RIFLE: Rapid Identification of Microorganisms by Fragment Length Evaluation. - Henning Hermjakob; Robert Giegerich; Walter Arnold (ISMB, 1997)

SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world. - Henning Hermjakob; Claire O'Donovan; Maria Jesus Martin; Fiona Lang; Rolf Apweiler (German Conference on Bioinformatics, 1998)

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. - T. Heinemeyer; Edgar Wingender; Ingmar Reuter; Henning Hermjakob; Alexander E. Kel; Olga V. Kel-Margoulis; Elena V. Ignatieva; Elena A. Ananko; Olga A. Podkolodnaya; Fedor A. Kolpakov; Nikolay L. Podkolodny; Nikolay A. Kolchanov (Nucleic Acids Res., 1998)

Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotation. - Arno Velds; Henning Hermjakob; Rolf Apweiler (German Conference on Bioinformatics, 1999)

Swissknife - 'lazy parsing' of SWISS-PROT entries. - Henning Hermjakob; Wolfgang Fleischmann; Rolf Apweiler (Bioinform., 1999)

InterPro-an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Bioinform., 2000)

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. - Paul J. Kersey; Henning Hermjakob; Rolf Apweiler (Bioinform., 2000)

A comparison of signal sequence prediction methods using a test set of signal peptides. - Kerstin M. L. Menne; Henning Hermjakob; Rolf Apweiler (Bioinform., 2000)

Towards a New Curation Environment for the TrEMBL Database. - Kai J. Runte; Henning Hermjakob; Rolf Apweiler (German Conference on Bioinformatics, 2001)

The InterPro database, an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Nucleic Acids Res., 2001)

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)

IntAct: an open source molecular interaction database. - Henning Hermjakob; Luisa Montecchi-Palazzi; Chris Lewington; Sugath Mudali; Samuel Kerrien; Sandra E. Orchard; Martin Vingron; Bernd Roechert; Peter Roepstorff; Alfonso Valencia; Hanah Margalit; John Armstrong; et al. (Nucleic Acids Res., 2004)

The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments. - Sandra E. Orchard; Luisa Montecchi-Palazzi; Henning Hermjakob; Rolf Apweiler (Pacific Symposium on Biocomputing, 2005)

Dasty and UniProt DAS: a perfect pair for protein feature visualization. - Philip Jones; Nisha Vinod; Thomas A. Down; Andre Hackmann; Andreas Kähäri; Ernst Kretschmann; Antony F. Quinn; Daniela Wieser; Henning Hermjakob; Rolf Apweiler (Bioinform., 2005)

Development and implementation of the PSI MI standard for molecular interaction. - Samuel Kerrien; Henning Hermjakob (WSC, 2006)

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. - Richard G. Côté; Philip Jones; Rolf Apweiler; Henning Hermjakob (BMC Bioinform., 2006)

PRIDE: a public repository of protein and peptide identifications for the proteomics community. - Philip Jones; Richard G. Côté; Lennart Martens; Antony F. Quinn; Chris F. Taylor; William Derache; Henning Hermjakob; Rolf Apweiler (Nucleic Acids Res., 2006)

An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases. - Sebastian Klie; Lennart Martens; Juan Antonio Vizcaíno; Richard G. Côté; Philip Jones; Rolf Apweiler; Alexander Hinneburg; Henning Hermjakob (German Conference on Bioinformatics, 2007)

Analysing latent topics in large-scale proteomics. - Sebastian Klie; Alexander Hinneburg; Lennart Martens; Juan Antonio Vizcaíno; Richard G. Côté; Philip Jones; Rolf Apweiler; Henning Hermjakob (LWA, 2007)

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. - Richard G. Côté; Philip Jones; Lennart Martens; Samuel Kerrien; Florian Reisinger; Quan Lin; Rasko Leinonen; Rolf Apweiler; Henning Hermjakob (BMC Bioinform., 2007)

Pride Wizard: generation of standards compliant quantitative proteomics data. - Neil Swainston; Jennifer A. Siepen; Andrew R. Jones; Sarah R. Hart; Henning Hermjakob; Philip Jones; Simon J. Hubbard (BMC Syst. Biol., 2007)

