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 using one of the “type-specifi...
Source: WormBase - March 18, 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 WormBase release (...
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, searching by a human disease na...
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 genes, molecul...
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, regulatory, and predic...
Source: WormBase - November 27, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest tutorials protein interaction WS267 Source Type: news
New SPELL server: Fresh look and faster
Please note that we have moved the WormBase SPELL tool to a new server on the Amazon Cloud: https://spell.wormbase.org. This should not affect any of our users, as the ‘Tools’ link on the main WormBase menu bar will take you to this new URL.
SPELL (Serial Pattern of Expression Levels Locator) is a query-driven search engine for microarray, RNAseq and Proteomics data. Given a small set of query genes, SPELL identifies which datasets are most informative for these genes, then within those datasets, additional genes are identified with expression profiles most similar to the query set. WormBase SPELL has colle...
Source: WormBase - November 16, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news tutorials SPELL tools Source Type: news
