DIP: the Database of Interacting Proteins. - Ioannis Xenarios; Danny W. Rice; Lukasz Salwínski; Marisa K. Baron; Edward M. Marcotte; David Eisenberg 001 (Nucleic Acids Res., 2000)

Mining literature for protein-protein interactions. - Edward M. Marcotte; Ioannis Xenarios; David Eisenberg 001 (Bioinform., 2001)

DIP: The Database of Interacting Proteins: 2001 update. - Ioannis Xenarios; Esteban Fernandez 002; Lukasz Salwínski; Xiaoqun Joyce Duan; Michael J. Thompson; Edward M. Marcotte; David Eisenberg 001 (Nucleic Acids Res., 2001)

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. - Ioannis Xenarios; Lukasz Salwínski; Xiaoqun Joyce Duan; Patrick Higney; Sul-Min Kim; David S. Eisenberg (Nucleic Acids Res., 2002)

An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments. - Abhishek Garg; Ioannis Xenarios; Luis Mendoza; Giovanni De Micheli (RECOMB, 2007)

Dynamic simulation of regulatory networks using SQUAD. - Alessandro Di Cara; Abhishek Garg; Giovanni De Micheli; Ioannis Xenarios; Luis Mendoza (BMC Bioinform., 2007)

Synchronous versus asynchronous modeling of gene regulatory networks. - Abhishek Garg; Alessandro Di Cara; Ioannis Xenarios; Luis Mendoza; Giovanni De Micheli (Bioinform., 2008)

Probabilistic base calling of Solexa sequencing data. - Jacques Rougemont; Arnaud Amzallag; Christian Iseli; Laurent Farinelli; Ioannis Xenarios; Felix Naef (BMC Bioinform., 2008)

R-Coffee: a web server for accurately aligning noncoding RNA sequences. - Sébastien Moretti; Andreas Wilm; Desmond G. Higgins; Ioannis Xenarios; Cédric Notredame (Nucleic Acids Res., 2008)

Modeling stochasticity and robustness in gene regulatory networks. - Abhishek Garg; Kartik Mohanram; Alessandro Di Cara; Giovanni De Micheli; Ioannis Xenarios (Bioinform., 2009)

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. - Olivier Martin 002; Armand Valsesia; Amalio Telenti; Ioannis Xenarios; Brian J. Stevenson (Bioinform., 2009)

MIMAS 3.0 is a Multiomics Information Management and Annotation System. - Alexandre Gattiker; Leandro Hermida; Robin Liechti; Ioannis Xenarios; Olivier Collin; Jacques Rougemont; Michael Primig (BMC Bioinform., 2009)

The Microbe browser for comparative genomics. - Alexandre Gattiker; Christophe Dessimoz; Adrian Schneider; Ioannis Xenarios; Marco Pagni; Jacques Rougemont (Nucleic Acids Res., 2009)

EuroDia: a beta-cell gene expression resource. - Robin Liechti; Gábor Csárdi; Sven Bergmann; Frédéric Schütz; Thierry Sengstag; Sylvia F. Boj; Joan-Marc Servitja; Jorge Ferrer; Leentje Van Lommel; Frans Schuit; Sonia Klinger; Bernard Thorens; et al. (Database J. Biol. Databases Curation, 2010)

OpenFluDB, a database for human and animal influenza virus. - Robin Liechti; Anne Gleizes; Dmitry Kuznetsov; Lydie Bougueleret; Philippe Le Mercier; Amos Bairoch; Ioannis Xenarios (Database J. Biol. Databases Curation, 2010)

FastEpistasis: a high performance computing solution for quantitative trait epistasis. - Thierry Schüpbach; Ioannis Xenarios; Sven Bergmann; Karen Kapur (Bioinform., 2010)

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. - Brigitte Boeckmann; Marc Robinson-Rechavi; Ioannis Xenarios; Christophe Dessimoz (Briefings Bioinform., 2011)

Visualization and quality assessment of de novo genome assemblies. - Oksana Riba-Grognuz; Laurent Keller; Laurent Falquet; Ioannis Xenarios; Yannick Wurm (Bioinform., 2011)

