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7 results on '"Foulger, R."'

1. Human and mouse essentiality screens as a resource for disease gene discovery

Author

Cacheiro, Pilar, Muñoz-Fuentes, Violeta, Westerberg, Henrik, Scott, R. H., Siddiq, A., Sieghart, A., Smith, K. R., Sosinsky, A., Spooner, W., Stevens, H. E., Stuckey, A., Sultana, R., Thomas, E. R. A., Konopka, Tomasz, Thompson, S. R., Tregidgo, C., Tucci, A., Walsh, E., Watters, S. A., Welland, M. J., Williams, E., Witkowska, K., Wood, S. M., Zarowiecki, M., Hsu, Chih-Wei, Marschall, Susan, Lengger, Christoph, Maier, Holger, Seisenberger, Claudia, Bürger, Antje, Kühn, Ralf, Schick, Joel, Hörlein, Andreas, Oritz, Oskar, Giesert, Florian, Christiansen, Audrey, Beig, Joachim, Kenyon, Janet, Codner, Gemma, Fray, Martin, Johnson, Sara J, Cleak, James, Szoke-Kovacs, Zsombor, Lafont, David, Vancollie, Valerie E, McLaren, Robbie S B, Lanza, Denise G, Hughes-Hallett, Lena, Rowley, Christine, Sanderson, Emma, Galli, Antonella, Tuck, Elizabeth, Green, Angela, Tudor, Catherine, Siragher, Emma, Dabrowska, Monika, Mazzeo, Cecilia Icoresi, Beaudet, Arthur L, Griffiths, Mark, Gannon, David, Doe, Brendan, Cockle, Nicola, Kirton, Andrea, Bottomley, Joanna, Ingle, Catherine, Ryder, Edward, Gleeson, Diane, Ramirez-Solis, Ramiro, Heaney, Jason D, Birling, Marie-Christine, Pavlovic, Guillaume, Ayadi, Abdel, Hamid, Meziane, About, Ghina Bou, Champy, Marie-France, Jacobs, Hugues, Wendling, Olivia, Leblanc, Sophie, Vasseur, Laurent, Fuchs, Helmut, Chesler, Elissa J, Kumar, Vivek, White, Jacqueline K, Svenson, Karen L, Wiegand, Jean-Paul, Anderson, Laura L, Wilcox, Troy, Clark, James, Ryan, Jennifer, Denegre, James, Gailus-Durner, Valerie, Stearns, Tim, Philip, Vivek, Witmeyer, Catherine, Bates, Lindsay, Seavey, Zachary, Stanley, Pamela, Willet, Amelia, Roper, Willson, Creed, Julie, Moore, Michayla, Sorg, Tania, Dorr, Alex, Fraungruber, Pamelia, Presby, Rose, Mckay, Matthew, Nguyen-Bresinsky, Dong, Goodwin, Leslie, Urban, Rachel, Kane, Coleen, Murray, Stephen A, Prochazka, Jan, Novosadova, Vendula, Lelliott, Christopher J, Wardle-Jones, Hannah, Wells, Sara, Teboul, Lydia, Cater, Heather, Stewart, Michelle, Hough, Tertius, Wurst, Wolfgang, Dickinson, Mary E, Sedlacek, Radislav, Adams, David J, Seavitt, John R, Tocchini-Valentini, Glauco, Mammano, Fabio, Braun, Robert E, McKerlie, Colin, Herault, Yann, de Angelis, Martin Hrabě, Mallon, Ann-Marie, Bucan, Maja, Lloyd, K C Kent, Brown, Steve D M, Parkinson, Helen, Meehan, Terrence F, Smedley, Damian, Consortium, Genomics England Research, Consortium, International Mouse Phenotyping, Ambrose, J. C., Arumugam, P., Baple, E. L., Nutter, Lauryl M J, Bleda, M., Boardman-Pretty, F., Boissiere, J. M., Boustred, C. R., Brittain, H., Caulfield, M. J., Chan, G. C., Craig, C. E. H., Daugherty, L. C., de Burca, A., Peterson, Kevin A, Devereau, A., Elgar, G., Foulger, R. E., Fowler, T., Furió-Tarí, P., Hackett, J. M., Halai, D., Hamblin, A., Henderson, S., Holman, J. E., Haselimashhadi, Hamed, Hubbard, T. J. P., Ibáñez, K., Jackson, R., Jones, L. J., Kasperaviciute, D., Kayikci, M., Lahnstein, L., Lawson, K., Leigh, S. E. A., Leong, I. U. S., Flenniken, Ann M, Lopez, F. J., Maleady-Crowe, F., Mason, J., McDonagh, E. M., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A. C., Odhams, C. A., Patch, C., Morgan, Hugh, Perez-Gil, D., Polychronopoulos, D., Pullinger, J., Rahim, T., Rendon, A., Riesgo-Ferreiro, P., Rogers, T., Ryten, M., Savage, K., Sawant, K., Cacheiro, Pilar [0000-0002-6335-8208], Muñoz-Fuentes, Violeta [0000-0003-3574-546X], Nutter, Lauryl MJ [0000-0001-9619-146X], Peterson, Kevin A [0000-0001-8353-3694], Haselimashhadi, Hamed [0000-0001-7334-2421], Konopka, Tomasz [0000-0003-3042-4712], Hsu, Chih-Wei [0000-0002-9591-9567], Lanza, Denise G [0000-0001-8750-6933], Heaney, Jason D [0000-0001-8475-8828], Fuchs, Helmut [0000-0002-5143-2677], Gailus-Durner, Valerie [0000-0002-6076-0111], Lelliott, Christopher J [0000-0001-8087-4530], Adams, David J [0000-0001-9490-0306], Mammano, Fabio [0000-0003-3751-1691], McKerlie, Colin [0000-0002-2232-0967], Herault, Yann [0000-0001-7049-6900], de Angelis, Martin Hrabě [0000-0002-7898-2353], Lloyd, KC Kent [0000-0002-5318-4144], Smedley, Damian [0000-0002-5836-9850], Apollo - University of Cambridge Repository, Queen Mary University of London (QMUL), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, The Jackson Laboratory [Bar