WormBase ParaSite is hiring
Got a passion for parasitic worm genomics? Join our team! We’re hiring a bioinformatician at University of Glasgow. The succesful applicant will work on a range of data analysis, data integration, curatorial and community-engagement activities for WormBase ParaSite (WB-PS). This will include driving annotation improvements within WB-PS by developing new workflows, and enabling updates from the research community. The post is available either for an experienced bioinformatician or a less experienced bioinformatician that wants to further develop their skills. For more information and to apply click here. (Source: WormBase)
Source: WormBase - March 30, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news positions available Wormbase Parasite Source Type: news
New release of the Alliance of Genome Resources
Check out the latest release (5.1.0) of the Alliance of Genome Resources for your favorite worm gene and get great comparative data across the major model organisms. A notable addition to this Alliance release are the member pages which link to organism or GO related data within the Alliance and to the model organism database or the GO Consortium. These pages can be accessed from the “Members” menu at the top of Alliance web pages. See the complete release notes for the 5.1.0 release. (Source: WormBase)
Source: WormBase - March 15, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news release notes Uncategorized Alliance of Genome Resources Source Type: news
FEBS Junior Sections initiative
Students and young researchers from some of the national Societies have created the ‘FEBS Junior Sections‘, an initiative to connect young scientists in the molecular life sciences across Europe. They organise online events and the next one is a talk on C. elegans.
FEBS Junior Sections/Young NVBMB invite you to an online talk on “Elucidating the molecular mechanisms of protein aggregation in C. elegans as a living model system”.
Time: 10 March 2022, 19:00 (CET)
Registration: https://network.febs.org/posts/young-nvbmb-febs-junior-sections-present-tessa-sinnige (Source: WormBase)
Source: WormBase - March 7, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news meetings talk Source Type: news
Two new chapters in WormBook, GENETICS
Check out these new chapters in WormBook, GENETICS: “Mechanisms of sex determination and X-chromosome dosage compensation” by Barbara Meyer and “Germ granules and gene regulation in the Caenorhabditis elegans germline” by Carolyn Phillips and Dustin Updike. (Source: WormBase)
Source: WormBase - March 6, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news
Service status update: WormBase tools back online
Several WormBase tools that were unavailable this morning (see blog post below) during server upgrades are now back online. Thank you for your patience. (Source: WormBase)
Source: WormBase - March 1, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news service status tools Source Type: news
Please note that some WormBase tools are down
Please note that because of server upgrades that we are doing the following WormBase tools are not available for use, including the Author First Pass form. We apologize for any inconvenience caused. The following tools are currently out of service:
SimpleMine
Gene Set Enrichment Analysis
Gene Name Sanitizer
Expression Dataset Locator
RNA-Seq FPKM Gene Search
Gene-pair Ontology Graph
Terms Ontology Graph
Wormicloud (Source: WormBase)
Source: WormBase - March 1, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news service status tools Source Type: news
C. elegans mutation accumulation lines ready soon
Ladies and Gentlemen,
We are writing to announce that the C. elegans mutation accumulation lines for which we wrote a grant proposal back in 2017 and for which you all generously provided letters of support are now almost ready for public dissemination. First things first: THANK YOU ALL! We surely would not have been able to do this project without your kind support. Details follow. Please feel free to advertise this resource to your friends and neighbors, and to think up cool things to do with them. We made them for everyone to use!
-Charlie Baer (University of Florida) and Vaishali Katju (Texas A&M Un...
Source: WormBase - February 28, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news C. elegans lines C.elegans Source Type: news
New chapter about DNA repair in WormBook, GENETICS
Check out this new chapter in WormBook, GENETICS, “DNA repair, recombination, and damage signaling” by Anton Gartner and JoAnne Engebrecht. (Source: WormBase)
Source: WormBase - February 14, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news paper of interest wormbook Source Type: news
Announcing the Mentor-Mentee matches for 2022
With gratitude to all those who agreed to be mentors, and with thanks to the C. elegans Community Mentor Match program committee, we announce this year’s mentor-mentee matches.
