Entschlüsselung von Proteinfunktionen mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzähnlichkeiten. - Peer Bork (Informatik in den Biowissenschaften, 1993)

A fast, sensitive pattern-matching approach for protein sequences. - K. Rohde; Peer Bork (Comput. Appl. Biosci., 1993)

GeneQuiz: A Workbench for Sequence Analysis. - Michael Scharf; Reinhard Schneider 002; Georg Casari; Peer Bork; Alfonso Valencia; Christos A. Ouzounis; Chris Sander (ISMB, 1994)

The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. - Christos A. Ouzounis; Alfonso Valencia; Javier Tamames; Peer Bork; Chris Sander (ECAL, 1995)

Von Genomsequenzen zu Proteinfunktionen. - Peer Bork (Informationstechnik Tech. Inform., 1996)

Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region. - Thomas Dandekar; Katrin Beyer; Peer Bork; Vera Sonntag-Buck; Gilles Flouriot; Frank Gannon; W. Keller; Sonja Schreiber (German Conference on Bioinformatics, 1997)

Associative Data Base of Biomolecuiar Sequences. - Jens Hanke; Peer Bork; Jens G. Reich (German Conference on Bioinformatics, 1997)

Towards detection of sequence orthologs. - Yan P. Yuan; Oliver Eulenstein; Martin Vingron; Peer Bork (German Conference on Bioinformatics, 1997)

The Sequence Alerting Server - a new WEB server. - Hedvig Hegyi; J. M. Lai; Peer Bork (Comput. Appl. Biosci., 1997)

Pathway alignment: Application in the comparative analysis of glycolysis. - Thomas Dandekar; Stefan Schuster; Martijn A. Huynen; Peer Bork (German Conference on Bioinformatics, 1998)

Frame: detection of genomic sequencing errors. - Nigel P. Brown; Chris Sander; Peer Bork (Bioinform., 1998)

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches. - Thomas Dandekar; Katrin Beyer; Peer Bork; Mary-Rose Kenealy; Kostas Pantopoulos; Matthias W. Hentze; Vera Sonntag-Buck; Gilles Flouriot; Frank Gannon; Sonja Schreiber (Bioinform., 1998)

Towards detection of orthologues in sequence databases. - Yan P. Yuan; Oliver Eulenstein; Martin Vingron; Peer Bork (Bioinform., 1998)

Applying Logic Programming to Derive Novel Functional Information of Genomes. - Arvind K. Bansal; Peer Bork (PADL, 1999)

Comparing genes and genomes (abstract): from polymorphism to phylogeny. - Peer Bork (RECOMB, 1999)

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. - Frank Eisenhaber; Peer Bork (Bioinform., 1999)

Associative database of protein sequences. - Jens Hanke; Gerrit Lehmann; Peer Bork; Jens G. Reich (Bioinform., 1999)

SMART: identification and annotation of domains from signalling and extracellular protein sequences. - Chris P. Ponting; Jörg Schultz; Frank Milpetz; Peer Bork (Nucleic Acids Res., 1999)

NAIL-Network Analysis Interface for Linking HMMER results. - Luis Sánchez-Pulido; Yan P. Yuan; Miguel A. Andrade; Peer Bork (Bioinform., 2000)

HGBASE: a database of SNPs and other variations in and around human genes. - Anthony J. Brookes; Heikki Lehväslaiho; Marianne Siegfried; Jana G. Boehm; Yan P. Yuan; Chandra M. Sarkar; Peer Bork; J. Flavio R. Ortigao (Nucleic Acids Res., 2000)

SMART: a web-based tool for the study of genetically mobile domains. - Jörg Schultz; Richard R. Copley; Tobias Doerks; Chris P. Ponting; Peer Bork (Nucleic Acids Res., 2000)

Comparative analysis of protein interaction networks. - Peer Bork (ECCB, 2002)

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites - 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; et al. (Briefings Bioinform., 2002)

A Versatile Structural Domain Analysis Server Using Profile Weight Matrices. - Steffen Schmidt; Peer Bork; Thomas Dandekar (J. Chem. Inf. Comput. Sci., 2002)

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. - D. Fredman; Marianne Siegfried; Yan P. Yuan; Peer Bork; Heikki Lehväslaiho; Anthony J. Brookes (Nucleic Acids Res., 2002)

Recent improvements to the SMART domain-based sequence annotation resource. - Ivica Letunic; Leo Goodstadt; Nicholas J. Dickens; Tobias Doerks; Jörg Schultz; Richard Mott; Francesca D. Ciccarelli; Richard R. Copley; Chris P. Ponting; Peer Bork (Nucleic Acids Res., 2002)