Harbor] (JAX), Baylor College of Medicine (BCM), Baylor University, University of Pennsylvania, The Hospital for sick children [Toronto] (SickKids), Mount Sinai Hospital [Toronto, Canada] (MSH), MRC Harwell Institute [UK], Helmholtz Zentrum München = German Research Center for Environmental Health, Institut Clinique de la Souris (ICS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), French National Infrastructure for Mouse Phenogenomics (PHENOMIN), Institute of Molecular Genetics of the Czech Academy of Sciences (IMG / CAS), Czech Academy of Sciences [Prague] (CAS), The Wellcome Trust Sanger Institute [Cambridge], Technische Universität München = Technical University of Munich (TUM), Ludwig-Maximilians-Universität München (LMU), CNR - Italian National Research Council (CNR), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), German Center for Diabetes Research - Deutsches Zentrum für Diabetesforschung [Neuherberg] (DZD), University of California [Davis] (UC Davis), University of California (UC), J C Ambrose, P Arumugam, E L Baple, M Bleda, F Boardman-Pretty, J M Boissiere, C R Boustred, H Brittain, M J Caulfield, G C Chan, C E H Craig, L C Daugherty, A de Burca, A Devereau, G Elgar, R E Foulger, T Fowler, P Furió-Tarí, J M Hackett, D Halai, A Hamblin, S Henderson, J E Holman, T J P Hubbard, K Ibáñez, R Jackson, L J Jones, D Kasperaviciute, M Kayikci, L Lahnstein, K Lawson, S E A Leigh, I U S Leong, F J Lopez, F Maleady-Crowe, J Mason, E M McDonagh, L Moutsianas, M Mueller, N Murugaesu, A C Need, C A Odhams, C Patch, D Perez-Gil, D Polychronopoulos, J Pullinger, T Rahim, A Rendon, P Riesgo-Ferreiro, T Rogers, M Ryten, K Savage, K Sawant, R H Scott, A Siddiq, A Sieghart, K R Smith, A Sosinsky, W Spooner, H E Stevens, A Stuckey, R Sultana, E R A Thomas, S R Thompson, C Tregidgo, A Tucci, E Walsh, S A Watters, M J Welland, E Williams, K Witkowska, S M Wood, M Zarowiecki, Susan Marschall, Christoph Lengger, Holger Maier, Claudia Seisenberger, Antje Bürger, Ralf Kühn, Joel Schick, Andreas Hörlein, Oskar Oritz, Florian Giesert, Joachim Beig, Janet Kenyon, Gemma Codner, Martin Fray, Sara J Johnson, James Cleak, Zsombor Szoke-Kovacs, David Lafont, Valerie E Vancollie, Robbie S B McLaren, Lena Hughes-Hallett, Christine Rowley, Emma Sanderson, Antonella Galli, Elizabeth Tuck, Angela Green, Catherine Tudor, Emma Siragher, Monika Dabrowska, Cecilia Icoresi Mazzeo, Mark Griffiths, David Gannon, Brendan Doe, Nicola Cockle, Andrea Kirton, Joanna Bottomley, Catherine Ingle, Edward Ryder, Diane Gleeson, Ramiro Ramirez-Solis, Marie-Christine Birling, Guillaume Pavlovic, Abdel Ayadi, Meziane Hamid, Ghina Bou About, Marie-France Champy, Hugues Jacobs, Olivia Wendling, Sophie Leblanc, Laurent Vasseur, Elissa J Chesler, Vivek Kumar, Jacqueline K White, Karen L Svenson, Jean-Paul Wiegand, Laura L Anderson, Troy Wilcox, James Clark, Jennifer Ryan, James Denegre, Tim Stearns, Vivek Philip, Catherine Witmeyer, Lindsay Bates, Zachary Seavey, Pamela Stanley, Amelia Willet, Willson Roper, Julie Creed, Michayla Moore, Alex Dorr, Pamelia Fraungruber, Rose Presby, Matthew Mckay, Dong Nguyen-Bresinsky, Leslie Goodwin, Rachel Urban, Coleen Kane, Herault, Yann, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
0301 basic medicine, Mutation rate, Cancer Research, [SDV]Life Sciences [q-bio], General Physics and Astronomy, methods [Genetic Association Studies], Disease, VARIANTS, Mice, Essential, 0302 clinical medicine, IMPC, Genetics research, Lethal allele, 2.1 Biological and endogenous factors, Aetiology, lcsh:Science, Organism, ComputingMilieux_MISCELLANEOUS, Disease gene, Mice, Knockout, 0303 health sciences, Multidisciplinary, Genes, Essential, genetics [Disease], Genomics, R/BIOCONDUCTOR PACKAGE, DATABASE, UPDATE, GENOME, [SDV] Life Sciences [q-bio], Knockout mouse, Identification (biology), ddc:500, International Mouse Phenotyping Consortium, Technology Platforms, Biotechnology, Knockout, Science, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Genetics, medicine, Animals, Humans, Genetic variation, Clinical genetics, Gene, Genetic Association Studies, 030304 developmental biology, Disease model, Prevention, Human Genome, General Chemistry, medicine.disease, Developmental disorder, Good Health and Well Being, 030104 developmental biology, Genomics England Research Consortium, Genes, lcsh:Q, Generic health relevance, 030217 neurology & neurosurgery, Rare disease
Abstract