A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. - Martial Sankar; Karen S. Osmont; Jakub Rolcik; Bojan Gujas; Danuse Tarkowska; Miroslav Strnad; Ioannis Xenarios; Christian S. Hardtke (Bioinform., 2011)

ViralZone: a knowledge resource to understand virus diversity. - Chantal Hulo; Edouard De Castro; Patrick Masson; Lydie Bougueleret; Amos Bairoch; Ioannis Xenarios; Philippe Le Mercier (Nucleic Acids Res., 2011)

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. - Paolo Di Tommaso; Sébastien Moretti; Ioannis Xenarios; Miquel Orobitg; Alberto Montanyola; Jia-Ming Chang; Jean-François Taly; Cédric Notredame (Nucleic Acids Res., 2011)

Biocurators and Biocuration: surveying the 21st century challenges. - Sarah W. Burge; Teresa K. Attwood; Alex Bateman; Tanya Z. Berardini; J. Michael Cherry; Claire O'Donovan; Ioannis Xenarios; Pascale Gaudet (Database J. Biol. Databases Curation, 2012)

Rhea - a manually curated resource of biochemical reactions. - Rafael Alcántara; Kristian B. Axelsen; Anne Morgat; Eugeni Belda; Elisabeth Coudert; Alan J. Bridge; Hong Cao; Paula de Matos; Marcus Ennis; Steve Turner; Gareth I. Owen; Lydie Bougueleret; et al. (Nucleic Acids Res., 2012)

ExPASy: SIB bioinformatics resource portal. - Panu Artimo; Manohar Jonnalagedda; Konstantin Arnold; Delphine Baratin; Gábor Csárdi; Edouard De Castro; Severine Duvaud; Volker Flegel; Arnaud Fortier; Elisabeth Gasteiger; Aurélien Grosdidier; Céline Hernandez; et al. (Nucleic Acids Res., 2012)

The UniProt-GO Annotation database in 2011. - Emily C. Dimmer; Rachael P. Huntley; Yasmin Alam-Faruque; Tony Sawford; Claire O'Donovan; Maria Jesus Martin; Benoit Bely; Paul Browne; Wei Mun Chan; Ruth Y. Eberhardt; Michael Gardner; Kati Laiho; et al. (Nucleic Acids Res., 2012)

UniPathway: a resource for the exploration and annotation of metabolic pathways. - Anne Morgat; Eric Coissac; Elisabeth Coudert; Kristian B. Axelsen; Guillaume Keller; Amos Bairoch; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios; Alain Viari (Nucleic Acids Res., 2012)

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. - Nicola Bonzanni; Abhishek Garg; K. Anton Feenstra; Judith Schütte; Sarah Kinston; Diego Miranda-Saavedra; Jaap Heringa; Ioannis Xenarios; Berthold Göttgens (Bioinform., 2013)

Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1. - Marco Pagni; Hélène Niculita-Hirzel; Loïc Pellissier; Anne Dubuis; Ioannis Xenarios; Antoine Guisan; Ian R. Sanders; Jérôme Goudet; Nicolas Guex (Bioinform., 2013)

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. - Thierry Schüpbach; Marco Pagni; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios; Lorenzo Cerutti (Bioinform., 2013)

Application of text-mining for updating protein post-translational modification annotation in UniProtKB. - Anne-Lise Veuthey; Alan J. Bridge; Julien Gobeill; Patrick Ruch; Johanna R. McEntyre; Lydie Bougueleret; Ioannis Xenarios (BMC Bioinform., 2013)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

ViralZone: recent updates to the virus knowledge resource. - Patrick Masson; Chantal Hulo; Edouard De Castro; Hans Bitter; Lore Gruenbaum; Laurent Essioux; Lydie Bougueleret; Ioannis Xenarios; Philippe Le Mercier (Nucleic Acids Res., 2013)

