acids Res. 46(Database-Issue): D493-D496 (2018) - [j100]Na L. Gao, Chengwei Zhang, Zhanbing Zhang, Songnian Hu
, Martin J. Lercher, Xing-Ming Zhao, Peer Bork, Zhi Liu, Wei-Hua Chen
:
MVP: a microbe-phage interaction database. Nucleic Acids Res. 46(Database-Issue): D700-D707 (2018) - [j99]Youssef Darzi
, Ivica Letunic
, Peer Bork, Takuji Yamada:
iPath3.0: interactive pathways explorer v3. Nucleic Acids Res. 46(Webserver-Issue): W510-W513 (2018) - [j98]Lisa Maier
, Mihaela Pruteanu
, Michael Kuhn
, Georg Zeller
, Anja Telzerow
, Exene Erin Anderson, Ana Rita Brochado
, Keith Conrad Fernandez
, Hitomi Dose, Hirotada Mori, Kiran Raosaheb Patil
, Peer Bork, Athanasios Typas
:
Extensive impact of non-antibiotic drugs on human gut bacteria. Nat. 555(7698): 623-628 (2018) - 2017
- [j97]Paul Saary
, Kristoffer Forslund
, Peer Bork, Falk Hildebrand
:
RTK: efficient rarefaction analysis of large datasets. Bioinform. 33(16): 2594-2595 (2017) - [j96]Robert D. Finn, Teresa K. Attwood
, Patricia C. Babbitt, Alex Bateman
, Peer Bork, Alan J. Bridge
, Hsin-Yu Chang
, Zsuzsanna Dosztányi
, Sara El-Gebali
, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday
, Hongzhan Huang, Xiaosong Huang
, Ivica Letunic
, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer
, Huaiyu Mi, Jaina Mistry, Darren A. Natale
, Marco Necci
, Gift Nuka, Christine A. Orengo, Young Mi Park
, Sebastien Pesseat
, Damiano Piovesan
, Simon C. Potter
, Neil D. Rawlings
, Nicole Redaschi
, Lorna J. Richardson
, Catherine Rivoire
, Amaia Sangrador-Vegas
, Christian J. A. Sigrist
, Ian Sillitoe, Ben Smithers
, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas
, Silvio C. E. Tosatto
, Cathy H. Wu
, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
:
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45(Database-Issue): D190-D199 (2017) - [j95]Damian Szklarczyk, John H. Morris
, Helen Cook
, Michael Kuhn
, Stefan Wyder
, Milan Simonovic, Alberto Santos
, Nadezhda T. Doncheva
, Alexander Roth, Peer Bork, Lars Juhl Jensen
, Christian von Mering
:
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 45(Database-Issue): D362-D368 (2017) - [j94]Daniel R. Mende
, Ivica Letunic
, Jaime Huerta-Cepas
, Simone S. Li
, Kristoffer Forslund
, Shinichi Sunagawa
, Peer Bork:
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Res. 45(Database-Issue): D529-D534 (2017) - [j93]Wei-Hua Chen
, Guanting Lu, Xiao Chen, Xing-Ming Zhao, Peer Bork:
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. Nucleic Acids Res. 45(Database-Issue): D940-D944 (2017) - [j92]Matthew J. Betts
, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki
, Pablo Minguez
, Luca Parca
, Frederick P. Roth, Anne-Claude Gavin
, Peer Bork, Robert B. Russell
:
Systematic identification of phosphorylation-mediated protein interaction switches. PLoS Comput. Biol. 13(3) (2017) - 2016
- [j91]Jens Roat Kultima, Luís Pedro Coelho
, Kristoffer Forslund
, Jaime Huerta-Cepas
, Simone S. Li
, Marja Driessen, Anita Yvonne Voigt
, Georg Zeller
, Shinichi Sunagawa
, Peer Bork:
MOCAT2: a metagenomic assembly, annotation and profiling framework. Bioinform. 32(16): 2520-2523 (2016) - [j90]Samy Deghou, Georg Zeller
, Murat Iskar, Marja Driessen, Mercedes Castillo, Vera van Noort
, Peer Bork:
CART - a chemical annotation retrieval toolkit. Bioinform. 32(18): 2869-2871 (2016) - [j89]Jaime Huerta-Cepas
, Damian Szklarczyk, Kristoffer Forslund
, Helen Cook
, Davide Heller, Mathias C. Walter
, Thomas Rattei
, Daniel R. Mende
, Shinichi Sunagawa
, Michael Kuhn
, Lars Juhl Jensen
, Christian von Mering
, Peer Bork
:
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44(Database-Issue): 286-293 (2016) - [j88]Damian Szklarczyk, Alberto Santos
