Maintenance Service Interruption: Thursday, November 28, 2019.
WormBase will be unavailable for approximately one hour on Thursday, November 28, 2019 starting at 12:00 PM ET (UTC -4). We apologize in advance for the disruption and plan to have service restored as quickly as possible. (Source: WormBase)
Source: WormBase - November 26, 2019 Category: Genetics & Stem Cells Authors: Todd Harris Tags: Uncategorized Source Type: news

WS273 version of WormBase
Please note that the WS273 version of WormBase is live on our website.  The release notes for this version contain a detailed report of the various entities (eg. gene, allele) and the number of sequence and biological annotations. Some of the highlights are: C.elegans Nanopore data has been integrated and is being used to improve UTR annotation. Further work on improving our automatic transcript annotation is ongoing. This release includes a few hundred gene splits in Pristionchus pacificus predicted by the Sommer lab based on IsoSeq analysis. More will be included in future releases. (Source: WormBase)
Source: WormBase - November 22, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes WS273 Source Type: news

Please cite the original papers where possible
When you write a paper, wherever possible cite the original, primary papers so the authors get credit. If you have used data amalgamated by WormBase, then please cite WormBase with the release version. (Source: WormBase)
Source: WormBase - November 21, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news Source Type: news

C. elegans meetings at the TAGC 2019
The C. elegans community is having sessions at The Allied Genetics Conference (TAGC), April 22-26, 2020 in Washington DC, organized by Martha Soto and Mike Boxem. Note that the abstract and early registration deadline is December 5. The C. elegans relevant page of the TAGC is here. (Source: WormBase)
Source: WormBase - November 13, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news meetings Source Type: news

Check out the new chapter in WormBook, GENETICS
Check out the latest chapter in WormBook, GENETICS: Developmental Plasticity and Cellular Reprogramming in Caenorhabditis elegans, by Joel Rothman and Sophie Jarriault. (Source: WormBase)
Source: WormBase - November 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news

Check out the WormBase paper in NAR
If you’d like to read about the latest developments at WormBase—literature curation efforts, features about the web interface, data mining options for users, and how WormBase as a founding member, interacts with the Alliance of Genome Resources to aid in cross-species data comparisons, check out our paper in Nucleic Acids Research. (Source: WormBase)
Source: WormBase - November 4, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication Featured Papers news paper of interest wormbase Source Type: news

C. elegans Development, Cell Biology, and Gene Expression Meeting
Dear Members of the Worm Community, We are happy to announce that registration is now open for: C. elegans Development, Cell Biology, and Gene Expression Meeting, within the larger TAGC 2020 Meeting, April 22–26, 2020. Conference website:    https://genetics-gsa.org/tagc-2020/   Location:  Washington, DC, USA (Gaylord National Resort & Convention Center)Abstract Submission Deadline*: December 5, 2019Registration Deadline:  December 5, 2019Early Discount:  December 5, 2019Submit a Workshop Proposal: by November 1, 2019Travel Award Deadline:&...
Source: WormBase - October 12, 2019 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: meetings Source Type: news

Join the CGC Team at the University of Minnesota!
Love worms and want to serve your community? Join the CGC and be instrumental in distributing C. elegans to the worldwide research community.  After 27 years of dedication to fulfilling our C. elegans needs, Theresa Stiernagle is retiring. The CGC seeks a replacement with significant worm experience (picking, scoring phenotypes, familiarity with interpreting genotypes, etc.), extreme attention to detail, and the ability to work efficiently and independently. An official job posting will be forthcoming, but in the meantime, inquiries can be made at cgc@umn.edu. (Source: WormBase)
Source: WormBase - October 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news positions available cgc Source Type: news

New chapter in WormBook, GENETICS
Check out the latest new chapter in WormBook, GENETICS: TOR Signaling in Caenorhabditis elegans Development, Metabolism and Aging, by T. Keith Blackwell, Aileen K. Sewell, Ziyun Wu and Min Han. (Source: WormBase)
Source: WormBase - October 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news

Call for Proposals for Undiagnosed Disease Network Gene Function Studies
The Call for Proposals for Undiagnosed Disease Network Gene Function Studies has been posted on the UDN website: https://undiagnosed.hms.harvard.edu/research/funding-opportunities/ Researchers outside of the United State can apply. (Source: WormBase)
Source: WormBase - September 22, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news grants Undiagnosed disease network Source Type: news

microPublications now indexed in Europe PMC!
microPublications are now integrated in the search, citation network, text-mining pipeline, ORCID claiming and other tools and services provided by Europe PMC. Indexing in Europe PMC increases the visibility of your microPublication, making it easier for others to find and cite your research. To learn more, visit the Europe PMC website. Thank you for supporting Open Science by sharing your data with the community! (Source: WormBase)
Source: WormBase - September 20, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news micropublication Source Type: news

