Ioannis Xenarios

Publication Activity (10 Years)

Years Active: 2000-2022
Publications (10 Years): 17

Top Topics

Protein Families

Chemical Reactions

Dynamical Model

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

PLoS Comput. Biol.

Publications

Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios
Towards mouse genetic-specific RNA-sequencing read mapping. PLoS Comput. Biol. 18 (9) (2022)
Rick Wertenbroek, Simone Rubinacci, Ioannis Xenarios, Yann Thoma, Olivier Delaneau
XSI - a genotype compression tool for compressive genomics in large biobanks. Bioinform. 38 (15) (2022)
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, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
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. Briefings Bioinform. 22 (2) (2021)
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, Filip Claes, Scott H. Newman, Marc A. Suchard, Guy Baele, Marius Gilbert
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. Bioinform. 36 (7) (2020)
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, Ioannis Xenarios, Sylvain Poux, Nicole Redaschi, Alan Bridge, The UniProt Consortium
Enzyme annotation in UniProtKB using Rhea. Bioinform. 36 (6) (2020)
Amel Bekkar, Anita Nasrallah, Nicolas Guex, Lluis Fajas, Ioannis Xenarios, Isabel C. Lopez-Mejia
PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. Bioinform. 36 (20) (2020)
Thierry Lombardot, Anne Morgat, Kristian B. Axelsen, Lucila Aimo, Nevila Hyka-Nouspikel, Anne Niknejad, Alexandr Ignatchenko, Ioannis Xenarios, Elisabeth Coudert, Nicole Redaschi, Alan Bridge
Updates in Rhea: SPARQLing biochemical reaction data. Nucleic Acids Res. 47 (Database-Issue) (2019)
Maria Livia Famiglietti, Anne Estreicher, Lionel Breuza, Sylvain Poux, Nicole Redaschi, Ioannis Xenarios, Alan Bridge
An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. Database J. Biol. Databases Curation 2019 (2019)
Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline A. L. MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Comput. Biol. 14 (8) (2018)
Simone Casale Brunet, Thierry Schüpbach, Nicolas Guex, Christian Iseli, Alan Bridge, Dmitry Kuznetsov, Christian J. A. Sigrist, Phillippe Lemercier, Ioannis Xenarios, Endri Bezati
Towards in the Field Fast Pathogens Detection Using FPGAs. FPL (2018)
Amel Bekkar, Anne Estreicher, Anne Niknejad, Cristina Casals-Casas, Alan Bridge, Ioannis Xenarios, Julien Dorier, Isaac Crespo
Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. Database J. Biol. Databases Curation 2018 (2018)
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, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan Bridge
Updates in Rhea - an expert curated resource of biochemical reactions. Nucleic Acids Res. 45 (Database-Issue) (2017)
Sara Schulthess, Anastasia Chasapi, Ioannis Xenarios, Martial Sankar, Claire Clivaz
HumaReC project: digital New Testament and continuous data publishing. DH (2017)
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45 (Database-Issue) (2017)
Megan Druce, Chantal Hulo, Patrick Masson, Paula Sommer, Ioannis Xenarios, Philippe Le Mercier, Tulio de Oliveira
Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. Database J. Biol. Databases Curation 2016 (2016)
Ayush Singhal, Robert Leaman, Natalie L. Catlett, Thomas Lemberger, Johanna R. McEntyre, Shawn W. Polson, Ioannis Xenarios, Cecilia N. Arighi, Zhiyong Lu
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database J. Biol. Databases Curation 2016 (2016)
Julien Dorier, Isaac Crespo, Anne Niknejad, Robin Liechti, Martin Ebeling, Ioannis Xenarios
Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method. BMC Bioinform. 17 (2016)
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, Alan Bridge
The SwissLipids knowledgebase for lipid biology. Bioinform. 31 (17) (2015)
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. 31 (7) (2015)
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, Abhishek Garg, Khalil Zaman, Hans-Anton Lehr, Brian J. Stevenson, Curzio Rüegg, George Coukos, Jean-François Delaloye, Ioannis Xenarios, Marie-Agnes Doucey
