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- affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
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2020 – today
- 2022
[j112]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)- 2021
- [j111]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 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) - [j110]Ivica Letunic, Supriya Khedkar, Peer Bork:
SMART: recent updates, new developments and status in 2020. Nucleic Acids Res. 49(Database-Issue): D458-D460 (2021) - [j109]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) - [j108]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) - 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 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 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, Youngmi 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 Rask 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 Rask 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]Sean D. Hooper, Peer Bork:
Medusa: a simple tool for interaction graph analysis. Bioinform. 21(24): 4432-4433 (2005) - [j32]Raimund Tenhaken, Tobias Doerks, Peer Bork:
DCD - a novel plant specific domain in proteins involved in development and programmed cell death. BMC Bioinform. 6: 169 (2005) - [j31]Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu:
InterPro, progress and status in 2005. Nucleic Acids Res. 33(Database-Issue): 201-205 (2005) - [j30]Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork:
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33(Database-Issue): 433-437 (2005) - [j29]Parantu K. Shah, Lars Juhl Jensen, Stéphanie Boué, Peer Bork:
Extraction of Transcript Diversity from Scientific Literature. PLoS Comput. Biol. 1(1) (2005) - 2004
- [j28]Torsten Crass, Iris Antes, Rico Basekow, Peer Bork, Christian Buning, Maik Christensen, Holger Claussen, Christian Ebeling, Peter Ernst, Valérie Gailus-Durner, Karl-Heinz Glatting, Rolf Gohla, Frank Gößling, Korbinian Grote, Karsten R. Heidtke, Alexander Herrmann, Sean O'Keeffe, O. Kießlich, Sven Kolibal, Jan O. Korbel, Thomas Lengauer, Ines Liebich, Mark van der Linden, Hannes Luz, Kathrin Meissner, Christian von Mering, Heinz-Theodor Mevissen, Hans-Werner Mewes, Holger Michael, Martin Mokrejs, Tobias Müller, Heike Pospisil, Matthias Rarey, Jens G. Reich, Ralf Schneider, Dietmar Schomburg, Steffen Schulze-Kremer, Knut Schwarzer, Ingolf Sommer, Stephan Springstubbe, Sándor Suhai, Gnanasekaran Thoppae, Martin Vingron, Jens Warfsmann, Thomas Werner, Daniel Wetzler, Edgar Wingender, Ralf Zimmer:
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinform. 20(2): 268-270 (2004) - [j27]Mikita Suyama, David Torrents, Peer Bork:
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Bioinform. 20(12): 1968-1970 (2004) - [j26]Antonio J. Pérez-Pulido, Carolina Perez-Iratxeta, Peer Bork, Guillermo Thode, Miguel A. Andrade:
Gene annotation from scientific literature using mappings between keyword systems. Bioinform. 20(13): 2084-2091 (2004) - [j25]Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, Peer Bork:
SMART 4.0: towards genomic data integration. Nucleic Acids Res. 32(Database-Issue): 142-144 (2004) - [j24]Lars Juhl Jensen, Julien Lagarde, Christian von Mering, Peer Bork:
ArrayProspector: a web resource of functional associations inferred from microarray expression data. Nucleic Acids Res. 32(Web-Server-Issue): 445-448 (2004) - [c11]