New Chapter in WormBook, GENETICS
Check out the latest chapter in WormBook, GENETICS: Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes by Asher D. Cutter, Levi T. Morran and Patrick C. Phillips. (Source: WormBase)
Source: WormBase - September 9, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news paper of interest wormbook Source Type: news

C. elegans as a model for studying human diseases
There is a growing body of literature showing that C. elegans is a great model that contributes to the study of human disease.  Recently Dr. Andy Golden alerted us to this bit of news: Check out the show ‘Diagnosis’ on Netflix by the New York Times (episode 4). There is a very rare disease caused by mutations in the human KCNMA1 gene. If you study slo-1, perhaps you can help these patients. (Source: WormBase)
Source: WormBase - September 4, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news

New chapter in WormBook (GENETICS): The Caenorhabditis elegans Transgenic Toolbox
Check out this useful chapter ‘The Caenorhabditis elegans Transgenic Toolbox‘ by Jeremy Nance and Christian Frøkjær-Jensen in the latest issue of WormBook, GENETICS. (Source: WormBase)
Source: WormBase - August 26, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Featured Papers paper of interest tools wormbook Source Type: news

WormBase workshop talks at the 2019 IWM available on Youtube
Talks delivered at the WormBase workshop as part of the International C. elegans meeting at UCLA in June 2019 are now available on Youtube. Please note that these are recordings done at the workshop with external cameras and microphones, so apologies if they are not of the highest quality.  They are linked from their titles below– Introduction to the WormBase webpages and widgets WormBase data mining tools: SimpleMine, WormMine, BioMart WormBase ontologies and gene set enrichment analysis WormBase JBrowse: tutorial and demo Community curation Introduction to the Alliance of Genome Resources   (Source: WormBase)
Source: WormBase - August 2, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication meetings news tutorials IWM Source Type: news

Looking for naming conventions and guidelines?
If you have started a new worm lab or are looking for nomenclature guidelines for genes, alleles and other genetic entities, please consult this page of our online user guide–https://wormbase.org/about/userguide/nomenclature#f1il048b3g6e2597cmdjkh–10 Different types of properly named entities (genes, alleles, strains, trangenes, etc.) in published papers are identified by text-mining and other WormBase tools and/or via manual curation. Following official nomenclature guidelines makes your data discoverable by WormBase and thus to the whole community! (Source: WormBase)
Source: WormBase - July 25, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news tutorials nomenclature Source Type: news

If you haven ’t signed up with WormBase, please consider doing so!
Several interactions with WormBase require that you have a WBPerson identification.  Use this form to request one, if you don’t have one already. In addition, you can also add or update your intellectual lineage. (Source: WormBase)
Source: WormBase - July 18, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news Source Type: news

New and Improved Author First Pass Pipeline!
Community curation is a valuable part of WormBase. For the past ten years, C. elegans researchers have participated in our ‘Author First Pass’ pipeline using a web-based form to alert WormBase curators to entities and data types in their newly published papers. We are very excited to announce a new and improved ‘Author First Pass’ pipeline that uses the Textpresso Central text mining system to automatically extract entities and identify data types in new C. elegans papers. As before, corresponding authors will receive an email (Help WormBase curate your paper!) shortly after publication of thei...
Source: WormBase - June 5, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community new features news author first pass data type text mining Textpresso Source Type: news

Come and talk to WormBase staff at the IWM 2019!
It’s that year again when worm breeders and worm lovers will be at UCLA from June 20th-24th for the International Worm Meeting. WormBase will be there in full force and will participate in several events–talks, workshops and booths. WormBase staff will be at our booth during the poster sessions in Pauley Pavilion, come talk to us and feel free to ask any questions related to data and data querying and give us your suggestions and comments. Also, take the opportunity to visit the microPublication booth and find out how to micropublish your results. WormBase related events at IWM 2019 include– Thursda...
Source: WormBase - June 3, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community meetings news Source Type: news

New VC2010 and improved CB4856 genomes published
The VC2010 genome assembly has just been published in Genome Research as an open-access article. This assembly is largely derived from a completely isogenic VC2010-derived strain, PD1074, that is now available from the CGC. In related news, Junho Lee and his lab have simultaneously published an open-access article on their substantially improved genome assembly for Hawaiian C. elegans (CB4856). (Source: WormBase)
Source: WormBase - May 24, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news paper of interest genomes new genome Source Type: news