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. - Roland Krause; Christian von Mering; Peer Bork (Bioinform., 2003)

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. - Francesca D. Ciccarelli; Elisa Izaurralde; Peer Bork (BMC Bioinform., 2003)

Information extraction from full text scientific articles: Where are the keywords? - Parantu K. Shah; Carolina Perez-Iratxeta; Peer Bork; Miguel A. Andrade (BMC Bioinform., 2003)

STRING: a database of predicted functional associations between proteins. - Christian von Mering; Martijn A. Huynen; Daniel Jaeggi; Steffen Schmidt; Peer Bork; Berend Snel (Nucleic Acids Res., 2003)

The InterPro Database, 2003 brings increased coverage and new features. - 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; et al. (Nucleic Acids Res., 2003)

Update on XplorMed: a web server for exploring scientific literature. - Carolina Perez-Iratxeta; Antonio J. Pérez-Pulido; Peer Bork; Miguel A. Andrade (Nucleic Acids Res., 2003)

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. - 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; et al. (Nucleic Acids Res., 2003)

Extracting Regulatory Gene Expression Networks From Pubmed. - Jasmin Saric; Lars Juhl Jensen; Peer Bork; Rossitza Ouzounova; Isabel Rojas (ACL, 2004)

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. - Torsten Crass; Iris Antes; Rico Basekow; Peer Bork; Christian Buning; Maik Christensen; Holger Claussen 002; Christian Ebeling; Peter Ernst; Valérie Gailus-Durner; Karl-Heinz Glatting; Rolf Gohla; et al. (Bioinform., 2004)

Gene annotation from scientific literature using mappings between keyword systems. - Antonio J. Pérez-Pulido; Carolina Perez-Iratxeta; Peer Bork; Guillermo Thode; Miguel A. Andrade (Bioinform., 2004)

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. - Mikita Suyama; David Torrents; Peer Bork (Bioinform., 2004)

ArrayProspector: a web resource of functional associations inferred from microarray expression data. - Lars Juhl Jensen; Julien Lagarde; Christian von Mering; Peer Bork (Nucleic Acids Res., 2004)

SMART 4.0: towards genomic data integration. - Ivica Letunic; Richard R. Copley; Steffen Schmidt; Francesca D. Ciccarelli; Tobias Doerks; Jörg Schultz; Chris P. Ponting; Peer Bork (Nucleic Acids Res., 2004)

The WHy domain mediates the response to desiccation in plants and bacteria. - Francesca D. Ciccarelli; Peer Bork (Bioinform., 2005)

Medusa: a simple tool for interaction graph analysis. - Sean D. Hooper; Peer Bork (Bioinform., 2005)

Comparison of computational methods for the identification of cell cycle-regulated genes. - Ulrik de Lichtenberg; Lars Juhl Jensen; Anders Fausbøll; Thomas Skøt Jensen; Peer Bork; Søren Brunak (Bioinform., 2005)

DCD - a novel plant specific domain in proteins involved in development and programmed cell death. - Raimund Tenhaken; Tobias Doerks; Peer Bork (BMC Bioinform., 2005)

STRING: known and predicted protein-protein associations, integrated and transferred across organisms. - Christian von Mering; Lars Juhl Jensen; Berend Snel; Sean D. Hooper; Markus Krupp; Mathilde Foglierini; Nelly Jouffre; Martijn A. Huynen; Peer Bork (Nucleic Acids Res., 2005)

InterPro, progress and status in 2005. - 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; et al. (Nucleic Acids Res., 2005)

Extraction of Transcript Diversity from Scientific Literature. - Parantu K. Shah; Lars Juhl Jensen; Stéphanie Boué; Peer Bork (PLoS Comput. Biol., 2005)

Extraction of regulatory gene/protein networks from Medline. - Jasmin Saric; Lars Juhl Jensen; Rossitza Ouzounova; Isabel Rojas; Peer Bork (Bioinform., 2006)

LSAT: learning about alternative transcripts in MEDLINE. - Parantu K. Shah; Peer Bork (Bioinform., 2006)

SMART 5: domains in the context of genomes and networks. - Ivica Letunic; Richard R. Copley; Birgit Pils; Stefan Pinkert; Jörg Schultz; Peer Bork (Nucleic Acids Res., 2006)

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. - Mikita Suyama; David Torrents; Peer Bork (Nucleic Acids Res., 2006)

Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes. - Mikita Suyama; Eoghan D. Harrington; Peer Bork; David Torrents (PLoS Comput. Biol., 2006)

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. - Ivica Letunic; Peer Bork (Bioinform., 2007)