, Christian von Mering
, Lars Juhl Jensen
, Peer Bork
, Michael Kuhn
:
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 44(Database-Issue): 380-384 (2016) - [j87]Michael Kuhn
, Ivica Letunic
, Lars Juhl Jensen
, Peer Bork
:
The SIDER database of drugs and side effects. Nucleic Acids Res. 44(Database-Issue): 1075-1079 (2016) - [j86]Ivica Letunic
, Peer Bork
:
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44(Webserver-Issue): W242-W245 (2016) - 2015
- [j85]Alex L. Mitchell
, Hsin-Yu Chang
, Louise C. Daugherty
, Matthew Fraser
, Sarah Hunter
, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat
, Amaia Sangrador-Vegas
, Maxim Scheremetjew
, Claudia Rato
, Siew-Yit Yong
, Alex Bateman
, Marco Punta
, Teresa K. Attwood
, Christian J. A. Sigrist
, Nicole Redaschi
, Catherine Rivoire
, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork
, Ivica Letunic
, Julian Gough, Matt E. Oates
, Daniel H. Haft, Hongzhan Huang, Darren A. Natale
, Cathy H. Wu
, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas
, Robert D. Finn
:
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43(Database-Issue): 213-221 (2015) - [j84]Ivica Letunic
, Tobias Doerks, Peer Bork
:
SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 43(Database-Issue): 257-260 (2015) - [j83]Damian Szklarczyk, Andrea Franceschini
, Stefan Wyder
, Kristoffer Forslund
, Davide Heller, Jaime Huerta-Cepas
, Milan Simonovic, Alexander Roth, Alberto Santos
, Kalliopi Tsafou, Michael Kuhn
, Peer Bork
, Lars Juhl Jensen
, Christian von Mering
:
STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43(Database-Issue): 447-452 (2015) - [j82]Pablo Minguez
, Ivica Letunic
, Luca Parca
, Luz Garcia-Alonso
, Joaquín Dopazo, Jaime Huerta-Cepas
, Peer Bork
:
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res. 43(Database-Issue): 494-502 (2015) - [j81]Kristoffer Forslund
, Falk Hildebrand
, Trine Nielsen
, Gwen Falony
, Emmanuelle Le Chatelier, Shinichi Sunagawa
, Edi Prifti
, Sara Vieira-Silva
, Valborg Gudmundsdottir
, Helle Krogh Pedersen
, Manimozhiyan Arumugam
, Karsten Kristiansen
, Anita Yvonne Voigt
, Henrik Vestergaard
, Rajna Hercog, Paul I. Costea
, Jens Roat Kultima, Junhua Li
, Torben Jørgensen
, Florence Levenez, Joël Dore
, Henrik Bjørn Nielsen, Søren Brunak
, Jeroen Raes
, Torben Hansen
, Jun Wang, S. Dusko Ehrlich, Peer Bork
, Oluf Pedersen
:
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nat. 528(7582): 262-266 (2015) - 2014
- [j80]Sean Powell
, Kristoffer Forslund
, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Jaime Huerta-Cepas
, Toni Gabaldón
, Thomas Rattei
, Christopher J. Creevey, Michael Kuhn
, Lars Juhl Jensen
, Christian von Mering
, Peer Bork
:
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42(Database-Issue): 231-239 (2014) - [j79]Michael Kuhn
, Damian Szklarczyk, Sune Pletscher-Frankild
, Thomas H. Blicher, Christian von Mering
, Lars Juhl Jensen
, Peer Bork
:
STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res. 42(Database-Issue): 401-407 (2014) - [j78]Manimozhiyan Arumugam, Jeroen Raes
, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Brüls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas
, Leyden Fernández, Laurent Gautier, Torben Hansen
, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, Henrik Bjørn Nielsen, Trine Nielsen
, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Pontén, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang
, Francisco Guarner, Oluf Pedersen
, Willem M. de Vos, Søren Brunak, Joël Dore, MetaHIT consortium, Jean Weissenbach, S. Dusko Ehrlich, Peer Bork
