Peer Bork

132 papers A* 1A 2B 2C 2Journal 118Unranked 7
YearRankTypeTitle / Venue / Authors
2023 — conf
Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities.
CoRDI
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
2023 J jnl
InterPro in 2022.
Nucleic Acids Res.
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
2023 J jnl
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Nucleic Acids Res.
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
2023 J jnl
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Nucleic Acids Res.
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
2023 J jnl
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Nucleic Acids Res.
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
2022 J jnl
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.
Nucleic Acids Res.
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
2022 J jnl
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Bioinform.
Thea Van Rossum, Paul I. Costea, Lucas Paoli, Renato Alves, Roman Thielemann, Shinichi Sunagawa, Peer Bork
2021 J jnl
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.
Nucleic Acids Res.
Ivica Letunic, Peer Bork
2021 J jnl
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Nucleic Acids Res.
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
2021 J jnl
SMART: recent updates, new developments and status in 2020.
Nucleic Acids Res.
Ivica Letunic, Supriya Khedkar, Peer Bork
2021 J jnl
The InterPro protein families and domains database: 20 years on.
Nucleic Acids Res.
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
2021 J jnl
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Nucleic Acids Res.
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
2020 J jnl
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Bioinform.
Yuanyue Li, Michael Kuhn, Anne-Claude Gavin, Peer Bork
2020 J jnl
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Nucleic Acids Res.
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
2019 J jnl
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Nucleic Acids Res.
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
2019 J jnl
Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Nucleic Acids Res.
Ivica Letunic, Peer Bork
2019 J jnl
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Nucleic Acids Res.
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
2019 J jnl
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Nucleic Acids Res.
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
2018 J jnl
20 years of the SMART protein domain annotation resource.
Nucleic Acids Res.
Ivica Letunic, Peer Bork
2018 J jnl
Extensive impact of non-antibiotic drugs on human gut bacteria.
Nat.
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
2018 J jnl
MVP: a microbe-phage interaction database.
Nucleic Acids Res.
Na L. Gao, Chengwei Zhang, Zhanbing Zhang, Songnian Hu, Martin J. Lercher, Xing-Ming Zhao, Peer Bork, Zhi Liu, Wei-Hua Chen
2018 J jnl
iPath3.0: interactive pathways explorer v3.
Nucleic Acids Res.
Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada
2017 J jnl
InterPro in 2017 - beyond protein family and domain annotations.
Nucleic Acids Res.
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
2017 J jnl
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.
Wei-Hua Chen, Guanting Lu, Xiao Chen, Xing-Ming Zhao, Peer Bork
2017 J jnl
RTK: efficient rarefaction analysis of large datasets.
Bioinform.
Paul Saary, Kristoffer Forslund, Peer Bork, Falk Hildebrand
2017 J jnl
Systematic identification of phosphorylation-mediated protein interaction switches.
PLoS Comput. Biol.
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
2017 J jnl
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Nucleic Acids Res.
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
2017 J jnl
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Nucleic Acids Res.
Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
2016 J jnl
CART - a chemical annotation retrieval toolkit.
Bioinform.
Samy Deghou, Georg Zeller, Murat Iskar, Marja Driessen, Mercedes Castillo, Vera van Noort, Peer Bork
2016 J jnl
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Nucleic Acids Res.
Ivica Letunic, Peer Bork
2016 J jnl
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Bioinform.
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
2016 J jnl
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Nucleic Acids Res.
Damian Szklarczyk, Alberto Santos, Christian von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn
2016 J jnl
The SIDER database of drugs and side effects.
Nucleic Acids Res.
Michael Kuhn, Ivica Letunic, Lars Juhl Jensen, Peer Bork
2016 J jnl
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Nucleic Acids Res.
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
2015 J jnl
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Nat.
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
2015 J jnl
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res.
Pablo Minguez, Ivica Letunic, Luca Parca, Luz Garcia-Alonso, Joaquín Dopazo, Jaime Huerta-Cepas, Peer Bork
2015 J jnl
SMART: recent updates, new developments and status in 2015.
Nucleic Acids Res.
Ivica Letunic, Tobias Doerks, Peer Bork
2015 J jnl
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Nucleic Acids Res.
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
2015 J jnl
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res.
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
2014 J jnl
Addendum: Enterotypes of the human gut microbiome.
Nat.
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
2014 J jnl
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication".
PLoS Comput. Biol.
Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork
2014 J jnl
STITCH 4: integration of protein-chemical interactions with user data.