STRING 7 - recent developments in the integration and prediction of protein interactions. - Christian von Mering; Lars Juhl Jensen; Michael Kuhn 004; Samuel Chaffron; Tobias Doerks; Beate Krüger; Berend Snel; Peer Bork (Nucleic Acids Res., 2007)

New developments in the InterPro database. - 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; et al. (Nucleic Acids Res., 2007)

Update of the G2D tool for prioritization of gene candidates to inherited diseases. - Carolina Perez-Iratxeta; Peer Bork; Miguel A. Andrade-Navarro (Nucleic Acids Res., 2007)

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. - 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; et al. (APBC, 2008)

Sircah: a tool for the detection and visualization of alternative transcripts. - Eoghan D. Harrington; Peer Bork (Bioinform., 2008)

SuperTarget and Matador: resources for exploring drug-target relationships. - Stefan Günther; Michael Kuhn 004; Mathias Dunkel; Monica Campillos; Christian Senger; Evangelia Petsalaki; Jessica Ahmed; Eduardo Garcia Urdiales; Andreas Gewiess; Lars Juhl Jensen; Reinhard Schneider 002; Roman Skoblo; et al. (Nucleic Acids Res., 2008)

4DXpress: a database for cross-species expression pattern comparisons. - 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; et al. (Nucleic Acids Res., 2008)

eggNOG: automated construction and annotation of orthologous groups of genes. - Lars Juhl Jensen; Philippe Julien; Michael Kuhn 004; Christian von Mering; Jean Muller; Tobias Doerks; Peer Bork (Nucleic Acids Res., 2008)

STITCH: interaction networks of chemicals and proteins. - Michael Kuhn 004; Christian von Mering; Monica Campillos; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2008)

NetworKIN: a resource for exploring cellular phosphorylation networks. - Rune Linding; Lars Juhl Jensen; Adrian Pasculescu; Marina Olhovsky; Karen Colwill; Peer Bork; Michael B. Yaffe; Tony Pawson (Nucleic Acids Res., 2008)

KEGG Atlas mapping for global analysis of metabolic pathways. - Shujiro Okuda; Takuji Yamada; Masami Hamajima; Masumi Itoh; Toshiaki Katayama; Peer Bork; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2008)

InterPro: the integrative protein signature database. - 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; et al. (Nucleic Acids Res., 2009)

STRING 8 - a global view on proteins and their functional interactions in 630 organisms. - Lars Juhl Jensen; Michael Kuhn 004; Manuel Stark; Samuel Chaffron; Christopher J. Creevey; Jean Muller; Tobias Doerks; Philippe Julien; Alexander Roth 001; Milan Simonovic; Peer Bork; Christian von Mering (Nucleic Acids Res., 2009)

SMART 6: recent updates and new developments. - Ivica Letunic; Tobias Doerks; Peer Bork (Nucleic Acids Res., 2009)

SmashCommunity: a metagenomic annotation and analysis tool. - Manimozhiyan Arumugam; Eoghan D. Harrington; Konrad U. Foerstner; Jeroen Raes; Peer Bork (Bioinform., 2010)

SmashCell: a software framework for the analysis of single-cell amplified genome sequences. - Eoghan D. Harrington; Manimozhiyan Arumugam; Jeroen Raes; Peer Bork; David A. Relman (Bioinform., 2010)

AQUA: automated quality improvement for multiple sequence alignments. - Jean Muller; Christopher J. Creevey; Julie Dawn Thompson; Detlev Arendt; Peer Bork (Bioinform., 2010)

STITCH 2: an interaction network database for small molecules and proteins. - Michael Kuhn 004; Damian Szklarczyk; Andrea Franceschini; Monica Campillos; Christian von Mering; Lars Juhl Jensen; Andreas Beyer; Peer Bork (Nucleic Acids Res., 2010)

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. - Jean Muller; Damian Szklarczyk; Philippe Julien; Ivica Letunic; Alexander Roth 001; Michael Kuhn 004; Sean Powell; Christian von Mering; Tobias Doerks; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2010)

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology. - Stefan M. Woerner; Yan P. Yuan; Axel Benner; Sebastian Korff; Magnus von Knebel Doeberitz; Peer Bork (Nucleic Acids Res., 2010)

Drug-Induced Regulation of Target Expression. - Murat Iskar; Monica Campillos; Michael Kuhn 004; Lars Juhl Jensen; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2010)

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. - Ivica Letunic; Peer Bork (Nucleic Acids Res., 2011)