IntAct - open source resource for molecular interaction data. - Samuel Kerrien; Yasmin Alam-Faruque; Bruno Aranda; I. Bancarz; Alan J. Bridge; C. Derow; Emily Dimmer; Marc Feuermann; A. Friedrichsen; Rachael P. Huntley; C. Kohler; Jyoti Khadake; et al. (Nucleic Acids Res., 2007)

EBI Proteomics Services. - Henning Hermjakob (DILS, 2008)

ENFIN - An Integrative Structure for Systems Biology. - Florian Reisinger; Manuel Corpas; John M. Hancock; Henning Hermjakob; Ewan Birney; Pascal Kahlem (DILS, 2008)

The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world. - Sandra E. Orchard; Henning Hermjakob (Briefings Bioinform., 2008)

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. - Tony Chiang; Nianhua Li; Sandra E. Orchard; Samuel Kerrien; Henning Hermjakob; Robert Gentleman; Wolfgang Huber (Bioinform., 2008)

Dasty2, an Ajax protein DAS client. - Rafael C. Jiménez; Antony F. Quinn; Alexander García Castro; Alberto Labarga; Kieran O'Neill; Fernando Martinez; Gustavo A. Salazar; Henning Hermjakob (Bioinform., 2008)

InteroPORC: automated inference of highly conserved protein interaction networks. - Magali Michaut; Samuel Kerrien; Luisa Montecchi-Palazzi; Franck Chauvat; Corinne Cassier-Chauvat; Jean-Christophe Aude; Pierre Legrain; Henning Hermjakob (Bioinform., 2008)

The Protein Feature Ontology: a tool for the unification of protein feature annotations. - Gabrielle A. Reeves; Karen Eilbeck; Michele Magrane; Claire O'Donovan; Luisa Montecchi-Palazzi; Midori A. Harris; Sandra E. Orchard; Rafael C. Jiménez; Andreas Prlic; Tim J. P. Hubbard; Henning Hermjakob; Janet M. Thornton (Bioinform., 2008)

Integrating biological data - the Distributed Annotation System. - Andrew M. Jenkinson; Mario Albrecht; Ewan Birney; Hagen Blankenburg; Thomas A. Down; Robert D. Finn; Henning Hermjakob; Tim J. P. Hubbard; Rafael C. Jiménez; Philip Jones; Andreas Kähäri; Eugene Kulesha; et al. (BMC Bioinform., 2008)

InteroPORC: an automated tool to predict highly conserved protein interaction networks. - Magali Michaut; Samuel Kerrien; Luisa Montecchi-Palazzi; Corinne Cassier-Chauvat; Franck Chauvat; Jean-Christophe Aude; Pierre Legrain; Henning Hermjakob (BMC Bioinform., 2008)

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. - Kieran O'Neill; Alexander García Castro; Anita Schwegmann; Rafael C. Jiménez; Dan Jacobson; Henning Hermjakob (BMC Bioinform., 2008)

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. - Richard G. Côté; Philip Jones; Lennart Martens; Rolf Apweiler; Henning Hermjakob (Nucleic Acids Res., 2008)

PRIDE: new developments and new datasets. - Philip Jones; Richard G. Côté; Sang Yun Cho; Sebastian Klie; Lennart Martens; Antony F. Quinn; David Thorneycroft; Henning Hermjakob (Nucleic Acids Res., 2008)

ISPIDER Central: an integrated database web-server for proteomics. - Jennifer A. Siepen; Khalid Belhajjame; Julian N. Selley; Suzanne M. Embury; Norman W. Paton; Carole A. Goble; Stephen G. Oliver; Robert Stevens 001; Lucas Zamboulis; Nigel J. Martin 001; Alexandra Poulovassilis; Philip Jones; et al. (Nucleic Acids Res., 2008)

Reactome knowledgebase of human biological pathways and processes. - Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft 001; Bernard de Bono; Phani V. Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alexander Kanapin; Suzanna Lewis; et al. (Nucleic Acids Res., 2009)

The systematic annotation of the three main GPCR families in Reactome. - Bijay Jassal; Steven Jupe; Michael Caudy; Ewan Birney; Lincoln Stein; Henning Hermjakob; Peter D'Eustachio (Database J. Biol. Databases Curation, 2010)

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. - Alexey V. Antonov; Esther Schmidt; Sabine Dietmann; Maria Krestyaninova; Henning Hermjakob (Nucleic Acids Res., 2010)