HAMAP in 2013, new developments in the protein family classification and annotation system. - Ivo Pedruzzi; Catherine Rivoire; Andrea H. Auchincloss; Elisabeth Coudert; Guillaume Keller; Edouard De Castro; Delphine Baratin; Béatrice A. Cuche; Lydie Bougueleret; Sylvain Poux; Nicole Redaschi; Ioannis Xenarios; et al. (Nucleic Acids Res., 2013)

New and continuing developments at PROSITE. - Christian J. A. Sigrist; Edouard De Castro; Lorenzo Cerutti; Béatrice A. Cuche; Nicolas Hulo; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios (Nucleic Acids Res., 2013)

Reconciliation of metabolites and biochemical reactions for metabolic networks. - Thomas Bernard; Alan J. Bridge; Anne Morgat; Sébastien Moretti; Ioannis Xenarios; Marco Pagni (Briefings Bioinform., 2014)

The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. - Filip Claes; Dmitry Kuznetsov; Robin Liechti; Sophie von Dobschütz; Bao Dinh Truong; Anne Gleizes; Daniele Conversa; Alessandro Colonna; Ettore Demaio; Sabina Ramazzotto; Fairouz Larfaoui; Julio Pinto; et al. (Database J. Biol. Databases Curation, 2014)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes. - Antonio Rausell; Pejman Mohammadi 001; Paul J. McLaren; István Bartha; Ioannis Xenarios; Jacques Fellay; Amalio Telenti (PLoS Comput. Biol., 2014)

The SwissLipids knowledgebase for lipid biology. - Lucila Aimo; Robin Liechti; Nevila Hyka-Nouspikel; Anne Niknejad; Anne Gleizes; Lou Götz; Dmitry Kuznetsov; Fabrice P. A. David; F. Gisou van der Goot; Howard Riezman; Lydie Bougueleret; Ioannis Xenarios; et al. (Bioinform., 2015)

Cooperative development of logical modelling standards and tools with CoLoMoTo. - Aurélien Naldi; Pedro T. Monteiro 001; Christoph Müssel; Hans A. Kestler; Denis Thieffry; Ioannis Xenarios; Julio Saez-Rodriguez; Tomás Helikar; Claudine Chaouiya (Bioinform., 2015)

TRAL: tandem repeat annotation library. - Elke Schaper; Alexander Korsunsky; Julija Pecerska; Antonio Messina; Riccardo Murri; Heinz Stockinger; Stefan Zoller; Ioannis Xenarios; Maria Anisimova (Bioinform., 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)

Updates in Rhea - a manually curated resource of biochemical reactions. - Anne Morgat; Kristian B. Axelsen; Thierry Lombardot; Rafael Alcántara; Lucila Aimo; Mohamed Zerara; Anne Niknejad; Eugeni Belda; Nevila Hyka-Nouspikel; Elisabeth Coudert; Nicole Redaschi; Lydie Bougueleret; et al. (Nucleic Acids Res., 2015)

HAMAP in 2015: updates to the protein family classification and annotation system. - Ivo Pedruzzi; Catherine Rivoire; Andrea H. Auchincloss; Elisabeth Coudert; Guillaume Keller; Edouard De Castro; Delphine Baratin; Béatrice A. Cuche; Lydie Bougueleret; Sylvain Poux; Nicole Redaschi; Ioannis Xenarios; et al. (Nucleic Acids Res., 2015)

Angiogenic Activity of Breast Cancer Patients' Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches. - Nicolas Guex; Isaac Crespo; Sylvian Bron; Assia Ifticene-Treboux; Eveline Faes-van't Hull; Solange Kharoubi; Robin Liechti; Patricia Werffeli; Mark Ibberson; Francois Majo; Michäel Nicolas; Julien Laurent; et al. (PLoS Comput. Biol., 2015)

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. - Megan Druce; Chantal Hulo; Patrick Masson; Paula Sommer; Ioannis Xenarios; Philippe Le Mercier; Tulio de Oliveira (Database J. Biol. Databases Curation, 2016)

