Literature DB >> 12519966

WormBase: a cross-species database for comparative genomics.

Todd W Harris1, Raymond Lee, Erich Schwarz, Keith Bradnam, Daniel Lawson, Wen Chen, Darin Blasier, Eimear Kenny, Fiona Cunningham, Ranjana Kishore, Juancarlos Chan, Hans-Michael Muller, Andrei Petcherski, Gudmundur Thorisson, Allen Day, Tamberlyn Bieri, Anthony Rogers, Chao-Kung Chen, John Spieth, Paul Sternberg, Richard Durbin, Lincoln D Stein.   

Abstract

WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.

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Year:  2003        PMID: 12519966      PMCID: PMC165500          DOI: 10.1093/nar/gkg053

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


  14 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.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

3.  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

4.  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

5.  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

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.  Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment.

Authors:  W J Kent; A M Zahler
Journal:  Genome Res       Date:  2000-08       Impact factor: 9.043

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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  47 in total

1.  A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors.

Authors:  Shuichi Wada; Miki Tokuoka; Eiichi Shoguchi; Kenji Kobayashi; Anna Di Gregorio; Antonietta Spagnuolo; Margherita Branno; Yuji Kohara; Daniel Rokhsar; Michael Levine; Hidetoshi Saiga; Nori Satoh; Yutaka Satou
Journal:  Dev Genes Evol       Date:  2003-05-08       Impact factor: 0.900

2.  SPINE 2: a system for collaborative structural proteomics within a federated database framework.

Authors:  Chern-Sing Goh; Ning Lan; Nathaniel Echols; Shawn M Douglas; Duncan Milburn; Paul Bertone; Rong Xiao; Li-Chung Ma; Deyou Zheng; Zeba Wunderlich; Tom Acton; Gaetano T Montelione; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2003-06-01       Impact factor: 16.971

3.  RPG: the Ribosomal Protein Gene database.

Authors:  Akihiro Nakao; Maki Yoshihama; Naoya Kenmochi
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects.

Authors:  Kristin C Gunsalus; Wan-Chen Yueh; Philip MacMenamin; Fabio Piano
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes.

Authors:  Todd Wylie; John C Martin; Michael Dante; Makedonka Dautova Mitreva; Sandra W Clifton; Asif Chinwalla; Robert H Waterston; Richard K Wilson; James P McCarter
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  UniProt: the Universal Protein knowledgebase.

Authors:  Rolf Apweiler; Amos Bairoch; Cathy H Wu; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Darren A Natale; Claire O'Donovan; Nicole Redaschi; Lai-Su L Yeh
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

7.  ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins.

Authors:  Thierry Hotelier; Ludovic Renault; Xavier Cousin; Vincent Negre; Pascale Marchot; Arnaud Chatonnet
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  TropGENE-DB, a multi-tropical crop information system.

Authors:  Manuel Ruiz; Mathieu Rouard; Louis Marie Raboin; Marc Lartaud; Pierre Lagoda; Brigitte Courtois
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

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

Authors:  Todd W Harris; 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
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

10.  The Rice PIPELINE: a unification tool for plant functional genomics.

Authors:  Junshi Yazaki; Keiichi Kojima; Kouji Suzuki; Naoki Kishimoto; Shoshi Kikuchi
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

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