The IntAct molecular interaction database in 2010. - Bruno Aranda; P. Achuthan; Yasmin Alam-Faruque; Irina M. Armean; Alan J. Bridge; C. Derow; Marc Feuermann; A. T. Ghanbarian; Samuel Kerrien; Jyoti Khadake; Jules Kerssemakers; C. Leroy; et al. (Nucleic Acids Res., 2010)

The Ontology Lookup Service: bigger and better. - Richard G. Côté; Florian Reisinger; Lennart Martens; Harald Barsnes; Juan Antonio Vizcaíno; Henning Hermjakob (Nucleic Acids Res., 2010)

The Proteomics Identifications database: 2010 update. - Juan Antonio Vizcaíno; Richard G. Côté; Florian Reisinger; Harald Barsnes; Joseph M. Foster; Jonathan Rameseder; Henning Hermjakob; Lennart Martens (Nucleic Acids Res., 2010)

The Reactome BioMart. - Robin Haw; David Croft 001; Christina K. Yung; Nelson Ndegwa; Peter D'Eustachio; Henning Hermjakob; Lincoln D. Stein (Database J. Biol. Databases Curation, 2011)

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. - Nelson Ndegwa; Richard G. Côté; David Ovelleiro; Peter D'Eustachio; Henning Hermjakob; Juan Antonio Vizcaíno; David Croft 001 (Database J. Biol. Databases Curation, 2011)

Dasty3, a WEB framework for DAS. - Jose M. Villaveces; Rafael C. Jiménez; Leyla J. García; Gustavo A. Salazar; Bernat Gel; Nicola J. Mulder; Maria Jesus Martin; Alexander García Castro; Henning Hermjakob (Bioinform., 2011)

easyDAS: Automatic creation of DAS servers. - Bernat Gel; Andrew M. Jenkinson; Rafael C. Jiménez; Xavier Messeguer Peypoch; Henning Hermjakob (BMC Bioinform., 2011)

DAS Writeback: A Collaborative Annotation System. - Gustavo A. Salazar; Rafael C. Jiménez; Alexander García Castro; Henning Hermjakob; Nicola J. Mulder; Edwin H. Blake (BMC Bioinform., 2011)

Reactome: a database of reactions, pathways and biological processes. - David Croft 001; Gavin O'Kelly; Guanming Wu; Robin Haw; Marc Gillespie; Lisa Matthews; Michael Caudy; Phani V. Garapati; Gopal Gopinath; Bijay Jassal; Steven Jupe; Irina Kalatskaya; et al. (Nucleic Acids Res., 2011)

Delivering 'Cool URIs' That Do Not Change. - Nick S. Juty; Nicolas Le Novère; Henning Hermjakob; Camille Laibe (SWAT4LS, 2012)

PRIDE: Quality control in a proteomics data repository. - Attila Csordas; David Ovelleiro; Rui Wang; Joseph M. Foster; Daniel Rios; Juan Antonio Vizcaíno; Henning Hermjakob (Database J. Biol. Databases Curation, 2012)

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. - Steven Lewis; Attila Csordas; Sarah A. Killcoyne; Henning Hermjakob; Michael R. Hoopmann; Robert L. Moritz; Eric W. Deutsch; John Boyle (BMC Bioinform., 2012)

The IntAct molecular interaction database in 2012. - Samuel Kerrien; Bruno Aranda; Lionel Breuza; Alan J. Bridge; Fiona Broackes-Carter; Carol Chen; Margaret J. Duesbury; Marine Dumousseau; Marc Feuermann; Ursula Hinz; Christine Jandrasits; Rafael C. Jiménez; et al. (Nucleic Acids Res., 2012)

Improvements in the protein identifier cross-reference service. - Samuel P. Wein; Richard G. Côté; Marine Dumousseau; Florian Reisinger; Henning Hermjakob; Juan Antonio Vizcaíno (Nucleic Acids Res., 2012)

The Apoptosis Gene Ontology project and the IntAct-Apoptosis dataset: updating the conceptual representation of apoptosis. - Pablo Porras; Paola Roncaglia; Emily Dimmer; Jane Lomax; Rachael P. Huntley; Sandra E. Orchard; Marine Dumousseau; Samuel Kerrien; Henning Hermjakob (IWBBIO, 2013)

Towards the Collaborative Curation of the Registry underlying identifiers.org. - Nick S. Juty; Nicolas Le Novère; Henning Hermjakob; Camille Laibe (Database J. Biol. Databases Curation, 2013)