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery., Discovery of causal variants for monogenic disorders has been facilitated by whole exome and genome sequencing, but does not provide a diagnosis for all patients. Here, the authors propose a Full Spectrum of Intolerance to Loss-of-Function (FUSIL) categorization that integrates gene essentiality information to aid disease gene discovery.

Published
2020
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2. Improving interpretation of cardiac phenotypes and enhancing discovery with expanded knowledge in the gene ontology

Author

Lovering, R, Roncaglia, P, Howe, D, Laulederkind, S, Khodiyar, V, Berardini, T, Tweedie, S, Foulger, R, Osumi-Sutherland, D, Campbell, N, Huntley, R, Talmud, P, Blake, J, Breckenridge, R, Riley, P, Lambiase, P, Elliott, P, Clapp, L, Tinker, A, and Hill, D

Subjects
Proteomics, data curation, Heart Diseases, Computational Biology, Heart, Molecular Sequence Annotation, Original Articles, arrhythmias, cardiac, electrophysiology, Gene Ontology, Phenotype, Databases, Genetic, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Humans, genetics, transcriptome
Abstract

Supplemental Digital Content is available in the text., Background: A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. Methods and Results: In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. As a result, the Gene Ontology now contains terms that comprehensively describe the roles of proteins in cardiac muscle cell action potential, electrical coupling, and the transmission of the electrical impulse from the sinoatrial node to the ventricles. Evaluating the effectiveness of this approach to inform data analysis demonstrated that Gene Ontology annotations, analyzed within an expanded ontological context of heart processes, can help to identify candidate genes associated with arrhythmic disease risk loci. Conclusions: We determined that a combination of curation and ontology development for heart-specific genes and processes supports the identification and downstream analysis of genes responsible for the spread of the cardiac action potential through the heart. Annotating these genes and processes in a structured format facilitates data analysis and supports effective retrieval of gene-centric information about cardiac defects.

