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

T. W. Harris
2004 Nucleic Acids Research  
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  ...  ACKNOWLEDGEMENTS WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and the British Medical Research Council.  ...  RESOURCES FOR THE BIOINFORMATICIST WormBase offers many tools for those researchers interested in data mining and programmatic analysis of the resource.  ... 
doi:10.1093/nar/gkh066 pmid:14681445 pmcid:PMC308800 fatcat:afby3v5drfe6pfuzqbumxqkb6a

WormBase 2014: new views of curated biology

Todd W. Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian Grove, Kevin Howe, Ranjana Kishore, Raymond Lee (+21 others)
2013 Nucleic Acids Research  
WormBase now houses the reference genomic sequence annotation for >20 nematode species.  ...  GENOMES AND SPECIES The C. elegans reference genome and sequence annotation Careful manual curation of the C. elegans reference genome sequence and annotation continues to be a key activity for WormBase  ... 
doi:10.1093/nar/gkt1063 pmid:24194605 pmcid:PMC3965043 fatcat:lh2mkgbydvfwrdngdv7nz3icme

WormBase: a modern Model Organism Information Resource

2019 Nucleic Acids Research  
WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic  ...  We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.  ...  ACKNOWLEDGEMENTS The authors wish to thank funding agencies for their ongoing support of WormBase and members of the C. elegans research community whose results form the foundation and purpose of WormBase  ... 
doi:10.1093/nar/gkz920 pmid:31642470 pmcid:PMC7145598 fatcat:6gcdoykkt5fmjji2i67akl3sw4

WormBase 2012: more genomes, more data, new website

K. Yook, T. W. Harris, T. Bieri, A. Cabunoc, J. Chan, W. J. Chen, P. Davis, N. de la Cruz, A. Duong, R. Fang, U. Ganesan, C. Grove (+27 others)
2011 Nucleic Acids Research  
Since its release in 2000, WormBase (http://www .wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential  ...  Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing.  ...  Finally, as we have transitioned from a single species to a multi-species resource, we built a new website released as a public beta version in September 2011.  ... 
doi:10.1093/nar/gkr954 pmid:22067452 pmcid:PMC3245152 fatcat:4jkq3undtzc6lporuvo3nteium

Methods and strategies for gene structure curation in WormBase

G. W. Williams, P. A. Davis, A. S. Rogers, T. Bieri, P. Ozersky, J. Spieth
2011 Database: The Journal of Biological Databases and Curation  
The Caenorhabditis elegans genome sequence was published over a decade ago; this was the first published genome of a multi-cellular organism and now the WormBase project has had a decade of experience  ...  In one of its roles as a central repository for nematode biology, WormBase continues to refine the gene structure annotations using sequence similarity and other computational methods, as well as information  ...  This system has been found to be easy to extend to the other nematode species that are being curated in WormBase and it is easy to add new types of evidence for a gene structure change.  ... 
doi:10.1093/database/baq039 pmid:21543339 pmcid:PMC3092607 fatcat:nptcyaxhirhwpatcl6aylqeb5u

Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes [chapter]

Christian Grove, Scott Cain, Wen J. Chen, Paul Davis, Todd Harris, Kevin L. Howe, Ranjana Kishore, Raymond Lee, Michael Paulini, Daniela Raciti, Mary Ann Tuli, Kimberly Van Auken (+1 others)
2018 Msphere  
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  ...  Comparative Genomics Other Nematode Genomes WormBase contains genomic data from many nematode species beyond C. elegans (http:// www.wormbase.org/species/all).  ... 
doi:10.1007/978-1-4939-7737-6_14 pmid:29761466 fatcat:pmvjwlblwrf6fkwid5fm272sfq

Toward 959 nematode genomes

Sujai Kumar, Georgios Koutsovoulos, Gaganjot Kaur, Mark Blaxter
2012 Worm  
The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model  ...  To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/).  ...  We thank all our colleagues around the world who are sequencing nematode genomes and adding information to the wiki.  ... 
doi:10.4161/worm.19046 pmid:24058822 pmcid:PMC3670170 fatcat:bnsl3sgtx5bxnelky6lnvfccui

Nematode phospholipid metabolism: an example of closing the genome–structure–function circle

Soon Goo Lee, Joseph M. Jez
2014 Trends in Parasitology  
As an example of how genome data, structural biology, and biochemistry integrate into a research cycle targeting parasites, we summarize the discovery of the phosphobase methylation pathway for phospholipid  ...  The growing availability of nematode genomes supports the discovery of new pathways that differ from host organisms and are a starting point for structural and functional studies of novel antiparasitic  ...  Combining genomics, structural biology, biochemistry, and parasitology A hallmark feature in modern drug discovery and development is a research cycle that combines genomic information, structural biology  ... 
doi:10.1016/j.pt.2014.03.001 pmid:24685202 pmcid:PMC4040950 fatcat:jjcaggeqtzafzmt6zeapdfyxzm

KinFin: Software for taxon-aware analysis of clustered protein sequences [article]