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. - Gerhard Mayer; Luisa Montecchi-Palazzi; David Ovelleiro; Andrew R. Jones; Pierre-Alain Binz; Eric W. Deutsch; Matthew Chambers; Marius Kallhardt; Fredrik Levander; James Shofstahl; Sandra E. Orchard; Juan Antonio Vizcaíno; et al. (Database J. Biol. Databases Curation, 2013)

Capturing cooperative interactions with the PSI-MI format. - Kim Van Roey; Sandra E. Orchard; Samuel Kerrien; Marine Dumousseau; Sylvie Ricard-Blum; Henning Hermjakob; Toby J. Gibson (Database J. Biol. Databases Curation, 2013)

BioJS: an open source JavaScript framework for biological data visualization. - John Gómez; Leyla J. García; Gustavo A. Salazar; Jose M. Villaveces; Swanand P. Gore; Alexander García Castro; Maria Jesus Martin; Guillaume Launay; Rafael Alcántara; Noemi del-Toro; Marine Dumousseau; Sandra E. Orchard; et al. (Bioinform., 2013)

iAnn: an event sharing platform for the life sciences. - Rafael C. Jiménez; Juan P. Albar; Jong Bhak; Marie-Claude Blatter; Thomas Blicher; Michelle D. Brazas; Catherine Brooksbank; Aidan Budd; Javier De Las Rivas; Jacqueline Dreyer; Marc A. van Driel; Michael J. Dunn; et al. (Bioinform., 2013)

Path2Models: large-scale generation of computational models from biochemical pathway maps. - Finja Büchel; Nicolas Rodriguez 001; Neil Swainston; Clemens Wrzodek; Tobias Czauderna; Roland Keller; Florian Mittag; Michael Schubert; Mihai Glont; Martin Golebiewski; Martijn P. van Iersel; Sarah M. Keating; et al. (BMC Syst. Biol., 2013)

The EBI enzyme portal. - Rafael Alcántara; Joseph Onwubiko; Hong Cao; Paula de Matos; Jennifer A. Cham; Julius O. B. Jacobsen; Gemma L. Holliday; Julia D. Fischer; Syed Asad Rahman; Bijay Jassal; Mickael Goujon; Francis Rowland; et al. (Nucleic Acids Res., 2013)

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. - Juan Antonio Vizcaíno; Richard G. Côté; Attila Csordas; José A. Dianes; Antonio Fabregat; Joseph M. Foster; Johannes Griss; Emanuele Alpi; Melih Birim; Javier Contell; Gavin O'Kelly; Andreas Schoenegger; et al. (Nucleic Acids Res., 2013)

A new reference implementation of the PSICQUIC web service. - Noemi del-Toro; Marine Dumousseau; Sandra E. Orchard; Rafael C. Jiménez; Eugenia Galeota; Guillaume Launay; Johannes Goll; Karin Breuer; Keiichiro Ono; Lukasz Salwínski; Henning Hermjakob (Nucleic Acids Res., 2013)

BioModels linked dataset. - Sarala M. Wimalaratne; Pierre Grenon; Henning Hermjakob; Nicolas Le Novère; Camille Laibe (BMC Syst. Biol., 2014)

BioJS: an open source standard for biological visualisation - its status in 2014. - Manuel Corpas; Rafael C. Jiménez; Seth Carbon; Alexander García Castro; Leyla Jael Castro; Tatyana Goldberg; John Gómez; Alex Kalderimis; Suzanna E. Lewis; Ian Mulvany; Aleksandra Pawlik; Francis Rowland; et al. (F1000Research, 2014)

The Reactome pathway knowledgebase. - David Croft 001; Antonio Fabregat Mundo; Robin Haw; Marija Milacic; Joel Weiser; Guanming Wu; Michael Caudy; Phani V. Garapati; Marc Gillespie; Maulik R. Kamdar; Bijay Jassal; Steven Jupe; et al. (Nucleic Acids Res., 2014)

The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. - Sandra E. Orchard; Mais G. Ammari; Bruno Aranda; Lionel Breuza; Leonardo Briganti; Fiona Broackes-Carter; Nancy H. Campbell; Gayatri Chavali; Carol Chen; Noemi del-Toro; Margaret J. Duesbury; Marine Dumousseau; et al. (Nucleic Acids Res., 2014)