Published
2018

3. The Gene Ontology in 2010: extensions and refinements

Author

Berardini, Tz, Li, D, Huala, E, Bridges, S, Burgess, S, Mccarthy, F, Carbon, S, Lewis, Se, Mungall, Cj, Abdulla, A, Wood, V, Feltrin, E, Valle, Giorgio, Chisholm, Rl, Fey, P, Gaudet, P, Kibbe, W, Basu, S, Bushmanova, Y, Eilbeck, K, Siegele, Da, Mcintosh, B, Renfro, D, Zweifel, A, Hu, Jc, Ashburner, M, Tweedie, S, ALAM FARUQUE, Y, Apweiler, R, Auchinchloss, A, Bairoch, A, Barrell, D, Binns, D, Blatter, Mc, Bougueleret, L, Boutet, E, Breuza, L, Bridge, A, Browne, P, Chan, Wm, Coudert, E, Daugherty, L, Dimmer, E, Eberhardt, R, Estreicher, A, Famiglietti, L, FERRO ROJAS, S, Feuermann, M, Foulger, R, GRUAZ GUMOWSKI, N, Hinz, U, Huntley, R, Jimenez, S, Jungo, F, Keller, G, Laiho, K, Legge, D, Lemercier, P, Lieberherr, D, Magrane, M, O'Donovan, C, Pedruzzi, I, Poux, S, Rivoire, C, Roechert, B, Sawford, T, Schneider, M, Stanley, E, Stutz, A, Sundaram, S, Tognolli, M, Xenarios, I, Harris, Ma, Deegan, Ji, Ireland, A, Lomax, J, Jaiswal, P, Chibucos, M, Giglio, Mg, Wortman, J, Hannick, L, Madupu, R, Botstein, D, Dolinski, K, Livstone, Ms, Oughtred, R, Blake, Ja, Bult, C, Diehl, Ad, Dolan, M, Drabkin, H, Eppig, Jt, Hill, Dp, Ni, L, Ringwald, M, Sitnikov, D, Collmer, C, TORTO ALALIBO, T, Laulederkind, S, Shimoyama, M, Twigger, S, D'Eustachio, P, Matthews, L, Balakrishnan, R, Binkley, G, Cherry, Jm, Christie, Kr, Costanzo, Mc, Engel, Sr, Fisk, Dg, Hirschman, Je, Hitz, Bc, Hong, El, Krieger, Cj, Miyasato, Sr, Nash, Rs, Park, J, Skrzypek, Ms, Weng, S, Wong, Ed, Aslett, M, Chan, J, Kishore, R, Sternberg, P, VAN AUKE, K, Khodiyar, Vk, Lovering, Rc, Talmud, Pj, Howe, D, Westerfield, M., Gene Ontology Consortium, Berardini, TZ., Li, D., Huala, E., Bridges, S., Burgess, S., McCarthy, F., Carbon, S., Lewis, SE., Mungall, CJ., Abdulla, A., Wood, V., Feltrin, E., Valle, G., Chisholm, RL., Fey, P., Gaudet, P., Kibbe, W., Basu, S., Bushmanova, Y., Eilbeck, K., Siegele, DA., McIntosh, B., Renfro, D., Zweifel, A., Hu, JC., Ashburner, M., Tweedie, S., Alam-Faruque, Y., Apweiler, R., Auchinchloss, A., Bairoch, A., Barrell, D., Binns, D., Blatter, MC., Bougueleret, L., Boutet, E., Breuza, L., Bridge, A., Browne, P., Chan, WM., Coudert, E., Daugherty, L., Dimmer, E., Eberhardt, R., Estreicher, A., Famiglietti, L., Ferro-Rojas, S., Feuermann, M., Foulger, R., Gruaz-Gumowski, N., Hinz, U., Huntley, R., Jimenez, S., Jungo, F., Keller, G., Laiho, K., Legge, D., Lemercier, P., Lieberherr, D., Magrane, M., O'Donovan, C., Pedruzzi, I., Poux, S., Rivoire, C., Roechert, B., Sawford, T., Schneider, M., Stanley, E., Stutz, A., Sundaram, S., Tognolli, M., Xenarios, I., Harris, MA., Deegan, JI., Ireland, A., Lomax, J., Jaiswal, P., Chibucos, M., Giglio, MG., Wortman, J., Hannick, L., Madupu, R., Botstein, D., Dolinski, K., Livstone, MS., Oughtred, R., Blake, JA., Bult, C., Diehl, AD., Dolan, M., Drabkin, H., Eppig, JT., Hill, DP., Ni, L., Ringwald, M., Sitnikov, D., Collmer, C., Torto-Alalibo, T., Laulederkind, S., Shimoyama, M., Twigger, S., D'Eustachio, P., Matthews, L., Balakrishnan, R., Binkley, G., Cherry, JM., Christie, KR., Costanzo, MC., Engel, SR., Fisk, DG., Hirschman, JE., Hitz, BC., Hong, EL., Krieger, CJ., Miyasato, SR., Nash, RS., Park, J., Skrzypek, MS., Weng, S., Wong, ED., Aslett, M., Chan, J., Kishore, R., Sternberg, P., Van Auke, K., Khodiyar, VK., Lovering, RC., Talmud, PJ., Howe, D., and Westerfield, M.