:
Addendum: Enterotypes of the human gut microbiome. Nat. 506(7489): 516 (2014) - [j77]Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort
, Peer Bork
:
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication". PLoS Comput. Biol. 10(7) (2014) - 2013
- [j76]Clare Pacini, Francesco Iorio
, Emanuel J. V. Gonçalves
, Murat Iskar
, Thomas Klabunde, Peer Bork
, Julio Saez-Rodriguez
:
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinform. 29(1): 132-134 (2013) - [j75]Pablo Minguez, Ivica Letunic
, Luca Parca
, Peer Bork
:
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic Acids Res. 41(Database-Issue): 306-311 (2013) - [j74]Andrea Franceschini
, Damian Szklarczyk, Sune Frankild
, Michael Kuhn
, Milan Simonovic, Alexander Roth, Jianyi Lin
, Pablo Minguez, Peer Bork
, Christian von Mering
, Lars Juhl Jensen
:
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41(Database-Issue): 808-815 (2013) - [j73]Wei-Hua Chen
, Xing-Ming Zhao, Vera van Noort
, Peer Bork
:
Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs. PLoS Comput. Biol. 9(5) (2013) - 2012
- [j72]Yi-Ping Phoebe Chen
, Peer Bork
:
The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). BMC Genom. 13(S-1): I1 (2012) - [j71]Sean Powell
, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Michael Kuhn
, Jean Muller
, Roland Arnold, Thomas Rattei
, Ivica Letunic
, Tobias Doerks, Lars Juhl Jensen
, Christian von Mering
, Peer Bork
:
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 40(Database-Issue): 284-289 (2012) - [j70]Ivica Letunic
, Tobias Doerks, Peer Bork
:
SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 40(Database-Issue): 302-305 (2012) - [j69]Sarah Hunter
, Philip Jones, Alex L. Mitchell
, Rolf Apweiler
, Teresa K. Attwood
, Alex Bateman
, Thomas Bernard
, David Binns, Peer Bork
, Sarah W. Burge
, Edouard De Castro
, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn
, Matthew Fraser
, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic
, David Lonsdale, Rodrigo Lopez
, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet
, Nicola J. Mulder
, Darren A. Natale
, Christine A. Orengo, Sebastien Pesseat, Marco Punta
, Antony F. Quinn
, Catherine Rivoire
, Amaia Sangrador-Vegas
, Jeremy D. Selengut, Christian J. A. Sigrist
, Maxim Scheremetjew
, John G. Tate
, Manjulapramila Thimmajanarthanan, Paul D. Thomas
, Cathy H. Wu
, Corin Yeats, Siew-Yit Yong
:
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40(Database-Issue): 306-312 (2012) - [j68]Michael Kuhn
, Damian Szklarczyk, Andrea Franceschini
, Christian von Mering
, Lars Juhl Jensen
, Peer Bork
:
STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res. 40(Database-Issue): 876-880 (2012) - [j67]Wei-Hua Chen
, Pablo Minguez
, Martin J. Lercher
, Peer Bork
:
OGEE: an online gene essentiality database. Nucleic Acids Res. 40(Database-Issue): 901-906 (2012) - 2011
- [j66]Damian Szklarczyk, Andrea Franceschini
, Michael Kuhn, Milan Simonovic, Alexander Roth, Pablo Minguez
, Tobias Doerks, Manuel Stark, Jean Muller
, Peer Bork
, Lars Juhl Jensen
, Christian von Mering
:
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39(Database-Issue): 561-568 (2011) - [j65]Takuji Yamada, Ivica Letunic
, Shujiro Okuda
, Minoru Kanehisa, Peer Bork
:
iPath2.0: interactive pathway explorer. Nucleic Acids Res. 39(Web-Server-Issue): 412-415 (2011) - [j64]Ivica Letunic
, Peer Bork
:
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39(Web-Server-Issue): 475-478 (2011) - [j63]Christopher J. Creevey, Jean Muller
, Tobias Doerks, Julie Dawn Thompson, Detlev Arendt, Peer Bork
:
