Ioannis Xenarios

Thierry Schüpbach, Marco Pagni, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, Lorenzo Cerutti: pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinformatics 29(9): 1215-1217 (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 Bioinformatics 14: 104 (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 Research 41(Database-Issue): 344-347 (2013)

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 Research 41(Database-Issue): 579-583 (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 Research 41(Database-Issue): 584-589 (2013)

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 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, 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 Research 40(Database-Issue): 565-570 (2012)

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 Research 40(Database-Issue): 754-760 (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 Research 40(Database-Issue): 761-769 (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 Research 40(Web-Server-Issue): 597-603 (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 in Bioinformatics 12(5): 423-435 (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. Bioinformatics 27(10): 1404-1412 (2011)

Oksana Riba-Grognuz, Laurent Keller, Laurent Falquet, Ioannis Xenarios, Yannick Wurm: Visualization and quality assessment of de novo genome assemblies. Bioinformatics 27(24): 3425-3426 (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 Research 39(Database-Issue): 576-582 (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 Research 39(Web-Server-Issue): 13-17 (2011)

Thierry Schüpbach, Ioannis Xenarios, Sven Bergmann, Karen Kapur: FastEpistasis: a high performance computing solution for quantitative trait epistasis. Bioinformatics 26(11): 1468-1469 (2010)

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. Bioinformatics 25(5): 662-663 (2009)

Abhishek Garg, Kartik Mohanram, Alessandro Di Cara, Giovanni De Micheli, Ioannis Xenarios: Modeling stochasticity and robustness in gene regulatory networks. Bioinformatics 25(12) (2009)

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 Bioinformatics 10 (2009)

Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont: The Microbe browser for comparative genomics. Nucleic Acids Research 37(Web-Server-Issue): 296-299 (2009)

Abhishek Garg, Alessandro Di Cara, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli: Synchronous versus asynchronous modeling of gene regulatory networks. Bioinformatics 24(17): 1917-1925 (2008)

Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef: Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 9 (2008)

Sébastien Moretti, Andreas Wilm, Desmond G. Higgins, Ioannis Xenarios, Cédric Notredame: R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Research 36(Web-Server-Issue): 10-13 (2008)

Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza: Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics 8 (2007)

Abhishek Garg, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli: An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments. RECOMB 2007: 62-76

Ioannis Xenarios, Lukasz Salwínski, Xiaoqun Joyce Duan, Patrick Higney, Sul-Min Kim, David Eisenberg: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Research 30(1): 303-305 (2002)

Edward M. Marcotte, Ioannis Xenarios, David Eisenberg: Mining literature for protein-protein interactions. Bioinformatics 17(4): 359-363 (2001)

Ioannis Xenarios, Esteban Fernandez, Lukasz Salwínski, Xiaoqun Joyce Duan, Michael J. Thompson, Edward M. Marcotte, David Eisenberg: DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Research 29(1): 239-241 (2001)

Ioannis Xenarios, Danny W. Rice, Lukasz Salwínski, Marisa K. Baron, Edward M. Marcotte, David Eisenberg: DIP: the Database of Interacting Proteins. Nucleic Acids Research 28(1): 289-291 (2000)