Subjects
Information Storage and Retrieval, Ontology (information science), Biology, Bioinformatics, World Wide Web, Set (abstract data type), 03 medical and health sciences, Annotation, User-Computer Interface, 0302 clinical medicine, Controlled vocabulary, Databases, Genetic, Genetics, Animals, Humans, Databases, Protein, Computational Biology/methods, Computational Biology/trends, Databases, Nucleic Acid, Genomics, Information Storage and Retrieval/methods, Internet, Software, Vocabulary, Controlled, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, Gene ontology, business.industry, Computational Biology, Usability, Articles, ComputingMethodologies_GENERAL, business, 030217 neurology & neurosurgery
Abstract

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

Published
2010

4. Corrigendum: Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project.

Author

Wheway, Gabrielle, Mitchison, Hannah M., Ambrose, J. C., Baple, E. L., Bleda, M., Boardman-Pretty, F., Boissiere, J. M., Boustred, C. R., Caulfield, M. J., Chan, G. C., Craig, C. E. H., Daugherty, L. C., de, Burca A., Devereau, A., Elgar, G., Foulger, R. E., Fowler, T., Furió-Tarí, P., Hackett, J. M., and Halai, D.

Subjects
GENOMES, MEDICAL care, STREET children
Abstract

Highlights from the article: Suitable gene panels with features overlapping the phenotype e.g., retinal dystrophy gene panel, Protein altering variants affecting genes not in the virtual gene 100,000 Genomes Project uses data provided by patients and Copyright of Frontiers in Genetics is the property of Frontiers Media S.A. and its content may.

Published
2019
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5. The Gene Ontology: enhancements for 2011

Author

P D'Eustachio, Benjamin C. Hitz, Julie Park, Paul Browne, Douglas G. Howe, Cynthia J. Krieger, Kalpana Karra, Stan Laulederkind, Karen R. Christie, Susan Tweedie, Eurie L. Hong, Lydie Bougueleret, Michele Magrane, Cathy R. Gresham, Rolf Apweiler, Lisa Matthews, Dong Li, Philippa J. Talmud, Ioannis Xenarios, J. M. Cherry, Tanya Z. Berardini, Deborah A. Siegele, Rama Balakrishnan, D. Sitnikov, A. Auchinchloss, Selina S. Dwight, Tony Sawford, Paul J. Kersey, Ruth C. Lovering, Ruth Y. Eberhardt, Ursula Hinz, Lakshmi Pillai, Sylvain Poux, Edith D. Wong, Klemens Pichler, Kati Laiho, Malcolm J. Gardner, Stephen G. Oliver, Lionel Breuza, Kara Dolinski, P Lemercier, Kristian B. Axelsen, Midori A. Harris, Adrienne E. Zweifel, H. Drabkin, Guillaume Keller, Marek S. Skrzypek, Daniel M. Staines, Fiona M. McCarthy, Nicholas H. Brown, Mark D. McDowall, Antonia Lock, Mary Shimoyama, Maria C. Costanzo, Teresia Buza, S. Jimenez, Rex L. Chisholm, Paul W. Sternberg, Hui Wang, Nadine Gruaz-Gumowski, Chantal Hulo, Rebecca E. Foulger, Melinda R. Dwinell, Judith A. Blake, Marcus C. Chibucos, B. K. McIntosh, C. D. Amundsen, Jane Lomax, L Famiglietti, Tom Hayman, Michael Tognolli, Eva Huala, James C. Hu, Patrick Masson, Maria Jesus Martin, Benoit Bely, Shuai Weng, Heather C. Wick, E. Dimmer, L. Ni, Catherine