Identifying Single Copy Orthologs in Metazoa. PLoS Comput. Biol. 7(12) (2011) - [j62]Xing-Ming Zhao, Murat Iskar
, Georg Zeller
, Michael Kuhn
, Vera van Noort
, Peer Bork
:
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data. PLoS Comput. Biol. 7(12) (2011) - 2010
- [j61]Jean Muller
, Christopher J. Creevey, Julie Dawn Thompson, Detlev Arendt, Peer Bork
:
AQUA: automated quality improvement for multiple sequence alignments. Bioinform. 26(2): 263-265 (2010) - [j60]Manimozhiyan Arumugam
, Eoghan D. Harrington, Konrad U. Foerstner
, Jeroen Raes
, Peer Bork
:
SmashCommunity: a metagenomic annotation and analysis tool. Bioinform. 26(23): 2977-2978 (2010) - [j59]Eoghan D. Harrington, Manimozhiyan Arumugam
, Jeroen Raes
, Peer Bork
, David A. Relman
:
SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Bioinform. 26(23): 2979-2980 (2010) - [j58]Jean Muller
, Damian Szklarczyk, Philippe Julien, Ivica Letunic
, Alexander Roth, Michael Kuhn, Sean Powell
, Christian von Mering
, Tobias Doerks, Lars Juhl Jensen
, Peer Bork
:
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): 190-195 (2010) - [j57]Michael Kuhn, Damian Szklarczyk, Andrea Franceschini
, Monica Campillos
, Christian von Mering
, Lars Juhl Jensen
, Andreas Beyer
, Peer Bork
:
STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res. 38(Database-Issue): 552-556 (2010) - [j56]Stefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, Peer Bork
:
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology. Nucleic Acids Res. 38(Database-Issue): 682-689 (2010) - [j55]Murat Iskar
, Monica Campillos
, Michael Kuhn, Lars Juhl Jensen
, Vera van Noort
, Peer Bork
:
Drug-Induced Regulation of Target Expression. PLoS Comput. Biol. 6(9) (2010)
2000 – 2009
- 2009
- [j54]Sarah Hunter
, Rolf Apweiler
, Teresa K. Attwood
, Amos Bairoch
, Alex Bateman
, David Binns, Peer Bork
, Ujjwal Das, Louise C. Daugherty
, Lauranne Duquenne, Robert D. Finn
, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic
, David Lonsdale, Rodrigo Lopez
, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry
, Alex L. Mitchell
, Nicola J. Mulder
, Darren A. Natale
, Christine A. Orengo, Antony F. Quinn
, Jeremy D. Selengut, Christian J. A. Sigrist
, Manjula Thimma, Paul D. Thomas
, Franck Valentin, Derek Wilson, Cathy H. Wu
, Corin Yeats:
InterPro: the integrative protein signature database. Nucleic Acids Res. 37(Database-Issue): 211-215 (2009) - [j53]Ivica Letunic
, Tobias Doerks, Peer Bork
:
SMART 6: recent updates and new developments. Nucleic Acids Res. 37(Database-Issue): 229-232 (2009) - [j52]Lars Juhl Jensen
, Michael Kuhn, Manuel Stark, Samuel Chaffron
, Christopher J. Creevey, Jean Muller
, Tobias Doerks, Philippe Julien, Alexander Roth, Milan Simonovic, Peer Bork
, Christian von Mering
:
STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37(Database-Issue): 412-416 (2009) - 2008
- [j51]Eoghan D. Harrington, Peer Bork
:
Sircah: a tool for the detection and visualization of alternative transcripts. Bioinform. 24(17): 1959-1960 (2008) - [j50]Lars Juhl Jensen
, Philippe Julien, Michael Kuhn, Christian von Mering
, Jean Muller
, Tobias Doerks, Peer Bork
:
eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 36(Database-Issue): 250-254 (2008) - [j49]Michael Kuhn, Christian von Mering
, Monica Campillos
, Lars Juhl Jensen
, Peer Bork
:
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res. 36(Database-Issue): 684-688 (2008) - [j48]Rune Linding, Lars Juhl Jensen
, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork
, Michael B. Yaffe, Tony Pawson:
NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 36(Database-Issue): 695-699 (2008) - [j47]Yannick Haudry, Hugo Bérubé, Ivica Letunic