Nucleic Acids Res.
Michael Kuhn, Damian Szklarczyk, Sune Pletscher-Frankild, Thomas H. Blicher, Christian von Mering, Lars Juhl Jensen, Peer Bork
2014 J jnl
eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res.
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
2013 J jnl
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Bioinform.
Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez
2013 J jnl
Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs.
PLoS Comput. Biol.
Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork
2013 J jnl
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
Nucleic Acids Res.
Pablo Minguez, Ivica Letunic, Luca Parca, Peer Bork
2013 J jnl
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Nucleic Acids Res.
Andrea Franceschini, Damian Szklarczyk, Sune Frankild, Michael Kuhn, Milan Simonovic, Alexander Roth, Jianyi Lin, Pablo Minguez, Peer Bork, Christian von Mering, Lars Juhl Jensen
2012 J jnl
InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Res.
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
2012 J jnl
OGEE: an online gene essentiality database.
Nucleic Acids Res.
Wei-Hua Chen, Pablo Minguez, Martin J. Lercher, Peer Bork
2012 J jnl
SMART 7: recent updates to the protein domain annotation resource.
Nucleic Acids Res.
Ivica Letunic, Tobias Doerks, Peer Bork
2012 J jnl
STITCH 3: zooming in on protein-chemical interactions.
Nucleic Acids Res.
Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Christian von Mering, Lars Juhl Jensen, Peer Bork
2012 J jnl
The Tenth Asia Pacific Bioinformatics Conference (APBC 2012).
BMC Genom.
Yi-Ping Phoebe Chen, Peer Bork
2012 J jnl
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res.
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
2011 J jnl
Identifying Single Copy Orthologs in Metazoa.
PLoS Comput. Biol.
Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie Dawn Thompson, Detlev Arendt, Peer Bork
2011 J jnl
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
Nucleic Acids Res.
Ivica Letunic, Peer Bork
2011 J jnl
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data.
PLoS Comput. Biol.
Xing-Ming Zhao, Murat Iskar, Georg Zeller, Michael Kuhn, Vera van Noort, Peer Bork
2011 J jnl
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Nucleic Acids Res.
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
2011 J jnl
iPath2.0: interactive pathway explorer.
Nucleic Acids Res.
Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, Peer Bork
2010 J jnl
AQUA: automated quality improvement for multiple sequence alignments.
Bioinform.
Jean Muller, Christopher J. Creevey, Julie Dawn Thompson, Detlev Arendt, Peer Bork
2010 J jnl
Drug-Induced Regulation of Target Expression.
PLoS Comput. Biol.
Murat Iskar, Monica Campillos, Michael Kuhn, Lars Juhl Jensen, Vera van Noort, Peer Bork
2010 J jnl
STITCH 2: an interaction network database for small molecules and proteins.
Nucleic Acids Res.
Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer, Peer Bork
2010 J jnl
SelTar
Nucleic Acids Res.
Stefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, Peer Bork
2010 J jnl
SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
Bioinform.
Eoghan D. Harrington, Manimozhiyan Arumugam, Jeroen Raes, Peer Bork, David A. Relman
2010 J jnl
SmashCommunity: a metagenomic annotation and analysis tool.
Bioinform.
Manimozhiyan Arumugam, Eoghan D. Harrington, Konrad U. Foerstner, Jeroen Raes, Peer Bork
2010 J jnl
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Nucleic Acids Res.
Jean Muller, Damian Szklarczyk, Philippe Julien, Ivica Letunic, Alexander Roth, Michael Kuhn, Sean Powell, Christian von Mering, Tobias Doerks, Lars Juhl Jensen, Peer Bork
2009 J jnl
InterPro: the integrative protein signature database.
Nucleic Acids Res.
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
2009 J jnl
SMART 6: recent updates and new developments.
Nucleic Acids Res.
Ivica Letunic, Tobias Doerks, Peer Bork
2009 J jnl
STRING 8 - a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Res.
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
2008 J jnl
4D
Nucleic Acids Res.
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
2008 B conf
Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress.
APBC
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
2008 J jnl
KEGG Atlas mapping for global analysis of metabolic pathways.
Nucleic Acids Res.
Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, Minoru Kanehisa
2008 J jnl
NetworKIN: a resource for exploring cellular phosphorylation networks.
Nucleic Acids Res.
Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, Tony Pawson
2008 J jnl
STITCH: interaction networks of chemicals and proteins.