UC Davis features micropublications
microPublication.org publishes brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative. Each article is peer reviewed and assigned a DOI. Included data is curated and, upon publication, deposited in third party referential databases (when available). Recently UC Davis featured an article, ‘Small Science Snippets: Micropubs Help Share Discoveries‘ about how one of their researchers used a micropublication to publish their results. Micropublish your results today! (Source: WormBase)
Source: WormBase - May 17, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news micropublication Source Type: news

WormBase updated to the WS270 release
Alliance orthologs Starting from WS270 we are using the Alliance of Genome Resources for orthologs between model organism genes. This should be more comprehensive and include the latest data from our sister databases. VC2010 genome An assembly and geneset of the VC2010 C.elegans strain has been added and work is ongoing to improve the integration and display of strain specific data. Additionally more mappings of N2 annotation will be included in future releases. (Source: WormBase)
Source: WormBase - May 15, 2019 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes Alliance of Genome Resources WS270 Source Type: news

An appreciation of Sydney Brenner
See this beautiful appreciation of Sydney Brenner by Peter Lawrence in DEVELOPMENT.   (Source: WormBase)
Source: WormBase - May 10, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news research community Sydney Brenner Source Type: news

SGD turns 25!
25 years ago the SGD (The Saccharomyces Genome Database) went online.  Happy Birthday SGD! SGD provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms. SGD collaborates with WormBase on several database-related projects including the Alliance of Genome Resources.  Check it out! (Source: WormBase)
Source: WormBase - May 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources SGD Source Type: news

Short WormBase downtime yesterday
WormBase went down at 2.54pm ET yesterday. The problem was caused ironically by a fault recovery mechanism that was introduced recently. The fault recovery mechanism takes faulty servers out of service and replaces them with healthy ones. The process involves two components:the detection of faulty servers and the creation of new ones. Two simultaneous problems in the two components lead to the failure. A false positive in detecting the faulty server caused the sever to be taken out of service, and a missing hard drive snapshot caused the failure to start new servers. To avoid such future occurrences we are looking into way...
Source: WormBase - May 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news

New chapter in WormBook, GENETICS, on sensing of physical stimuli in C. elegans
Check out the new chapter in WormBook, GENETICS–‘How Caenorhabditis elegans Senses Mechanical Stress, Temperature, and Other Physical Stimuli‘ by Miriam Goodman and Piali Sengupta. (Source: WormBase)
Source: WormBase - May 7, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news

Tuesday, April 30th – early registration deadline for IWM 2019
Please note that Tuesday, April 30th is the deadline for early registration for the International C. elegans conference at UCLA. (Source: WormBase)
Source: WormBase - April 29, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community meetings news IWM Source Type: news

Sydney Brenner passes away
Sydney Brenner, the Nobel prize-winning molecular biologist who pioneered the use of C. elegans as a model organism has passed away. https://www.nature.com/articles/d41586-019-01128-3 (Source: WormBase)
Source: WormBase - April 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news Source Type: news

WormBase is up to date with curation of protein-protein interactions
We have now curated all C. elegans protein-protein interactions (physical) from the published literature. In the current release, WS269, we have over 30,000 binary gene pair interactions. Please let us know if we have missed anything! (Source: WormBase)
Source: WormBase - March 29, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news curation protein interaction Source Type: news

Important Dates for the 22nd International C. elegans Conference
The abstract submission deadline for the 22nd International C. elegans Conference is March 28th! The conference will be held June 20-24, 2019 at UCLA. For more information visit the conference website. Abstract Submission Deadline: March 28 Submit an abstract Registration Discounted early registration: April 30 Discounted advance registration: May 1 – June 17 Register for the conference Housing Reservations Deadline: May 15 Make a housing reservation (Source: WormBase)
Source: WormBase - March 23, 2019 Category: Genetics & Stem Cells Authors: Todd Harris Tags: meetings news Source Type: news

Getting DNA sequence from JBrowse
There are two ways that users can download DNA sequence from JBrowse: in relation to a feature, like a gene, or by specific sequence coordinates. Getting Sequence for a Gene or Transcript To get the sequence for a gene, open any of the “Curated Genes” tracks and right click or control click on the feature and select “View Sequence” from the resulting popup menu. If you are using the main “Curated Genes” track, you’ll get a dialog box asking which transcript you want to view. It does this because it needs to know what subfeatures like exons and introns can be shown. If you’re ...
Source: WormBase - March 19, 2019 Category: Genetics & Stem Cells Authors: Scott Cain Tags: brief communication news tutorials jbrowse Source Type: news