BioModels Database: a public repository for sharing models of biological processes. - Vijayalakshmi Chelliah; Nick S. Juty; Camille Laibe; Henning Hermjakob; Nicolas Le Novère (Encyclopedia of Computational Neuroscience, 2014)

Shared resources, shared costs - leveraging biocuration resources. - Sandra E. Orchard; Henning Hermjakob (Database J. Biol. Databases Curation, 2015)

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. - Jose M. Villaveces; Rafael C. Jiménez; Pablo Porras; Noemi del-Toro; Margaret J. Duesbury; Marine Dumousseau; Sandra E. Orchard; H. Choi; Peipei Ping; N. C. Zong; Manor Askenazi; Bianca Habermann; et al. (Database J. Biol. Databases Curation, 2015)

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. - Yasset Pérez-Riverol; Julian Uszkoreit; Aniel Sánchez; Tobias Ternent; Noemi del-Toro; Henning Hermjakob; Juan Antonio Vizcaíno; Rui Wang (Bioinform., 2015)

SPARQL-enabled identifier conversion with Identifiers.org. - Sarala M. Wimalaratne; Jerven T. Bolleman; Nick S. Juty; Toshiaki Katayama; Michel Dumontier; Nicole Redaschi; Nicolas Le Novère; Henning Hermjakob; Camille Laibe (Bioinform., 2015)

Development of data representation standards by the human proteome organization proteomics standards initiative. - Eric W. Deutsch; Juan P. Albar; Pierre-Alain Binz; Martin Eisenacher; Andrew R. Jones; Gerhard Mayer; Gilbert S. Omenn; Sandra E. Orchard; Juan Antonio Vizcaíno; Henning Hermjakob (J. Am. Medical Informatics Assoc., 2015)

BioModels: ten-year anniversary. - Vijayalakshmi Chelliah; Nick S. Juty; Ishan Ajmera; Raza Ali; Marine Dumousseau; Mihai Glont; Michael Hucka; Gaël Jalowicki; Sarah M. Keating; Vincent Knight-Schrijver; Audald Lloret-Villas; Kedar Nath Natarajan; et al. (Nucleic Acids Res., 2015)

The complex portal - an encyclopaedia of macromolecular complexes. - Birgit H. M. Meldal; Oscar Forner-Martinez; Maria C. Costanzo; Jose M. Dana; Janos Demeter; Marine Dumousseau; Selina S. Dwight; Anna Gaulton; Luana Licata; Anna N. Melidoni; Sylvie Ricard-Blum; Bernd Roechert; et al. (Nucleic Acids Res., 2015)

Introducing the PRIDE Archive RESTful web services. - Florian Reisinger; Noemi del-Toro; Tobias Ternent; Henning Hermjakob; Juan Antonio Vizcaíno (Nucleic Acids Res., 2015)

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. - Sushil Tripathi; Steven Vercruysse; Konika Chawla; Karen R. Christie; Judith A. Blake; Rachael P. Huntley; Sandra E. Orchard; Henning Hermjakob; Liv Thommesen; Astrid Lægreid; Martin Kuiper (Database J. Biol. Databases Curation, 2016)

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. - Enrique Audain; Yassel Ramos; Henning Hermjakob; Darren R. Flower; Yasset Pérez-Riverol (Bioinform., 2016)

Organizational principles of the Reactome human BioPAX model using graph theory methods. - Aristotelis Kittas; Laura Bennett; Henning Hermjakob; Sophia Tsoka (J. Complex Networks, 2016)

The Reactome pathway Knowledgebase. - Antonio Fabregat; Konstantinos Sidiropoulos; Phani V. Garapati; Marc Gillespie; Kerstin Hausmann; Robin Haw; Bijay Jassal; Steven Jupe; Florian Korninger; Sheldon J. McKay; Lisa Matthews; Bruce May; et al. (Nucleic Acids Res., 2016)

2016 update of the PRIDE database and its related tools. - Juan Antonio Vizcaíno; Attila Csordas; Noemi del-Toro; José A. Dianes; Johannes Griss; Ilias Lavidas; Gerhard Mayer; Yasset Pérez-Riverol; Florian Reisinger; Tobias Ternent; Qing-Wei Xu; Rui Wang; et al. (Nucleic Acids Res., 2016)