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. - Damian Szklarczyk; Andrea Franceschini; Michael Kuhn 004; Milan Simonovic; Alexander Roth 001; Pablo Minguez; Tobias Doerks; Manuel Stark; Jean Muller; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2011)

iPath2.0: interactive pathway explorer. - Takuji Yamada; Ivica Letunic; Shujiro Okuda; Minoru Kanehisa; Peer Bork (Nucleic Acids Res., 2011)

Identifying Single Copy Orthologs in Metazoa. - Christopher J. Creevey; Jean Muller; Tobias Doerks; Julie Dawn Thompson; Detlev Arendt; Peer Bork (PLoS Comput. Biol., 2011)

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data. - Xing-Ming Zhao; Murat Iskar; Georg Zeller; Michael Kuhn 004; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2011)

The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). - Yi-Ping Phoebe Chen; Peer Bork (BMC Genom., 2012)

OGEE: an online gene essentiality database. - Wei-Hua Chen; Pablo Minguez; Martin J. Lercher; Peer Bork (Nucleic Acids Res., 2012)

InterPro in 2011: new developments in the family and domain prediction database. - 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; et al. (Nucleic Acids Res., 2012)

STITCH 3: zooming in on protein-chemical interactions. - Michael Kuhn 004; Damian Szklarczyk; Andrea Franceschini; Christian von Mering; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2012)

SMART 7: recent updates to the protein domain annotation resource. - Ivica Letunic; Tobias Doerks; Peer Bork (Nucleic Acids Res., 2012)

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. - Sean Powell; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth 001; Michael Kuhn 004; Jean Muller; Roland Arnold; Thomas Rattei; Ivica Letunic; Tobias Doerks; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2012)

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. - Clare Pacini; Francesco Iorio; Emanuel J. V. Gonçalves; Murat Iskar; Thomas Klabunde; Peer Bork; Julio Saez-Rodriguez (Bioinform., 2013)

STRING v9.1: protein-protein interaction networks, with increased coverage and integration. - Andrea Franceschini; Damian Szklarczyk; Sune Frankild; Michael Kuhn 004; Milan Simonovic; Alexander Roth 001; Jianyi Lin; Pablo Minguez; Peer Bork; Christian von Mering; Lars Juhl Jensen (Nucleic Acids Res., 2013)

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. - Pablo Minguez; Ivica Letunic; Luca Parca; Peer Bork (Nucleic Acids Res., 2013)

Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs. - Wei-Hua Chen; Xing-Ming Zhao; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2013)

STITCH 4: integration of protein-chemical interactions with user data. - Michael Kuhn 004; Damian Szklarczyk; Sune Pletscher-Frankild; Thomas H. Blicher; Christian von Mering; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2014)

eggNOG v4.0: nested orthology inference across 3686 organisms. - Sean Powell; Kristoffer Forslund; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth 001; Jaime Huerta-Cepas; Toni Gabaldón; Thomas Rattei; Christopher J. Creevey; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2014)

Addendum: Enterotypes of the human gut microbiome. - 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; et al. (Nat., 2014)

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication". - Wei-Hua Chen; Xing-Ming Zhao; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2014)

SMART: recent updates, new developments and status in 2015. - Ivica Letunic; Tobias Doerks; Peer Bork (Nucleic Acids Res., 2015)

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. - Pablo Minguez; Ivica Letunic; Luca Parca; Luz Garcia-Alonso; Joaquín Dopazo; Jaime Huerta-Cepas; Peer Bork (Nucleic Acids Res., 2015)

The InterPro protein families database: the classification resource after 15 years. - 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; et al. (Nucleic Acids Res., 2015)

STRING v10: protein-protein interaction networks, integrated over the tree of life. - Damian Szklarczyk; Andrea Franceschini; Stefan Wyder; Kristoffer Forslund; Davide Heller; Jaime Huerta-Cepas; Milan Simonovic; Alexander Roth 001; Alberto Santos; Kalliopi Tsafou; Michael Kuhn 004; Peer Bork; et al. (Nucleic Acids Res., 2015)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. - 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; et al. (Nat., 2015)

CART - a chemical annotation retrieval toolkit. - Samy Deghou; Georg Zeller; Murat Iskar; Marja Driessen; Mercedes Castillo; Vera van Noort; Peer Bork (Bioinform., 2016)

MOCAT2: a metagenomic assembly, annotation and profiling framework. - 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 (Bioinform., 2016)

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. - Jaime Huerta-Cepas; Damian Szklarczyk; Kristoffer Forslund; Helen Cook; Davide Heller; Mathias C. Walter; Thomas Rattei; Daniel R. Mende; Shinichi Sunagawa; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2016)