Nucleic Acids Res.
Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, Peer Bork
2008 J jnl
Sircah: a tool for the detection and visualization of alternative transcripts.
Bioinform.
Eoghan D. Harrington, Peer Bork
2008 J jnl
SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic Acids Res.
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
2008 J jnl
eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic Acids Res.
Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, Peer Bork
2007 J jnl
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Bioinform.
Ivica Letunic, Peer Bork
2007 J jnl
New developments in the InterPro database.
Nucleic Acids Res.
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
2007 J jnl
STRING 7 - recent developments in the integration and prediction of protein interactions.
Nucleic Acids Res.
Christian von Mering, Lars Juhl Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork
2007 J jnl
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Nucleic Acids Res.
Carolina Perez-Iratxeta, Peer Bork, Miguel A. Andrade-Navarro
2006 J jnl
Extraction of regulatory gene/protein networks from Medline.
Bioinform.
Jasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, Peer Bork
2006 J jnl
Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes.
PLoS Comput. Biol.
Mikita Suyama, Eoghan D. Harrington, Peer Bork, David Torrents
2006 J jnl
LSAT: learning about alternative transcripts in MEDLINE.
Bioinform.
Parantu K. Shah, Peer Bork
2006 J jnl
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Nucleic Acids Res.
Mikita Suyama, David Torrents, Peer Bork
2006 J jnl
SMART 5: domains in the context of genomes and networks.
Nucleic Acids Res.
Ivica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork
2005 J jnl
Comparison of computational methods for the identification of cell cycle-regulated genes.
Bioinform.
Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak
2005 J jnl
DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
BMC Bioinform.
Raimund Tenhaken, Tobias Doerks, Peer Bork
2005 J jnl
Extraction of Transcript Diversity from Scientific Literature.
PLoS Comput. Biol.
Parantu K. Shah, Lars Juhl Jensen, Stéphanie Boué, Peer Bork
2005 J jnl
InterPro, progress and status in 2005.
Nucleic Acids Res.
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
2005 J jnl
Medusa: a simple tool for interaction graph analysis.
Bioinform.
Sean D. Hooper, Peer Bork
2005 J jnl
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res.
Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork
2005 J jnl
The WHy domain mediates the response to desiccation in plants and bacteria.
Bioinform.
Francesca D. Ciccarelli, Peer Bork
2004 J jnl
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Nucleic Acids Res.
Lars Juhl Jensen, Julien Lagarde, Christian von Mering, Peer Bork
2004 J jnl
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Bioinform.
Mikita Suyama, David Torrents, Peer Bork
2004 A* conf
Extracting Regulatory Gene Expression Networks From Pubmed.
ACL
Jasmin Saric, Lars Juhl Jensen, Peer Bork, Rossitza Ouzounova, Isabel Rojas
2004 J jnl
Gene annotation from scientific literature using mappings between keyword systems.
Bioinform.
Antonio J. Pérez-Pulido, Carolina Perez-Iratxeta, Peer Bork, Guillermo Thode, Miguel A. Andrade
2004 J jnl
SMART 4.0: towards genomic data integration.
Nucleic Acids Res.
Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, Peer Bork
2004 J jnl
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Bioinform.
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
2003 J jnl
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Bioinform.
Roland Krause, Christian von Mering, Peer Bork
2003 J jnl
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Nucleic Acids Res.
Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M. A. Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Stanislaw Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson
2003 J jnl
Information extraction from full text scientific articles: Where are the keywords?
BMC Bioinform.
Parantu K. Shah, Carolina Perez-Iratxeta, Peer Bork, Miguel A. Andrade
2003 J jnl
STRING: a database of predicted functional associations between proteins.
Nucleic Acids Res.
Christian von Mering, Martijn A. Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, Berend Snel
2003 J jnl
The InterPro Database, 2003 brings increased coverage and new features.
Nucleic Acids Res.
Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov
2003 J jnl
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
BMC Bioinform.
Francesca D. Ciccarelli, Elisa Izaurralde, Peer Bork
2003 J jnl
Update on XplorMed: a web server for exploring scientific literature.
Nucleic Acids Res.
Carolina Perez-Iratxeta, Antonio J. Pérez-Pulido, Peer Bork, Miguel A. Andrade
2002 J jnl
A Versatile Structural Domain Analysis Server Using Profile Weight Matrices.
J. Chem. Inf. Comput. Sci.
Steffen Schmidt, Peer Bork, Thomas Dandekar
2002 C conf
Comparative analysis of protein interaction networks.