ComplexViewer: visualization of curated macromolecular complexes. - Colin W. Combe; Marine Sivade; Henning Hermjakob; Joshua Heimbach; Birgit H. M. Meldal; Gos Micklem; Sandra E. Orchard; Juri Rappsilber (Bioinform., 2017)

Reactome enhanced pathway visualization. - Konstantinos Sidiropoulos; Guilherme Viteri; Cristoffer Sevilla; Steven Jupe; Marissa Webber; Marija Orlic-Milacic; Bijay Jassal; Bruce May; Veronica Shamovsky; Corina Duenas; Karen Rothfels; Lisa Matthews; et al. (Bioinform., 2017)

Reactome pathway analysis: a high-performance in-memory approach. - Antonio Fabregat; Konstantinos Sidiropoulos; Guilherme Viteri; Oscar Forner-Martinez; Pablo Marín-García; Vicente Arnau; Peter D'Eustachio; Lincoln Stein; Henning Hermjakob (BMC Bioinform., 2017)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. - Eric W. Deutsch; Attila Csordas; Zhi Sun; Andrew F. Jarnuczak; Yasset Pérez-Riverol; Tobias Ternent; David S. Campbell; Manuel Bernal Llinares; Shujiro Okuda; Shin Kawano; Robert L. Moritz; Jeremy Carver; et al. (Nucleic Acids Res., 2017)

Open Targets: a platform for therapeutic target identification and validation. - Gautier Koscielny; Peter An; Denise Carvalho-Silva; Jennifer A. Cham; Luca Fumis; Rippa Gasparyan; Samiul Hasan; Nikiforos Karamanis; Michael Maguire; Eliseo Papa; Andrea Pierleoni; Miguel Pignatelli; et al. (Nucleic Acids Res., 2017)

AAgAtlas 1.0: a human autoantigen database. - Dan Wang; Liuhui Yang; Ping Zhang; Joshua LaBaer; Henning Hermjakob; Dong Li; Xiaobo Yu (Nucleic Acids Res., 2017)

Reactome diagram viewer: data structures and strategies to boost performance. - Antonio Fabregat; Konstantinos Sidiropoulos; Guilherme Viteri; Pablo Marín-García; Peipei Ping; Lincoln Stein; Peter D'Eustachio; Henning Hermjakob (Bioinform., 2018)

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. - M. Sivade Dumousseau; Diego Alonso-López; Mais G. Ammari; Glyn Bradley; Nancy H. Campbell; Arnaud Céol; Gianni Cesareni; Colin W. Combe; Javier De Las Rivas; Noemi del-Toro; Joshua Heimbach; Henning Hermjakob; et al. (BMC Bioinform., 2018)

A pipeline for identifying endogenous neuropeptides from spectral archives. - Mingze Bai; Mingmin He; Qifeng Sun; Huadong Liao; Kunxian Shu; Henning Hermjakob (Int. J. Data Min. Bioinform., 2018)

The Reactome Pathway Knowledgebase. - Antonio Fabregat; Steven Jupe; Lisa Matthews; Konstantinos Sidiropoulos; Marc Gillespie; Phani V. Garapati; Robin Haw; Bijay Jassal; Florian Korninger; Bruce May; Marija Milacic; Corina Duenas; et al. (Nucleic Acids Res., 2018)

BioModels: expanding horizons to include more modelling approaches and formats. - Mihai Glont; Tung V. N. Nguyen; Martin Graesslin; Robert Hälke; Raza Ali; Jochen Schramm; Sarala M. Wimalaratne; Varun B. Kothamachu; Nicolas Rodriguez 001; Maciej J. Swat; Jurgen Eils; Roland Eils; et al. (Nucleic Acids Res., 2018)

Reactome graph database: Efficient access to complex pathway data. - Antonio Fabregat; Florian Korninger; Guilherme Viteri; Konstantinos Sidiropoulos; Pablo Marín-García; Peipei Ping; Guanming Wu; Lincoln Stein; Peter D'Eustachio; Henning Hermjakob (PLoS Comput. Biol., 2018)

Reactome and ORCID - fine-grained credit attribution for community curation. - Guilherme Viteri; Lisa Matthews; Thawfeek M. Varusai; Marc Gillespie; Marija Milacic; Justin Cook; Joel Weiser; Solomon Shorser; Konstantinos Sidiropoulos; Antonio Fabregat; Robin Haw; Guanming Wu; et al. (Database J. Biol. Databases Curation, 2019)