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. - Ayush Singhal; Robert Leaman; Natalie L. Catlett; Thomas Lemberger 001; Johanna R. McEntyre; Shawn W. Polson; Ioannis Xenarios; Cecilia N. Arighi; Zhiyong Lu (Database J. Biol. Databases Curation, 2016)

Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method. - Julien Dorier; Isaac Crespo; Anne Niknejad; Robin Liechti; Martin Ebeling; Ioannis Xenarios (BMC Bioinform., 2016)

HumaReC project: digital New Testament and continuous data publishing. - Sara Schulthess; Anastasia Chasapi; Ioannis Xenarios; Martial Sankar; Claire Clivaz (DH, 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)

Updates in Rhea - an expert curated resource of biochemical reactions. - Anne Morgat; Thierry Lombardot; Kristian B. Axelsen; Lucila Aimo; Anne Niknejad; Nevila Hyka-Nouspikel; Elisabeth Coudert; Monica Pozzato; Marco Pagni; Sébastien Moretti; Steven Rosanoff; Joseph Onwubiko; et al. (Nucleic Acids Res., 2017)

Towards in the Field Fast Pathogens Detection Using FPGAs. - Simone Casale Brunet; Thierry Schüpbach; Nicolas Guex; Christian Iseli; Alan J. Bridge; Dmitry Kuznetsov; Christian J. A. Sigrist; Phillippe Lemercier; Ioannis Xenarios; Endri Bezati (FPL, 2018)

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. - Amel Bekkar; Anne Estreicher; Anne Niknejad; Cristina Casals-Casas; Alan J. Bridge; Ioannis Xenarios; Julien Dorier; Isaac Crespo (Database J. Biol. Databases Curation, 2018)

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. - Kyubum Lee; Maria Livia Famiglietti; Aoife McMahon; Chih-Hsuan Wei; Jacqueline A. L. MacArthur; Sylvain Poux; Lionel Breuza; Alan J. Bridge; Fiona Cunningham; Ioannis Xenarios; Zhiyong Lu (PLoS Comput. Biol., 2018)

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. - Maria Livia Famiglietti; Anne Estreicher; Lionel Breuza; Sylvain Poux; Nicole Redaschi; Ioannis Xenarios; Alan J. Bridge (Database J. Biol. Databases Curation, 2019)

Updates in Rhea: SPARQLing biochemical reaction data. - Thierry Lombardot; Anne Morgat; Kristian B. Axelsen; Lucila Aimo; Nevila Hyka-Nouspikel; Anne Niknejad; Alexandr Ignatchenko; Ioannis Xenarios; Elisabeth Coudert; Nicole Redaschi; Alan J. Bridge (Nucleic Acids Res., 2019)

PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. - Amel Bekkar; Anita Nasrallah; Nicolas Guex; Lluis Fajas; Ioannis Xenarios; Isabel C. Lopez-Mejia (Bioinform., 2020)

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. - Simon Dellicour; Philippe Lemey; Jean Artois; Tommy T. Lam; Alice Fusaro; Isabella Monne; Giovanni Cattoli; Dmitry Kuznetsov; Ioannis Xenarios; Gwenaelle Dauphin; Wantanee Kalpravidh; Sophie von Dobschütz; et al. (Bioinform., 2020)

Enzyme annotation in UniProtKB using Rhea. - Anne Morgat; Thierry Lombardot; Elisabeth Coudert; Kristian B. Axelsen; Teresa Batista Neto; Sebastien Gehant; Parit Bansal; Jerven T. Bolleman; Elisabeth Gasteiger; Edouard De Castro; Delphine Baratin; Monica Pozzato; et al. (Bioinform., 2020)

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. - Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S. Malik-Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C. Freeman; Paul D. Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; et al. (Briefings Bioinform., 2021)

XSI - a genotype compression tool for compressive genomics in large biobanks. - Rick Wertenbroek; Simone Rubinacci; Ioannis Xenarios; Yann Thoma; Olivier Delaneau (Bioinform., 2022)

Towards mouse genetic-specific RNA-sequencing read mapping. - Nastassia Gobet; Maxime Jan; Paul Franken; Ioannis Xenarios (PLoS Comput. Biol., 2022)