The SIDER database of drugs and side effects. - Michael Kuhn 004; Ivica Letunic; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2016)

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. - Ivica Letunic; Peer Bork (Nucleic Acids Res., 2016)

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. - Damian Szklarczyk; Alberto Santos; Christian von Mering; Lars Juhl Jensen; Peer Bork; Michael Kuhn 004 (Nucleic Acids Res., 2016)

RTK: efficient rarefaction analysis of large datasets. - Paul Saary; Kristoffer Forslund; Peer Bork; Falk Hildebrand (Bioinform., 2017)

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. - Wei-Hua Chen; Guanting Lu; Xiao Chen; Xing-Ming Zhao; Peer Bork (Nucleic Acids Res., 2017)

InterPro in 2017 - beyond protein family and domain annotations. - 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; et al. (Nucleic Acids Res., 2017)

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. - Daniel R. Mende; Ivica Letunic; Jaime Huerta-Cepas; Simone S. Li; Kristoffer Forslund; Shinichi Sunagawa; Peer Bork (Nucleic Acids Res., 2017)

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. - Damian Szklarczyk; John H. Morris; Helen Cook; Michael Kuhn 004; Stefan Wyder; Milan Simonovic; Alberto Santos; Nadezhda T. Doncheva; Alexander Roth 001; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2017)

Systematic identification of phosphorylation-mediated protein interaction switches. - 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 (PLoS Comput. Biol., 2017)

iPath3.0: interactive pathways explorer v3. - Youssef Darzi; Ivica Letunic; Peer Bork; Takuji Yamada (Nucleic Acids Res., 2018)

MVP: a microbe-phage interaction database. - Na L. Gao; Chengwei Zhang; Zhanbing Zhang; Songnian Hu; Martin J. Lercher; Xing-Ming Zhao; Peer Bork; Zhi Liu; Wei-Hua Chen (Nucleic Acids Res., 2018)

20 years of the SMART protein domain annotation resource. - Ivica Letunic; Peer Bork (Nucleic Acids Res., 2018)

Extensive impact of non-antibiotic drugs on human gut bacteria. - Lisa Maier; Mihaela Pruteanu; Michael Kuhn 004; Georg Zeller; Anja Telzerow; Exene Erin Anderson; Ana Rita Brochado; Keith Conrad Fernandez; Hitomi Dose; Hirotada Mori; Kiran Raosaheb Patil; Peer Bork; et al. (Nat., 2018)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. - 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 (Nucleic Acids Res., 2019)

Interactive Tree Of Life (iTOL) v4: recent updates and new developments. - Ivica Letunic; Peer Bork (Nucleic Acids Res., 2019)

InterPro in 2019: improving coverage, classification and access to protein sequence annotations. - 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; et al. (Nucleic Acids Res., 2019)

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. - 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 (Nucleic Acids Res., 2019)

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. - Yuanyue Li; Michael Kuhn 004; Anne-Claude Gavin; Peer Bork (Bioinform., 2020)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. - 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; et al. (Nucleic Acids Res., 2020)

The InterPro protein families and domains database: 20 years on. - 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; et al. (Nucleic Acids Res., 2021)

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. - 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 (Nucleic Acids Res., 2021)

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. - Ivica Letunic; Peer Bork (Nucleic Acids Res., 2021)

SMART: recent updates, new developments and status in 2020. - Ivica Letunic; Supriya Khedkar; Peer Bork (Nucleic Acids Res., 2021)

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. - 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 (Nucleic Acids Res., 2021)

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes. - Thea Van Rossum; Paul I. Costea; Lucas Paoli; Renato Alves; Roman Thielemann; Shinichi Sunagawa; Peer Bork (Bioinform., 2022)

The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. - 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; et al. (Nucleic Acids Res., 2022)

Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. - Nils Hoffmann; Irena Maus; Sebastian Beier; Peter Belmann; Jan Krüger; Andreas Tauch; Alexander Goesmann; Roland Eils; Peer Bork; Oliver Kohlbacher; Ursula Kummer; Rolf Backofen; et al. (CoRDI, 2023)

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. - Anthony Fullam; Ivica Letunic; Thomas S. B. Schmidt; Quinten R. Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn 004; Martin Larralde; Oleksandr M. Maistrenko; Lukas Malfertheiner; Alessio Milanese; João F. Matias Rodrigues; et al. (Nucleic Acids Res., 2023)

eggNOG 6.0: enabling comparative genomics across 12 535 organisms. - 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; et al. (Nucleic Acids Res., 2023)

InterPro in 2022. - 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; et al. (Nucleic Acids Res., 2023)

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. - 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; et al. (Nucleic Acids Res., 2023)