The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection.

Autor: Chantal Hulo, Patrick Masson, Edouard de Castro, Andrea H Auchincloss, Rebecca Foulger, Sylvain Poux, Jane Lomax, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier

Publikováno v: PLoS ONE, Vol 12, Iss 2, p e0171746 (2017)

Viruses are genetically diverse, infect a wide range of tissues and host cells and follow unique processes for replicating themselves. All these processes were investigated and indexed in ViralZone knowledge base. To facilitate standardizing data, a

Externí odkaz: https://doaj.org/article/27f0129d85384b578f86b2264c1e5a94

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

Autor: Adrian M. Altenhoff, Evgenia V. Kriventseva, Ioannis Xenarios, Brigitte Boeckmann, Christophe Dessimoz, Lydie Bougueleret, David Dylus, Sébastien Moretti, Toni Gabaldón, C-M Train, Eyal Privman

Medium to large phylogenetic gene trees constructed from datasets of different species density and taxonomic range are rarely topologically consistent because of missing phylogenetic signal, non-phylogenetic signal and error. In this study, we first

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fb328d50cefe7878cac991da5f8e27f8

The UniProt-GO Annotation database in 2011

Autor: Rachael P. Huntley, Florence Jungo, Tony Sawford, Harminder Sehra, Shyamala Sundaram, Phillippe Lemercier, Bernd Roechert, Silvia Braconi-Quintaje, Guillaume Keller, Madelaine Moinat, Sylvain Poux, Paul Browne, Rolf Apweiler, Kristian B. Axelsen, Kati Laiho, Andre Stutz, Janet James, Catherine Rivoire, Diego Poggioli, Wei Mun Chan, Ivo Pedruzzi, Anne Estreicher, Silvia Jimenez, Paula Duek Roggli, Michael Gardner, Serenella Ferro-Rojas, Claire O'Donovan, Patrick Masson, Maria Jesus Martin, Michele Magrane, Elizabeth Coudert, Benoit Bely, Michael Tognolli, Emmanuel Boutet, Isabelle Cusin, Andrea H. Auchincloss, Yasmin Alam-Faruque, Klemens Pichler, Nadine Gruaz-Gumowski, Chantal Hulo, Ursula Hinz, Ruth Y. Eberhardt, Duncan Legge, L Famiglietti, E. Dimmer, Michael Schneider, Marc Feuermann, Lionel Breuza, Arnaud Gos, Damien Lieberherr, Ghislaine Argoud-Puy, Marie-Claude Blatter, Lydie Bougueleret, Ioannis Xenarios, Alan Bridge

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, vol. 40, no. Database issue, pp. D565-D570

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 mil

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::841ea9e8f55688773d2ad655152eaaa4
http://doc.rero.ch/record/290953/files/gkr1048.pdf

The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection

Autor: Jane Lomax, Edouard de Castro, Chantal Hulo, Andrea H. Auchincloss, Rebecca E. Foulger, Sylvain Poux, Lydie Bougueleret, Ioannis Xenarios, Patrick Masson, Philippe Le Mercier

Publikováno v: PLoS ONE, Vol 12, Iss 2, p e0171746 (2017)
PLoS ONE

Viruses are genetically diverse, infect a wide range of tissues and host cells and follow unique processes for replicating themselves. All these processes were investigated and indexed in ViralZone knowledge base. To facilitate standardizing data, a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bcb6bbf16cc55dc6785ada5bd4188201
http://europepmc.org/articles/PMC5313201?pdf=render

Activities at the Universal Protein Resource (UniProt)

Autor: Borisas Bursteinas, L-S Yeh, Klemens Pichler, Guillaume Keller, C Casal-Casas, Gerritsen, A Da Silva, Prudence Mutowo, Xavier D. Martin, Peter B. McGarvey, Volynkin, J Lew, K Sonesson, M. C. Blatter, L Pureza, Rodrigo Lopez, Anne Estreicher, Alex Bateman, Ramona Britto, A-L Veuthey, Penelope Garmiri, Patrick Masson, Baris E. Suzek, Cathy H. Wu, Paul Gane, Maria Jesus Martin, Shyamala Sundaram, Yasmin Alam-Faruque, Ioannis Xenarios, Alan Bridge, WM Chan, Guoying Qi, L Famiglietti, Christian J. A. Sigrist, Nadine Gruaz-Gumowski, Chantal Hulo, Hermann Zellner, Matthew Corbett, Monica Pozzato, Thierry Lombardot, S Staehli, Jerven Bolleman, Sylvain Poux, Séverine Duvaud, Tony Sawford, Chuming Chen, Xavier Watkins, Yuqi Wang, Elisabeth Gasteiger, Kati Laiho, Qinghua Wang, M Bingley, Lydie Bougueleret, Kristian B. Axelsen, Yongxing Chen, Salvo Paesano, Andrew Nightingale, Nicole Redaschi, Emma Hatton-Ellis, John S. Garavelli, Delphine Baratin, Darren A. Natale, Gayatri Chavali, E de Castro, Leslie Arminski, Damien Lieberherr, Elena Cibrian-Uhalte, Catherine Rivoire, Bernd Roechert, Yerramalla, Hongzhan Huang, Alistair MacDougall, Edd Turner, Maria Victoria Schneider, Aleksandra Shypitsyna, Jie Zhang, Michele Magrane, Dolnide Dornevil, Lara, M Donnelly, F. Fazzini, Andrea H. Auchincloss, Emanuele Alpi, Benoit Bely, Brigitte Boeckmann, Rolf Apweiler, Rachael P. Huntley, Lionel Breuza, Sangya Pundir, Lorenzo Cerutti, Tunca Doğan, EB Casanova, P van Rensburg, Rabie Saidi, Jie Luo, Mickael Goujon, Laure Verbregue, Tony Wardell, W Liu, Andre Stutz, P Lemercier, Hamish McWilliam, Ivo Pedruzzi, P-A Binz, Sebastien Gehant, Béatrice A. Cuche, Carlos Bonilla, Duncan Legge, C. R. Vinayaka, Anne Morgat, Diego Poggioli, J Arganiska, Teresa Batista Neto, Emmanuel Boutet, Florence Jungo, Ursula Hinz, Parit Bansal, Sandra Orchard, Ricardo Antunes, Manuela Pruess, M Feuermann, S. Rosanoff, Claire O'Donovan, Cecilia N. Arighi, J. James, M Doche, Elisabeth Coudert, M De Giorgi, Reija Hieta, Sandrine Pilbout, Arnaud Gos, Michael Tognolli, Leyla Jael Garcia Castro, Lucila Aimo

Publikováno v: Nucleic Acids Research

The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dacc18afba0dcb8db8d93542e3ba0bff
http://europepmc.org/articles/PMC3965022