New GENETICS WormBook Chapter on Developmental Control of the Cell Cycle
Check out the new chapter of WormBook in GENETICS– ‘Developmental Control of the Cell Cycle: Insights from Caenorhabditis elegans‘ by Edward T. Kipreos and Sander van den Heuvel. (Source: WormBase)
Source: WormBase - March 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news

Gene Ontology Consortium turns 20
The Gene Ontology (GO) resource turns 20! Check out the latest paper describing this resource.  WormBase uses GO to describe the molecular function, cellular localization and the biological processes that a gene is involved in.  These annotations are displayed in the Gene Ontology widget on all gene pages in WormBase.  The ontology structure including the number of genes annotated to each term can be viewed via tools such as the Ontology Browser. GO Enrichment Analysis can be performed using tools on the GO website.  Data files (known as gene association files) of all the GO annotations in the latest Wo...
Source: WormBase - March 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news gene ontology Source Type: news

Paper of Interest: Identification of functional long non-coding RNAs in C. elegans.
This paper predicts 143 new multi-exonic lncRNA loci in C. elegans, along with ~3,000 possible new single-exon lncRNA loci.   (Source: WormBase)
Source: WormBase - March 1, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest Source Type: news

Biocurator position open at WormBase
A biocurator position is open at WormBase.  If you are interested and for further details please contact Paul Sternberg at pws@caltech.edu (Source: WormBase)
Source: WormBase - February 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news positions available Source Type: news

Integrated model organism data at the Alliance of Genome Resources
It is now possible to view integrated data from six different Model Organism Databases (MODs) and the Gene Ontology (GO) Consortium at the Alliance of Genome Resources (Alliance).  One can view gene descriptions, disease model data, orthology data, gene expression data and much more for the six major model organisms (yeast, worm, fly, zebrafish, mouse, rat) as well as human data on gene pages at the Alliance.   You can search by gene, disease or a GO term and be taken to a page where you will find integrated views of data relevant to all of the above mentioned organisms.   For example, searchi...
Source: WormBase - February 7, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources Source Type: news

New gene descriptions for the WS268 release of WormBase
The WS268 release of WormBase features new automated gene descriptions (displayed in the ‘Overview’ widget at the top of the gene page). In addition to the code being entirely rewritten, we have also added gene descriptions for a new worm species – Trichuris muris.   These automated gene descriptions are highly structured and are based on curated data such as orthology data, Gene Ontology (GO) annotations, Disease Ontology (DO) annotations, gene expression data, etc., in WormBase. The following data-types are included in the description of a given gene, when available: orthology to human ge...
Source: WormBase - January 14, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new datasets news WS268 Source Type: news

WormBase updated to the WS268 release
Please note that the WormBase website has been updated to the WS268 release.  Details about this release may be found in the Release Notes for WS268.  The notes include a list of files that we publish on our FTP site. (Source: WormBase)
Source: WormBase - January 13, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes new release WS268 Source Type: news

New chapter of WormBook in GENETICS
Check out the new chapter of WormBook in GENETICS about mitotic cell division by Lionel Pintard and Bruce Bowerman – ‘Mitotic Cell Division in Caenorhabditis elegans‘. (Source: WormBase)
Source: WormBase - January 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news

Paper of Interest: Comparative study of 81 genomes of parasitic and non-parasitic worms
Check out the paper ‘Comparative genomics of the major parasitic worms’ in Nature Genetics by the International Helminth Genomes Consortium and the ‘News and Views’ article by Paul Sternberg, ‘Opening up a large can of worms‘. (Source: WormBase)
Source: WormBase - December 5, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest genomes parasite genomes Source Type: news

Update on protein-protein interaction data in WormBase
Currently WormBase contains over 28,000 physical protein-protein interactions of which 1,500 protein-protein interactions have been curated by BioGRID as a collaboration with WormBase. Within the data set, over 17,000 protein-protein interactions are unique, and over 6,000 unique genes are involved in these interactions. In WormBase, protein-protein interaction data can be found as a subclass of physical interaction data in the ‘Interactions widget’ on the gene report page. The interactions widget provides all types of interaction data related to the gene of interest, such as physical, genetic, regula...
Source: WormBase - November 28, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest tutorials protein interaction WS267 Source Type: news