Literature DB >> 14681445

WormBase: a multi-species resource for nematode biology and genomics.

Todd W Harris1, Nansheng Chen, Fiona Cunningham, Marcela Tello-Ruiz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Juancarlos Chan, Chao-Kung Chen, Wen J Chen, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W Sternberg, Lincoln D Stein.   

Abstract

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system.

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Year:  2004        PMID: 14681445      PMCID: PMC308800          DOI: 10.1093/nar/gkh066

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  18 in total

1.  A gene expression map for Caenorhabditis elegans.

Authors:  S K Kim; J Lund; M Kiraly; K Duke; M Jiang; J M Stuart; A Eizinger; B N Wylie; G S Davidson
Journal:  Science       Date:  2001-09-14       Impact factor: 47.728

2.  Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map.

Authors:  S R Wicks; R T Yeh; W R Gish; R H Waterston; R H Plasterk
Journal:  Nat Genet       Date:  2001-06       Impact factor: 38.330

3.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

4.  The structure of the nervous system of the nematode Caenorhabditis elegans.

Authors:  J G White; E Southgate; J N Thomson; S Brenner
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1986-11-12       Impact factor: 6.237

5.  C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.

Authors:  Jérôme Reboul; Philippe Vaglio; Jean-François Rual; Philippe Lamesch; Monica Martinez; Christopher M Armstrong; Siming Li; Laurent Jacotot; Nicolas Bertin; Rekin's Janky; Troy Moore; James R Hudson; James L Hartley; Michael A Brasch; Jean Vandenhaute; Simon Boulton; Gregory A Endress; Sarah Jenna; Eric Chevet; Vasilis Papasotiropoulos; Peter P Tolias; Jason Ptacek; Mike Snyder; Raymond Huang; Mark R Chance; Hongmei Lee; Lynn Doucette-Stamm; David E Hill; Marc Vidal
Journal:  Nat Genet       Date:  2003-05       Impact factor: 38.330

6.  Post-embryonic cell lineages of the nematode, Caenorhabditis elegans.

Authors:  J E Sulston; H R Horvitz
Journal:  Dev Biol       Date:  1977-03       Impact factor: 3.582

7.  The embryonic cell lineage of the nematode Caenorhabditis elegans.

Authors:  J E Sulston; E Schierenberg; J G White; J N Thomson
Journal:  Dev Biol       Date:  1983-11       Impact factor: 3.582

8.  A global analysis of Caenorhabditis elegans operons.

Authors:  Thomas Blumenthal; Donald Evans; Christopher D Link; Alessandro Guffanti; Daniel Lawson; Jean Thierry-Mieg; Danielle Thierry-Mieg; Wei Lu Chiu; Kyle Duke; Moni Kiraly; Stuart K Kim
Journal:  Nature       Date:  2002-06-20       Impact factor: 49.962

9.  High-throughput gene mapping in Caenorhabditis elegans.

Authors:  Kathryn A Swan; Damian E Curtis; Kathleen B McKusick; Alexander V Voinov; Felipa A Mapa; Michael R Cancilla
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

Review 10.  Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors: 
Journal:  Science       Date:  1998-12-11       Impact factor: 47.728

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  64 in total

1.  The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.

Authors:  Olivier Tassy; Delphine Dauga; Fabrice Daian; Daniel Sobral; François Robin; Pierre Khoueiry; David Salgado; Vanessa Fox; Danièle Caillol; Renaud Schiappa; Baptiste Laporte; Anne Rios; Guillaume Luxardi; Takehiro Kusakabe; Jean-Stéphane Joly; Sébastien Darras; Lionel Christiaen; Magali Contensin; Hélène Auger; Clément Lamy; Clare Hudson; Ute Rothbächer; Michael J Gilchrist; Kazuhiro W Makabe; Kohji Hotta; Shigeki Fujiwara; Nori Satoh; Yutaka Satou; Patrick Lemaire
Journal:  Genome Res       Date:  2010-07-20       Impact factor: 9.043

2.  Molecular characterization of numr-1 and numr-2: genes that increase both resistance to metal-induced stress and lifespan in Caenorhabditis elegans.

Authors:  Brooke E Tvermoes; Windy A Boyd; Jonathan H Freedman
Journal:  J Cell Sci       Date:  2010-05-25       Impact factor: 5.285

3.  WormBase as an integrated platform for the C. elegans ORFeome.

Authors:  Nansheng Chen; Daniel Lawson; Keith Bradnam; Todd W Harris; Lincoln D Stein
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

4.  Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans.

Authors:  Gino Poulin; Yan Dong; Andrew G Fraser; Neil A Hopper; Julie Ahringer
Journal:  EMBO J       Date:  2005-06-30       Impact factor: 11.598

5.  Staying alive in adversity: transcriptome dynamics in the stress-resistant dauer larva.

Authors:  Suzan J Holt
Journal:  Funct Integr Genomics       Date:  2006-04-25       Impact factor: 3.410

6.  Graemlin: general and robust alignment of multiple large interaction networks.

Authors:  Jason Flannick; Antal Novak; Balaji S Srinivasan; Harley H McAdams; Serafim Batzoglou
Journal:  Genome Res       Date:  2006-08-09       Impact factor: 9.043

7.  Evolution of the metazoan protein phosphatase 2C superfamily.

Authors:  Adi Stern; Eyal Privman; Michal Rasis; Sara Lavi; Tal Pupko
Journal:  J Mol Evol       Date:  2006-12-06       Impact factor: 2.395

8.  A general model of G protein-coupled receptor sequences and its application to detect remote homologs.

Authors:  Markus Wistrand; Lukas Käll; Erik L L Sonnhammer
Journal:  Protein Sci       Date:  2006-02-01       Impact factor: 6.725

9.  Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library.

Authors:  Jean-François Rual; Julian Ceron; John Koreth; Tong Hao; Anne-Sophie Nicot; Tomoko Hirozane-Kishikawa; Jean Vandenhaute; Stuart H Orkin; David E Hill; Sander van den Heuvel; Marc Vidal
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

10.  Role of phosphatidylinositol-4-phosphate 5' kinase (ppk-1) in ovulation of Caenorhabditis elegans.

Authors:  Xiaojian Xu; Haisu Guo; Diane L Wycuff; Myeongwoo Lee
Journal:  Exp Cell Res       Date:  2007-03-24       Impact factor: 3.905

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