Angiogenic Activity of Breast Cancer Patients' Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches. PLoS Comput. Biol. 11 (3) (2015)
Elke Schaper, Alexander Korsunsky, Julija Pecerska, Antonio Messina, Riccardo Murri, Heinz Stockinger, Stefan Zoller, Ioannis Xenarios, Maria Anisimova
TRAL: tandem repeat annotation library. Bioinform. 31 (18) (2015)
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, Christoph Steinbeck, Ioannis Xenarios, Alan Bridge
Updates in Rhea - a manually curated resource of biochemical reactions. Nucleic Acids Res. 43 (Database-Issue) (2015)
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, Alan Bridge
HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res. 43 (Database-Issue) (2015)
Alex L. Mitchell, Hsin-Yu Chang, Louise C. Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K. Attwood, Christian J. A. Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt E. Oates, Daniel H. Haft, Hongzhan Huang, Darren A. Natale, Cathy H. Wu, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas, Robert D. Finn
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43 (Database-Issue) (2015)
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, Olivier Michielin, Patricia M. Palagi, Jacques Rougemont, Torsten Schwede, Christian von Mering, Erik van Nimwegen, Daniel Walther, Ioannis Xenarios, Mihaela Zavolan, Evgeny M. Zdobnov, Vincent Zoete, Ron D. Appel
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Antonio Rausell, Pejman Mohammadi, Paul J. McLaren, István Bartha, Ioannis Xenarios, Jacques Fellay, Amalio Telenti
Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes. PLoS Comput. Biol. 10 (7) (2014)
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, Philippe Le Mercier, Ioannis Xenarios, Gwenaelle Dauphin
The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. Database J. Biol. Databases Curation 2014 (2014)
Thomas Bernard, Alan Bridge, Anne Morgat, Sébastien Moretti, Ioannis Xenarios, Marco Pagni
Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings Bioinform. 15 (1) (2014)
Patrick Masson, Chantal Hulo, Edouard De Castro, Hans Bitter, Lore Gruenbaum, Laurent Essioux, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier
ViralZone: recent updates to the virus knowledge resource. Nucleic Acids Res. 41 (Database-Issue) (2013)
Anne-Lise Veuthey, Alan Bridge, Julien Gobeill, Patrick Ruch, Johanna R. McEntyre, Lydie Bougueleret, Ioannis Xenarios
Application of text-mining for updating protein post-translational modification annotation in UniProtKB. BMC Bioinform. 14 (2013)
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
Marco Pagni, Hélène Niculita-Hirzel, Loïc Pellissier, Anne Dubuis, Ioannis Xenarios, Antoine Guisan, Ian R. Sanders, Jérôme Goudet, Nicolas Guex
Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1. Bioinform. 29 (10) (2013)
Thierry Schüpbach, Marco Pagni, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, Lorenzo Cerutti
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinform. 29 (9) (2013)
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, Alan Bridge
HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 41 (Database-Issue) (2013)
Christian J. A. Sigrist, Edouard De Castro, Lorenzo Cerutti, Béatrice A. Cuche, Nicolas Hulo, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios
New and continuing developments at PROSITE. Nucleic Acids Res. 41 (Database-Issue) (2013)
Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinform. 29 (13) (2013)
Rafael Alcántara, Kristian B. Axelsen, Anne Morgat, Eugeni Belda, Elisabeth Coudert, Alan Bridge, Hong Cao, Paula de Matos, Marcus Ennis, Steve Turner, Gareth Owen, Lydie Bougueleret, Ioannis Xenarios, Christoph Steinbeck
Rhea - a manually curated resource of biochemical reactions. Nucleic Acids Res. 40 (Database-Issue) (2012)
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, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan Bridge, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek-Roggli, Ioannis Xenarios, Rolf Apweiler
The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 40 (Database-Issue) (2012)
Anne Morgat, Eric Coissac, Elisabeth Coudert, Kristian B. Axelsen, Guillaume Keller, Amos Bairoch, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, Alain Viari