Rivoire, Christopher J. Mungall, H. Sehra, P. Duek-Roggli, Maria Victoria Schneider, Dianna G. Fisk, Michael S. Livstone, Ivo Pedruzzi, Shyamala Sundaram, Donna K. Slonim, Isabelle Cusin, Stuart R. Miyasato, Timothy F. Lowry, Varsha K. Khodiyar, Seth Carbon, Elisabeth Coudert, Jürg Bähler, Juancarlos Chan, Evelyn Camon, Daniel P. Renfro, Anne Estreicher, M. C. Blatter, Robert S. Nash, P Gaudet, Sven Heinicke, K. Van Auken, Stacia R. Engel, Alan Bridge, Ralf Stephan, Mary E. Dolan, Shane C. Burgess, Petra Fey, Shur-Jen Wang, Damien Lieberherr, Duncan Legge, P. Porras Millán, Andre Stutz, Yasmin Alam-Faruque, Gail Binkley, Bernd Roechert, S. Branconi-Quintaje, Ghislaine Argoud-Puy, S. Basu, Kim Rutherford, M. Moinat, Monte Westerfield, Arnaud Gos, Eleanor J Stanley, Valerie Wood, Ranjana Kishore, Diego Poggioli, S. Ferro-Rojas, Victoria Petri, Florence Jungo, Suzanna E. Lewis, Emmanuel Boutet, Warren A. Kibbe, M Feuermann, Claire O'Donovan, W. M. Chan, J. James, David P. Hill, Rachael P. Huntley, M. Gwinn Giglio, Paul Thomas, Jodi E. Hirschman, Paola Roncaglia, Gene Ontology Consortium, Blake, JA., Dolan, M., Drabkin, H., Hill, DP., Ni, L., Sitnikov, D., Burgess, S., Buza, T., Gresham, C., McCarthy, F., Pillai, L., Wang, H., Carbon, S., Lewis, SE., Mungall, CJ., Gaudet, P., Chisholm, RL., Fey, P., Kibbe, WA., Basu, S., Siegele, DA., McIntosh, BK., Renfro, DP., Zweifel, AE., Hu, JC., Brown, NH., Tweedie, S., Alam-Faruque, Y., Apweiler, R., Auchinchloss, A., Axelsen, K., Argoud-Puy, G., Bely, B., Blatter, M-., Bougueleret, L., Boutet, E., Branconi, S., Breuza, L., Bridge, A., Browne, P., Chan, WM., Coudert, E., Cusin, I., Dimmer, E., Duek-Roggli, P., Eberhardt, R., Estreicher, A., Famiglietti, L., Ferro-Rojas, S., Feuermann, M., Gardner, M., Gos, A., Gruaz-Gumowski, N., Hinz, U., Hulo, C., Huntley, R., James, J., Jimenez, S., Jungo, F., Keller, G., Laiho, K., Legge, D., Lemercier, P., Lieberherr, D., Magrane, M., Martin, MJ., Masson, P., Moinat, M., O'Donovan, C., Pedruzzi, I., Pichler, K., Poggioli, D., Porras Millán, P., Poux, S., Rivoire, C., Roechert, B., Sawford, T., Schneider, M., Sehra, H., Stanley, E., Stutz, A., Sundaram, S., Tognolli, M., Xenarios, I., Foulger, R., Lomax, J., Roncaglia, P., Camon, E., Khodiyar, VK., Lovering, RC., Talmud, PJ., Chibucos, M., Gwinn Giglio, M., Dolinski, K., Heinicke, S., Livstone, MS., Stephan, R., Harris, MA., Oliver, SG., Rutherford, K., Wood, V., Bahler, J., Lock, A., Kersey, PJ., McDowall, MD., Staines, DM., Dwinell, M., Shimoyama, M., Laulederkind, S., Hayman, T., Wang, S-., Petri, V., Lowry, T., D'Eustachio, P., Matthews, L., Amundsen, CD., Balakrishnan, R., Binkley, G., Cherry, JM., Christie, KR., Costanzo, MC., Dwight, SS., Engel, SR., Fisk, DG., Hirschman, JE., Hitz, BC., Hong, EL., Karra, K., Krieger, CJ., Miyasato, SR., Nash, RS., Park, J., Skrzypek, MS., Weng, S., Wong, ED., Berardini, TZ., Li, D., Huala, E., Slonim, D., Wick, H., Thomas, P., Chan, J., Kishore, R., Sternberg, P., Van Auken, K., Howe, D., and Westerfield, M.