Dominik R Laetsch, Mark L Blaxter
2017 bioRxiv   pre-print
A common approach is to define gene families by clustering protein sequences based on sequence similarity, and analyse protein cluster presence and absence in different species groups as a guide to biology  ...  We illustrate the utility of the KinFin pipeline by addressing questions regarding the biology of filarial nematodes, which include parasites of veterinary and medical importance.  ...  Ensembl 18 comparative genomics resources.  ... 
doi:10.1101/159145 fatcat:7dtjocxdgjhv5klsp72wdqb7y4

Tackling Hypotheticals in Helminth Genomes

Nikola Palevich, Collette Britton, Laura Kamenetzky, Makedonka Mitreva, Marina de Moraes Mourão, Sasisekhar Bennuru, Thomas Quack, Larissa Lopes Silva Scholte, Rahul Tyagi, Barton E. Slatko
2018 Trends in Parasitology  
Inferring gene function for nematodes is therefore a major challenge, 71 especially where little genomic and transcriptomic information is available.  ...  also been identified from some nematode 155 species.  ...  WormBase ParaSite: web-accessible central data repository for information about Caenorhabditis elegans and related nematodes (http://www.wormbase.org).  ... 
doi:10.1016/j.pt.2017.11.007 pmid:29249363 fatcat:2iemihwk6zavdcojlcpn44myvm

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes

Todd Wylie, John Martin, Sahar Abubucker, Yong Yin, David Messina, Zhengyuan Wang, James P McCarter, Makedonka Mitreva
2008 BMC Genomics  
Nematode.net http://www.nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes.  ...  The NemaPath approach consists of two parts: 1) a backend tool to align and evaluate nematode genomic sequences (curated EST contigs) against the annotated Kyoto Encyclopedia of Genes and Genomes (KEGG  ...  Jarret Glasscock, Mike Dante, Billy Li, and Rick Meyer of the Genome Center at Washington University School of Medicine provided additional project feedback.  ... 
doi:10.1186/1471-2164-9-525 pmid:18983679 pmcid:PMC2588608 fatcat:gek5pi4yyfbcpagyizlmxog5hi

Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

Gary Schindelman, Jolene S Fernandes, Carol A Bastiani, Karen Yook, Paul W Sternberg
2011 BMC Bioinformatics  
The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species.  ...  Conclusions: We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species comparisons within the nematode community.  ...  suggestions; Norie de la Cruz for his work on the phenotype ontology search tool and fellow curators at WormBase for their valuable input.  ... 
doi:10.1186/1471-2105-12-32 pmid:21261995 pmcid:PMC3039574 fatcat:j7nmqr5wirfxpnxd65zx3lfmay

Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons

Nicolas J Wheeler, Paul M. Airs, Mostafa Zamanian, Krystyna Cwiklinski
2020 PLoS Neglected Tropical Diseases  
Recently there has been a coordinated global effort to generate, annotate, and curate genomic data from nematode species of medical and veterinary importance.  ...  nematode genome assemblies.  ...  The release of the B. malayi draft genome initiated a wave of target-based approaches that leverage genomic data, molecular biology, and rational target selection, which allow for the cloning, expression  ... 
doi:10.1371/journal.pntd.0008869 pmid:33196647 fatcat:ma5pbmcamvazbg55czvlbieozy

Phylum-Spanning Neuropeptide GPCR Identification and Prioritization: Shaping Drug Target Discovery Pipelines for Nematode Parasite Control

Louise E. Atkinson, Ciaran J. McCoy, Bethany A. Crooks, Fiona M. McKay, Paul McVeigh, Darrin McKenzie, Allister Irvine, John Harrington, Bruce A. Rosa, Makedonka Mitreva, Nikki J. Marks, Aaron G. Maule (+1 others)
2021 Frontiers in Endocrinology  
We show that, whilst parasitic nematodes possess a reduced complement of Ce-NP-GPCRs, several receptors are broadly conserved across nematode species.  ...  These data focus functional validation efforts towards the most appealing NP-GPCR targets and, in addition, the prioritization strategy employed here provides a blueprint for parasitic nematode target  ...  ACKNOWLEDGMENTS The authors wish to thank Dr James Cotton, Dr Shelly Michalski, and Dr Elodie Ghedin for providing resources and advice.  ... 
doi:10.3389/fendo.2021.718363 pmid:34659113 pmcid:PMC8515059 fatcat:2u6qqaebizbtdksklcek6kznua

Large-Scale Screening for Targeted Knockouts in the Caenorhabditis elegans Genome

2012 G3: Genes, Genomes, Genetics  
The nematode Caenorhabditis elegans is a powerful model system to study contemporary biological problems.  ...  This knowledge will usher in a new age of metazoan genetics in which the contribution to any biological process can be assessed for all genes.  ...  We thank the CGC, especially Aric Daul, who have provided a home for this resource and have sent out several thousand KO strains to the community.  ... 
doi:10.1534/g3.112.003830 pmid:23173093 pmcid:PMC3484672 fatcat:mnzvu7lnfrcenknlfeldrvc6de
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