ECCB
Peer Bork
2002 J jnl
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Nucleic Acids Res.
D. Fredman, Marianne Siegfried, Yan P. Yuan, Peer Bork, Heikki Lehväslaiho, Anthony J. Brookes
2002 J jnl
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites
Briefings Bioinform.
Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Sam Griffiths-Jones, Daniel H. Haft, Henning Hermjakob, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, Sue Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Florence Servant, Christian J. A. Sigrist
2002 J jnl
Recent improvements to the SMART domain-based sequence annotation resource.
Nucleic Acids Res.
Ivica Letunic, Leo Goodstadt, Nicholas J. Dickens, Tobias Doerks, Jörg Schultz, Richard Mott, Francesca D. Ciccarelli, Richard R. Copley, Chris P. Ponting, Peer Bork
2000 J jnl
HGBASE: a database of SNPs and other variations in and around human genes.
Nucleic Acids Res.
Anthony J. Brookes, Heikki Lehväslaiho, Marianne Siegfried, Jana G. Boehm, Yan P. Yuan, Chandra M. Sarkar, Peer Bork, J. Flavio R. Ortigao
2000 J jnl
NAIL-Network Analysis Interface for Linking HMMER results.
Bioinform.
Luis Sánchez-Pulido, Yan P. Yuan, Miguel A. Andrade, Peer Bork
2000 J jnl
SMART: a web-based tool for the study of genetically mobile domains.
Nucleic Acids Res.
Jörg Schultz, Richard R. Copley, Tobias Doerks, Chris P. Ponting, Peer Bork
1999 C conf
Applying Logic Programming to Derive Novel Functional Information of Genomes.
PADL
Arvind K. Bansal, Peer Bork
1999 J jnl
Associative database of protein sequences.
Bioinform.
Jens Hanke, Gerrit Lehmann, Peer Bork, Jens G. Reich
1999 B conf
Comparing genes and genomes (abstract): from polymorphism to phylogeny.
RECOMB
Peer Bork
1999 J jnl
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Bioinform.
Frank Eisenhaber, Peer Bork
1999 A ed.
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany
ISMB
Thomas Lengauer, Reinhard Schneider, Peer Bork, Douglas L. Brutlag, Janice I. Glasgow, Hans-Werner Mewes, Ralf Zimmer
1999 J jnl
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Nucleic Acids Res.
Chris P. Ponting, Jörg Schultz, Frank Milpetz, Peer Bork
1998 J jnl
Frame: detection of genomic sequencing errors.
Bioinform.
Nigel P. Brown, Chris Sander, Peer Bork
1998 — conf
Pathway alignment: Application in the comparative analysis of glycolysis.
German Conference on Bioinformatics
Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork
1998 J jnl
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Bioinform.
Thomas Dandekar, Katrin Beyer, Peer Bork, Mary-Rose Kenealy, Kostas Pantopoulos, Matthias W. Hentze, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, Sonja Schreiber
1998 J jnl
Towards detection of orthologues in sequence databases.
Bioinform.
Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork
1997 — conf
Associative Data Base of Biomolecuiar Sequences.
German Conference on Bioinformatics
Jens Hanke, Peer Bork, Jens G. Reich
1997 — conf
Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region.
German Conference on Bioinformatics
Thomas Dandekar, Katrin Beyer, Peer Bork, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, W. Keller, Sonja Schreiber
1997 J jnl
The Sequence Alerting Server - a new WEB server.
Comput. Appl. Biosci.
Hedvig Hegyi, J. M. Lai, Peer Bork
1997 — conf
Towards detection of sequence orthologs.
German Conference on Bioinformatics
Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork
1996 J jnl
Von Genomsequenzen zu Proteinfunktionen.
Informationstechnik Tech. Inform.
Peer Bork
1995 — conf
The Functional Composition of Living Machines as a Design Principle for Artificial Organisms.
ECAL
Christos A. Ouzounis, Alfonso Valencia, Javier Tamames, Peer Bork, Chris Sander
1994 A conf
GeneQuiz: A Workbench for Sequence Analysis.
ISMB
Michael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander
1993 J jnl
A fast, sensitive pattern-matching approach for protein sequences.
Comput. Appl. Biosci.
K. Rohde, Peer Bork
1993 — conf
Entschlüsselung von Proteinfunktionen mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzähnlichkeiten.
Informatik in den Biowissenschaften
Peer Bork