Subjects
Quality Control, 0303 health sciences, media_common.quotation_subject, Databases, Genetic, Molecular Sequence Annotation/standards, Vocabulary, Controlled, Inference, Molecular Sequence Annotation, Articles, Biology, Ontology (information science), World Wide Web, Open Biomedical Ontologies, 03 medical and health sciences, Annotation, 0302 clinical medicine, Resource (project management), Controlled vocabulary, Genetics, Social media, Function (engineering), 030217 neurology & neurosurgery, 030304 developmental biology, media_common
Abstract

The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.

Published
2011
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6. The Universal Protein Resource (UniProt) in 2010

Author

Elisabeth Gasteiger, Amos Bairoch, John Garavelli, Julius Jacobsen, Lionel Breuza, Rachael Huntley, Rolf Apweiler, Christian J. A. SIGRIST, Rebecca Foulger, Jerven Bolleman, Raja Mazumder, Ivo Pedruzzi, Florence Jungo, Anaïs Mottaz, Michael Tognolli, Emmanuel Boutet, Claire O'Donovan, Edward Turner, Sandra Orchard, Patrick Masson, Peter McGarvey, Nicole Redaschi, Sébastien Géhant, Michele Magrane, Anne Estreicher, Alan Bridge, Michel Schneider, Daniel Barrell, Benoit Bely, Anne Morgat, Sylvain Poux, Petra Langendijk-Genevaux, Maria-Jesus Martin, Catherine Rivoire, Elisabeth Coudert, Rasko Leinonen, Cecilia Arighi, UniProt Consortium, Apweiler, R., Martin, MJ., O'Donovan, C., Magrane, M., Alam-Faruque, Y., Antunes, R., Barrell, D., Bely, B., Bingley, M., Binns, D., Bower, L., Browne, P., Chan, WM., Dimmer, E., Eberhardt, R., Fedotov, A., Foulger, R., Garavelli, J., Huntley, R., Jacobsen, J., Kleen, M., Laiho, K., Leinonen, R., Legge, D., Lin, Q., Liu, W., Luo, J., Orchard, S., Patient, S., Poggioli, D., Pruess, M., Corbett, M., di Martino, G., Donnelly, M., van Rensburg, P., Bairoch, A., Bougueleret, L., Xenarios, I., Altairac, S., Auchincloss, A., Argoud-Puy, G., Axelsen, K., Baratin, D., Blatter, MC., Boeckmann, B., Bolleman, J., Bollondi, L., Boutet, E., Quintaje, SB., Breuza, L., Bridge, A., deCastro, E., Ciapina, L., Coral, D., Coudert, E., Cusin, I., Delbard, G., Doche, M., Dornevil, D., Roggli, PD., Duvaud, S., Estreicher, A., Famiglietti, L., Feuermann, M., Gehant, S., Farriol-Mathis, N., Ferro, S., Gasteiger, E., Gateau, A., Gerritsen, V., Gos, A., Gruaz-Gumowski, N., Hinz, U., Hulo, C., Hulo, N., James, J., Jimenez, S., Jungo, F., Kappler, T., Keller, G., Lachaize, C., Lane-Guermonprez, L., Langendijk-Genevaux, P., Lara, V., Lemercier, P., Lieberherr, D., de Oliveira Lima, T., Mangold, V., Martin, X., Masson, P., Moinat, M., Morgat, A., Mottaz, A., Paesano, S., Pedruzzi, I., Pilbout, S., Pillet, V., Poux, S., Pozzato, M., Redaschi, N., Rivoire, C., Roechert, B., Schneider, M., Sigrist, C., Sonesson, K., Staehli, S., Stanley, E., Stutz, A., Sundaram, S., Tognolli, M., Verbregue, L., Veuthey, AL., Yip, L., Zuletta, L., Wu, C., Arighi, C., Arminski, L., Barker, W., Chen, C., Chen, Y., Hu, ZZ., Huang, H., Mazumder, R., McGarvey, P., Natale, DA., Nchoutmboube, J., Petrova, N., Subramanian, N., Suzek, BE., Ugochukwu, U., Vasudevan, S., Vinayaka, CR., Yeh, LS., and Zhang, J.

Subjects
Proteomics, Internet, 0303 health sciences, Proteome, 030302 biochemistry & molecular biology, Computational Biology, Information Storage and Retrieval, Genome, Viral, Articles, Europe, 03 medical and health sciences, Algorithms, Animals, Computational Biology/methods, Computational Biology/trends, Databases, Nucleic Acid, Databases, Protein, Genome, Fungal, Humans, Information Storage and Retrieval/methods, Protein Isoforms, Software, Genetics, 030304 developmental biology
Abstract

The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.

Published
2009
Full Text
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7. Ongoing and future developments at the Universal Protein Resource