, Paul-Daniel Weeber, Julien Gagneur
, Charles Girardot
, Misha Kapushesky, Detlev Arendt, Peer Bork
, Alvis Brazma
, Eileen E. M. Furlong
, Joachim Wittbrodt
, Thorsten Henrich:
4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res. 36(Database-Issue): 847-853 (2008) - [j46]Stefan Günther, Michael Kuhn, Mathias Dunkel
, Monica Campillos
, Christian Senger, Evangelia Petsalaki
, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen
, Reinhard Schneider, Roman Skoblo, Robert B. Russell
, Philip E. Bourne, Peer Bork
, Robert Preissner
:
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res. 36(Database-Issue): 919-922 (2008) - [j45]Shujiro Okuda
, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork
, Susumu Goto, Minoru Kanehisa:
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res. 36(Web-Server-Issue): 423-426 (2008) - [c12]Yannick Haudry, Chuang Kee Ong, Laurence Ettwiller, Hugo Bérubé, Ivica Letunic, Misha Kapushesky, Paul-Daniel Weeber, Xi Wang, Julien Gagneur, Charles Girardot, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich:
Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. APBC 2008: 373-382 - 2007
- [j44]Ivica Letunic
, Peer Bork
:
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinform. 23(1): 127-128 (2007) - [j43]Nicola J. Mulder
, Rolf Apweiler
, Teresa K. Attwood
, Amos Bairoch
, Alex Bateman
, David Binns, Peer Bork
, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise C. Daugherty
, Mark Dibley, Robert D. Finn
, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter
, Daniel Kahn, Alexander Kanapin
, Anish Kejariwal, Alberto Labarga
, Petra S. Langendijk-Genevaux
, David Lonsdale, Rodrigo Lopez
, Ivica Letunic
, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry
, Alex L. Mitchell
, Anastasia N. Nikolskaya, Sandra E. Orchard
, Christine A. Orengo, Robert Petryszak
, Jeremy D. Selengut, Christian J. A. Sigrist
, Paul D. Thomas
, Franck Valentin, Derek Wilson, Cathy H. Wu
, Corin Yeats:
New developments in the InterPro database. Nucleic Acids Res. 35(Database-Issue): 224-228 (2007) - [j42]Christian von Mering
, Lars Juhl Jensen
, Michael Kuhn, Samuel Chaffron
, Tobias Doerks, Beate Krüger, Berend Snel
, Peer Bork
:
STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35(Database-Issue): 358-362 (2007) - [j41]Carolina Perez-Iratxeta, Peer Bork
, Miguel A. Andrade-Navarro
:
Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic Acids Res. 35(Web-Server-Issue): 212-216 (2007) - 2006
- [j40]Jasmin Saric, Lars Juhl Jensen
, Rossitza Ouzounova, Isabel Rojas, Peer Bork
:
Extraction of regulatory gene/protein networks from Medline. Bioinform. 22(6): 645-650 (2006) - [j39]Parantu K. Shah, Peer Bork
:
LSAT: learning about alternative transcripts in MEDLINE. Bioinform. 22(7): 857-865 (2006) - [j38]Ivica Letunic
, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork
:
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 34(Database-Issue): 257-260 (2006) - [j37]Mikita Suyama
, David Torrents
, Peer Bork
:
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34(Web-Server-Issue): 609-612 (2006) - [j36]Mikita Suyama
, Eoghan D. Harrington, Peer Bork
, David Torrents
:
Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes. PLoS Comput. Biol. 2(6) (2006) - 2005
- [j35]Ulrik de Lichtenberg
, Lars Juhl Jensen
, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork
, Søren Brunak
:
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinform. 21(7): 1164-1171 (2005) - [j34]Francesca D. Ciccarelli
, Peer Bork
:
The WHy domain mediates the response to desiccation in plants and bacteria. Bioinform. 21(8): 1304-1307 (2005) - [j33]