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. - Livia Perfetto; Marcio Luis Acencio; Glyn Bradley; Gianni Cesareni; Noemi del-Toro; Dávid Fazekas; Henning Hermjakob; Tamás Korcsmáros; Martin Kuiper; Astrid Lægreid; Prisca Lo Surdo; Ruth C. Lovering; et al. (Bioinform., 2019)

iProX: an integrated proteome resource. - Jie Ma; Tao Chen 005; Songfeng Wu; Chunyuan Yang; Mingze Bai; Kunxian Shu; Kenli Li 001; Guoqing Zhang 006; Zhong Jin; Fuchu He; Henning Hermjakob; Yunping Zhu (Nucleic Acids Res., 2019)

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. - Birgit H. M. Meldal; Hema Bye-A-Jee; Lukás Gajdos; Zuzana Hammerová; Aneta Horácková; Filip Melicher; Livia Perfetto; Daniel Pokorný; Milagros Rodríguez-López; Alzbeta Türková; Edith D. Wong; Zengyan Xie; et al. (Nucleic Acids Res., 2019)

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. - Livia Perfetto; Chiara Pastrello; Noemi del-Toro; Margaret J. Duesbury; Marta Iannuccelli; Max Kotlyar; Luana Licata; Birgit Meldal; Kalpana Panneerselvam; Simona Panni; N. Rahimzadeh; Sylvie Ricard-Blum; et al. (Database J. Biol. Databases Curation, 2020)

BioModels Parameters: a treasure trove of parameter values from published systems biology models. - Mihai Glont; Chinmay Arankalle; Krishan K. Tiwari; Tung V. N. Nguyen; Henning Hermjakob; Rahuman S. Malik-Sheriff (Bioinform., 2020)

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). - Dagmar Waltemath; Martin Golebiewski; Michael L. Blinov; Padraig Gleeson; Henning Hermjakob; Michael Hucka; Esther Thea Inau; Sarah M. Keating; Matthias König 003; Olga Krebs; Rahuman S. Malik-Sheriff; David P. Nickerson; et al. (J. Integr. Bioinform., 2020)

The omics discovery REST interface. - Gaurhari Dass; Manh-Tu Vu; Pan Xu; Enrique Audain; Marc-Phillip Hitz; Björn A. Grüning; Henning Hermjakob; Yasset Pérez-Riverol (Nucleic Acids Res., 2020)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

The reactome pathway knowledgebase. - Bijay Jassal; Lisa Matthews; Guilherme Viteri; Chuqiao Gong; Pascual Lorente; Antonio Fabregat; Konstantinos Sidiropoulos; Justin Cook; Marc Gillespie; Robin Haw; Fred Loney 001; Bruce May; et al. (Nucleic Acids Res., 2020)

BioModels - 15 years of sharing computational models in life science. - Rahuman S. Malik-Sheriff; Mihai Glont; Tung V. N. Nguyen; Krishan K. Tiwari; Matthew G. Roberts; Ashley Xavier; Manh T. Vu; Jinghao Men; Matthieu Maire; Sarubini Kananathan; Emma L. Fairbanks; Johannes P. Meyer; et al. (Nucleic Acids Res., 2020)

PhaSepDB: a database of liquid-liquid phase separation related proteins. - Kaiqiang You; Qi Huang; Chunyu Yu; Boyan Shen; Cristoffer Sevilla; Minglei Shi; Henning Hermjakob; Yang Chen 053; Tingting Li (Nucleic Acids Res., 2020)

A decoupled, modular and scriptable architecture for tools to curate data platforms. - Momo Langenstein; Henning Hermjakob; Manuel Bernal Llinares (Bioinform., 2021)

Identifiers.org: Compact Identifier services in the cloud. - Manuel Bernal Llinares; Javier Ferrer-Gómez; Nick S. Juty; Carole A. Goble; Sarala M. Wimalaratne; Henning Hermjakob (Bioinform., 2021)

IntAct App: a Cytoscape application for molecular interaction network visualization and analysis. - Eliot Ragueneau; Anjali Shrivastava; John H. Morris; Noemi del-Toro; Henning Hermjakob; Pablo Porras (Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Vasundra Touré; Steven Vercruysse; Marcio Luis Acencio; Ruth C. Lovering; Sandra E. Orchard; Glyn Bradley; Cristina Casals-Casas; Claudine Chaouiya; Noemi del-Toro; Åsmund Flobak; Pascale Gaudet; Henning Hermjakob; et al. (Bioinform., 2021)