Author

Vicente Lara, Arnaud Gos, Nikolas Pontikos, L. Bollondi, L Famiglietti, Barker Wc, Chuming Chen, Michael Tognolli, Patrick Masson, Salvo Paesano, Tony Sawford, Sandrine Pilbout, Jerven Bolleman, Jian Zhang, S Staehli, Elisabeth Gasteiger, David Binns, Ursula Hinz, Nadine Gruaz-Gumowski, Chantal Hulo, Maria Jesus Martin, M. Corbett, Veuthey Al, Paul Browne, Guillaume Keller, S. Jimenez, Roberts Nv, Brigitte Boeckmann, Natale Da, Suzek Be, Edward Turner, T. Kappler, Steven Rosanoff, Leslie Arminski, Florence Jungo, M Donnelly, P. Dubey, Ruth Y. Eberhardt, Lydie Bougueleret, Vivienne Baillie Gerritsen, Maria Victoria Schneider, Lionel Breuza, Isabelle Cusin, Delphine Baratin, E. Dimmer, Rachael P. Huntley, Julius O.B. Jacobsen, Arighi Cn, Quintaje Sb, Alan Bridge, Nicole Redaschi, Shyamala Sundaram, Peter B. McGarvey, Rebecca E. Foulger, Duncan Legge, Andre Stutz, Monica Pozzato, Raja Mazumder, Anne Morgat, M Doche, K Sonesson, Anne Estreicher, Blatter Mc, Manuela Pruess, Serenella Ferro, Séverine Duvaud, F. Fazzini, Rolf Apweiler, Natarajan Tg, E. Stanley, M Feuermann, Claire O'Donovan, J. James, Ivo Pedruzzi, Castro Lg, Wu Ch, M Bingley, W Liu, He Huang, Bernd Roechert, Laure Verbregue, Elisabeth Coudert, Ioannis Xenarios, M. Moinat, Sandra Orchard, P Lemercier, Damien Lieberherr, Ricardo Antunes, Ghislaine Argoud-Puy, Sebastien Gehant, Qiang Wang, Klemens Pichler, S. Patient, Nicolas Hulo, Diego Poggioli, J. Nchoutmboube, Emmanuel Boutet, H. Sehra, Chan Wm, Yasmin Alam-Faruque, M. Kleen, Van Rensburg P, Kati Laiho, Kristian B. Axelsen, John S. Garavelli, Christian J. A. Sigrist, Amos Marc Bairoch, Yongxing Chen, A. Fedotov, Yeh Ls, Sylvain Poux, Lynette Bower, Quan Lin, Daniel Barrell, Benoit Bely, U. Ugochukwu, Xavier D. Martin, Catherine Rivoire, E. Decastro, Jie Luo, Alain Gateau, Michele Magrane, Dolnide Dornevil, Vinayaka Cr, Andrea H. Auchincloss, Yuqi Wang, An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institut de Microélectronique, Electromagnétisme et Photonique - Laboratoire d'Hyperfréquences et Caractérisation (IMEP-LAHC), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Institut de minéralogie et de physique des milieux condensés (IMPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria), Université de Lausanne (UNIL), Université Pierre et Marie Curie - Paris 6 (UPMC)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), UniProt Consortium, Apweiler, R., Martin, MJ., O'Donovan, C., Magrane, M., Alam-Faruque, Y., Antunes, R., Barrell, D., Bely, B., Bingley, M., Binns, D., Bower, L., Browne, P., Chan, WM., Dimmer, E., Eberhardt, R., Fazzini, F., Fedotov, A., Foulger, R., Garavelli, J., Castro, LG., Huntley, R., Jacobsen, J., Kleen, M., Laiho, K., Legge, D., Lin, Q., Liu, W., Luo, J., Orchard, S., Patient, S., Pichler, K., Poggioli, D., Pontikos, N., Pruess, M., Rosanoff, S., Sawford, T., Sehra, H., Turner, E., Corbett, M., Donnelly, M., van Rensburg, P., Xenarios, I., Bougueleret, L., Auchincloss, A., Argoud-Puy, G., Axelsen, K., Bairoch, A., Baratin, D., Blatter, MC., Boeckmann, B., Bolleman, J., Bollondi, L., Boutet, E., Quintaje, SB., Breuza, L., Bridge, A., deCastro, E., Coudert, E., Cusin, I., Doche, M., Dornevil, D., Duvaud, S., Estreicher, A., Famiglietti, L., Feuermann, M., Gehant, S., Ferro, S., Gasteiger, E., Gateau, A., Gerritsen, V., Gos, A., Gruaz-Gumowski, N., Hinz, U., Hulo, C., Hulo, N., James, J., Jimenez, S., Jungo, F., Kappler, T., Keller, G., Lara, V., Lemercier, P., Lieberherr, D., Martin, X., Masson, P., Moinat, M., Morgat, A., Paesano, S., Pedruzzi, I., Pilbout, S., Poux, S., Pozzato, M., Redaschi, N., Rivoire, C., Roechert, B., Schneider, M., Sigrist, C., Sonesson, K., Staehli, S., Stanley, E., Stutz, A., Sundaram, S., Tognolli, M., Verbregue, L., Veuthey, AL., Wu, CH., Arighi, CN., Arminski, L., Barker, WC., Chen, C., Chen, Y., Dubey, P., Huang, H., Mazumder, R., McGarvey, P., Natale, DA., Natarajan, TG., Nchoutmboube, J., Roberts, NV., Suzek, BE., Ugochukwu, U., Vinayaka, CR., Wang, Q., Wang, Y., Yeh, LS., and Zhang, J.

Subjects
Proteomics, 0303 health sciences, Sequence database, 030302 biochemistry & molecular biology, Proteins, Articles, Computational biology, Biology, Bioinformatics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Systems Integration, Universal Protein Resource, 03 medical and health sciences, Information resource, Protein sequencing, Sequence Analysis, Protein, Metagenomics, UniProt Knowledgebase, Genetics, Databases, Protein/trends, Proteins/chemistry, Proteins/genetics, UniProt, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Databases, Protein, 030304 developmental biology
Abstract

International audience; The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.

Published
2011
Full Text
View/download PDF

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