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res. 40 (Database-Issue) (2012)
Sarah W. Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, J. Michael Cherry, Claire O'Donovan, Ioannis Xenarios, Pascale Gaudet
Biocurators and Biocuration: surveying the 21st century challenges. Database J. Biol. Databases Curation 2012 (2012)
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, Vassilios Ioannidis, Dmitri Kuznetsov, Robin Liechti, Sébastien Moretti, Khaled Mostaguir, Nicole Redaschi, Grégoire Rossier, Ioannis Xenarios, Heinz Stockinger
ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings Bioinform. 12 (5) (2011)
Chantal Hulo, Edouard De Castro, Patrick Masson, Lydie Bougueleret, Amos Bairoch, Ioannis Xenarios, Philippe Le Mercier
ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res. 39 (Database-Issue) (2011)
Paolo Di Tommaso, Sébastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, Cédric Notredame
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Martial Sankar, Karen S. Osmont, Jakub Rolcik, Bojan Gujas, Danuse Tarkowska, Miroslav Strnad, Ioannis Xenarios, Christian S. Hardtke
A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. Bioinform. 27 (10) (2011)
Oksana Riba-Grognuz, Laurent Keller, Laurent Falquet, Ioannis Xenarios, Yannick Wurm
genome assemblies. Bioinform. 27 (24) (2011)
Thierry Schüpbach, Ioannis Xenarios, Sven Bergmann, Karen Kapur
FastEpistasis: a high performance computing solution for quantitative trait epistasis. Bioinform. 26 (11) (2010)
Robin Liechti, Anne Gleizes, Dmitry Kuznetsov, Lydie Bougueleret, Philippe Le Mercier, Amos Bairoch, Ioannis Xenarios
OpenFluDB, a database for human and animal influenza virus. Database J. Biol. Databases Curation 2010 (2010)
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, Najib Naamane, Decio L. Eizirik, Lorella Marselli, Marco Bugliani, Piero Marchetti, Stephanie Lucas, Cecilia Holm, C. Victor Jongeneel, Ioannis Xenarios
EuroDia: a beta-cell gene expression resource. Database J. Biol. Databases Curation 2010 (2010)
Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig
MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinform. 10 (2009)
Abhishek Garg, Kartik Mohanram, Alessandro Di Cara, Giovanni De Micheli, Ioannis Xenarios
Modeling stochasticity and robustness in gene regulatory networks. Bioinform. 25 (12) (2009)
Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont
The Microbe browser for comparative genomics. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Olivier Martin, Armand Valsesia, Amalio Telenti, Ioannis Xenarios, Brian J. Stevenson
AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. Bioinform. 25 (5) (2009)
Sébastien Moretti, Andreas Wilm, Desmond G. Higgins, Ioannis Xenarios, Cédric Notredame
R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Abhishek Garg, Alessandro Di Cara, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli
Synchronous versus asynchronous modeling of gene regulatory networks. Bioinform. 24 (17) (2008)
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef
Probabilistic base calling of Solexa sequencing data. BMC Bioinform. 9 (2008)
Abhishek Garg, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli
Gene Perturbation Experiments. RECOMB (2007)
Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza
Dynamic simulation of regulatory networks using SQUAD. BMC Bioinform. 8 (2007)
Ioannis Xenarios, Lukasz Salwínski, Xiaoqun Joyce Duan, Patrick Higney, Sul-Min Kim, David S. Eisenberg
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30 (1) (2002)
Edward M. Marcotte, Ioannis Xenarios, David S. Eisenberg
Mining literature for protein-protein interactions. Bioinform. 17 (4) (2001)
Ioannis Xenarios, Esteban Fernandez, Lukasz Salwínski, Xiaoqun Joyce Duan, Michael J. Thompson, Edward M. Marcotte, David S. Eisenberg
DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res. 29 (1) (2001)
Ioannis Xenarios, Danny W. Rice, Lukasz Salwínski, Marisa K. Baron, Edward M. Marcotte, David S. Eisenberg
DIP: the Database of Interacting Proteins. Nucleic Acids Res. 28 (1) (2000)