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. - Anna Niarakis; Dagmar Waltemath; James A. Glazier; Falk Schreiber; Sarah M. Keating; David P. Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomás Helikar; Sylvain Soliman; et al. (Briefings Bioinform., 2022)

KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study. - Barbara Füzi; Rahuman S. Malik-Sheriff; Emma J. Manners; Henning Hermjakob; Gerhard F. Ecker (J. Cheminformatics, 2022)

The European Bioinformatics Institute (EMBL-EBI) in 2021. - Gaia Cantelli; Alex Bateman; Cath Brooksbank; Anton I. Petrov; Rahuman S. Malik-Sheriff; Michele Ide-Smith; Henning Hermjakob; Paul Flicek; Rolf Apweiler; Ewan Birney; Johanna R. McEntyre (Nucleic Acids Res., 2022)

iProX in 2021: connecting proteomics data sharing with big data. - Tao Chen 005; Jie Ma; Yi Liu; Zhiguang Chen 001; Nong Xiao 001; Yutong Lu; Yinjin Fu; Chunyuan Yang; Mansheng Li; Songfeng Wu; Xue Wang; Dongsheng Li; et al. (Nucleic Acids Res., 2022)

The reactome pathway knowledgebase 2022. - Marc Gillespie; Bijay Jassal; Ralf Stephan; Marija Milacic; Karen Rothfels; Andrea Senff-Ribeiro; Johannes Griss; Cristoffer Sevilla; Lisa Matthews; Chuqiao Gong; Chuan Deng; Thawfeek M. Varusai; et al. (Nucleic Acids Res., 2022)

Complex Portal 2022: new curation frontiers. - Birgit H. M. Meldal; Livia Perfetto; Colin W. Combe; Tiago Lubiana; João Vitor Ferreira Cavalcante; Hema Bye-A-Jee; Andra Waagmeester; Noemi del-Toro; Anjali Shrivastava; Elisabet Barrera; Edith D. Wong; Bernhard Mlecnik; et al. (Nucleic Acids Res., 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

The IntAct database: efficient access to fine-grained molecular interaction data. - Noemi del-Toro; Anjali Shrivastava; Eliot Ragueneau; Birgit Meldal; Colin W. Combe; Elisabet Barrera; Livia Perfetto; Karyn How; Prashansa Ratan; Gautam Shirodkar; Odilia Lu; Bálint Mészáros; et al. (Nucleic Acids Res., 2022)

The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study. - Simona Panni; Kalpana Panneerselvam; Pablo Porras; Margaret J. Duesbury; Livia Perfetto; Luana Licata; Henning Hermjakob; Sandra E. Orchard (Database J. Biol. Databases Curation, 2023)

Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness. - Romain David 001; Audrey S. Richard; Claire Connellan; Katharina B. Lauer; Maria Luisa Chiusano; Carole A. Goble; Martin Houde; Isabel Kemmer; Antje Keppler; Philippe Lieutaud; Christian Ohmann; Maria Panagiotopoulou; et al. (Data Sci. J., 2023)

Building an Ethical and Trustworthy Biomedical AI Ecosystem for the Translational and Clinical Integration of Foundational Models. - Simha Sankar Baradwaj; Destiny Gilliland; Jack Rincon; Henning Hermjakob; Yu Yan; Irsyad Adam; Gwyneth Lemaster; Dean Wang; Karol E. Watson; Alex A. T. Bui; Wei Wang; Peipei Ping (CoRR, 2024)

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. - Marija Orlic-Milacic; Karen Rothfels; Lisa Matthews; Adam J. Wright; Bijay Jassal; Veronica Shamovsky; Quang M. Trinh; Marc Gillespie; Cristoffer Sevilla; Krishna Tiwari; Eliot Ragueneau; Chuqiao Gong; et al. (Database J. Biol. Databases Curation, 2024)

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. - Marija Orlic-Milacic; Karen Rothfels; Lisa Matthews; Adam J. Wright; Bijay Jassal; Veronica Shamovsky; Quang M. Trinh; Marc Gillespie; Cristoffer Sevilla; Krishna Tiwari; Eliot Ragueneau; Chuqiao Gong; et al. (Zenodo, 2024)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)