Literature DB >> 29761466

Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.

Christian Grove1, Scott Cain2, Wen J Chen3, Paul Davis4, Todd Harris2, Kevin L Howe4, Ranjana Kishore3, Raymond Lee3, Michael Paulini4, Daniela Raciti3, Mary Ann Tuli3, Kimberly Van Auken3, Gary Williams4.   

Abstract

WormBase ( www.wormbase.org ) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.

Entities:  

Keywords:  Caenorhabditis elegans; Data mining; Genetics; Genomics; Model organism database; Nematodes; Ontologies; User guide

Mesh：

Substances：

Year:  2018        PMID： 29761466      PMCID： PMC6424801          DOI： 10.1007/978-1-4939-7737-6_14

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  56 in total

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

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

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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

3.  MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors:  Robert C Edgar
Journal:  Nucleic Acids Res       Date:  2004-03-19       Impact factor: 16.971

Review 4.  Caenorhabditis elegans: a versatile platform for drug discovery.

Authors:  Marta Artal-Sanz; Liesbeth de Jong; Nektarios Tavernarakis
Journal:  Biotechnol J       Date:  2006-12       Impact factor: 4.677

5.  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

6.  Genome-wide prediction of C. elegans genetic interactions.

Authors:  Weiwei Zhong; Paul W Sternberg
Journal:  Science       Date:  2006-03-10       Impact factor: 47.728

7.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi.

Authors:  Ravi S Kamath; Andrew G Fraser; Yan Dong; Gino Poulin; Richard Durbin; Monica Gotta; Alexander Kanapin; Nathalie Le Bot; Sergio Moreno; Marc Sohrmann; David P Welchman; Peder Zipperlen; Julie Ahringer
Journal:  Nature       Date:  2003-01-16       Impact factor: 49.962

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Authors:  Heng Li; Avril Coghlan; Jue Ruan; Lachlan James Coin; Jean-Karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang; Lars Bolund; Gane Ka-Shu Wong; Weimou Zheng; Paramvir Dehal; Jun Wang; Richard Durbin
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

Review 9.  A role for Caenorhabditis elegans in understanding the function and interactions of human disease genes.

Authors:  E Culetto; D B Sattelle
Journal:  Hum Mol Genet       Date:  2000-04-12       Impact factor: 6.150

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Journal:  Genome Biol       Date:  2007       Impact factor: 13.583
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  13 in total

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Authors:  Taylor N Medwig-Kinney; Jayson J Smith; Nicholas J Palmisano; Sujata Tank; Wan Zhang; David Q Matus
Journal:  Development       Date:  2020-01-02       Impact factor: 6.868

2.  Identification of Essential Genes in Caenorhabditis elegans with Lethal Mutations Maintained by Genetic Balancers.

Authors:  Shicheng Yu; Chaoran Zheng; Jeffrey Shih-Chieh Chu
Journal:  Methods Mol Biol       Date:  2022

3.  Using FlyBase: A Database of Drosophila Genes and Genetics.

Authors:  Victoria K Jenkins; Aoife Larkin; Jim Thurmond
Journal:  Methods Mol Biol       Date:  2022

4.  WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans.

Authors:  Basten L Snoek; Mark G Sterken; Margi Hartanto; Albert-Jan van Zuilichem; Jan E Kammenga; Dick de Ridder; Harm Nijveen
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

5.  Vennter - An interactive analysis tool for WormBase interaction data using Venn diagrams.

Authors:  Jaehyoung Cho; Sibyl Gao; Lincoln Stein; Paul W Sternberg
Journal:  MicroPubl Biol       Date:  2020-05-25

6.  Human Disease Ontology 2018 update: classification, content and workflow expansion.

Authors:  Lynn M Schriml; Elvira Mitraka; James Munro; Becky Tauber; Mike Schor; Lance Nickle; Victor Felix; Linda Jeng; Cynthia Bearer; Richard Lichenstein; Katharine Bisordi; Nicole Campion; Brooke Hyman; David Kurland; Connor Patrick Oates; Siobhan Kibbey; Poorna Sreekumar; Chris Le; Michelle Giglio; Carol Greene
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

7.  Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.

Authors:  Shawna Spoor; Chun-Huai Cheng; Lacey-Anne Sanderson; Bradford Condon; Abdullah Almsaeed; Ming Chen; Anthony Bretaudeau; Helena Rasche; Sook Jung; Dorrie Main; Kirstin Bett; Margaret Staton; Jill L Wegrzyn; F Alex Feltus; Stephen P Ficklin
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

8.  UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import in Caenorhabditis elegans.

Authors:  Tomer Shpilka; YunGuang Du; Qiyuan Yang; Andrew Melber; Nandhitha Uma Naresh; Joshua Lavelle; Sookyung Kim; Pengpeng Liu; Hilla Weidberg; Rui Li; Jun Yu; Lihua Julie Zhu; Lara Strittmatter; Cole M Haynes
Journal:  Nat Commun       Date:  2021-01-20       Impact factor: 14.919

9.  Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity.

Authors:  Julia Wang; Dongxue Mao; Fatima Fazal; Seon-Young Kim; Shinya Yamamoto; Hugo Bellen; Zhandong Liu
Journal:  Curr Protoc Bioinformatics       Date:  2019-09

10.  The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.

Authors:  Jennifer R Smith; G Thomas Hayman; Shur-Jen Wang; Stanley J F Laulederkind; Matthew J Hoffman; Mary L Kaldunski; Monika Tutaj; Jyothi Thota; Harika S Nalabolu; Santoshi L R Ellanki; Marek A Tutaj; Jeffrey L De Pons; Anne E Kwitek; Melinda R Dwinell; Mary E Shimoyama
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971
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