Read more about the program rollout.
Here’s a complete list of all 2022 matches.
To those of you who offered to mentor but were not selected for a match this year, undoubtedly there will be opportunities in the future!! In the meantime, please stay tuned for these and other opportunities to serve the community.
For those mentors and mentees who did match, the committee will contact you later in the year to se...
Source: WormBase - February 7, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: community external website news mentor match initiative Source Type: news
WormBase in 2022
Check out the paper “WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans” to read about new data and tools and the latest updates. Also, see guidelines for citing WormBase here. (Source: WormBase)
Source: WormBase - February 4, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: news paper of interest citing wormbase Source Type: news
New operons in C. briggsae
Kindly, Dr. Itai Antoine Toker made us aware of the paper Uyar et al. Genome Research 2012 (PMID: 22772596/ WBPaper00041271), which contains a genome-wide set of operon predictions for C. briggsae. The data was mapped forward to the current gene set using the Sequence IDs supplied. 1034 operons were captured from the publication, but because of the time between publication and extensive re-annotation of C. briggsae only 709 of these operons had enough information to allow us to map them precisely onto the genome and supplement the C. briggsae operon JBrowse track. If you find some interesting dataset you’d like WormB...
Source: WormBase - February 4, 2022 Category: Genetics & Stem Cells Authors: Magdalena Zarowiecki Tags: new datasets paper of interest C.briggsae Source Type: news
3D structures for all proteins
AlphaFold is an AI system, created in partnership between DeepMind and the EMBL-European Bioinformatics Institute (EMBL-EBI), that makes predictions of a protein’s structure from its amino-acid sequence. Go to their webpage to look at your favourite protein from C. elegans, Brugia, Onchocerca, Strongyloides, Trichuris or Wuchereria. If your favourite protein is missing, remember that any protein with >90% amino acid similarity is quite likely to have a very similar structure. And if you spot any structure that does not look right contact help@wormbase.org, and we’ll forward your feedback. (Source: WormBase)
Source: WormBase - February 3, 2022 Category: Genetics & Stem Cells Authors: Magdalena Zarowiecki Tags: external website news new datasets Uncategorized Source Type: news
New Chapter in WormBook, GENETICS – Natural Genetic Variation as a Tool
Check out this new chapter in WormBook, GENETICS, “Natural genetic variation as a tool for discovery in Caenorhabditis nematodes” by Erik C. Andersen and Matthew V. Rockman (published Jan 04, 2022). (Source: WormBase)
Source: WormBase - February 2, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: external website news paper of interest wormbook Source Type: news
Update on CeNeuro2022
Dear Participants of CeNeuro 2022,
We look forward to a rich and stimulating meeting this summer! To remind everyone, the date is set for July 24-27, 2022.
As uncertainty around the world continues, we cannot make a decision on the format at the moment. We desperately hope to be able to organize a hybrid meeting and welcome as many people as possible in person, in Vienna. However, we will re-evaluate this decision in mid/end of March and and if a hybrid meeting is not possible, we will still hold an online only meeting.
Regardless of the final format, please note that the deadline for abstract submission will be ...
Source: WormBase - January 5, 2022 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication meetings news Uncategorized Source Type: news
Two new genes in C. elegans!
After more than 20 years of careful manual curation of C. elegans, it is quite unusual to find new protein-coding genes. But in release WS283 we have no less than 2 new genes! We were alerted to the first one by Dr. Adam Norris from Southern Methodist University, Dallas, TX, USA. Working with WormBase curators, we were able to comprehensively annotate the new gene. As finding a new gene is such a remarkable event, Dr. Norris opted for writing a micropublication describing the new gene WBGene00306123 (Y97E10C.2). Iyengar, A; Diamantakis, S; Norris, A (2021), “A new gene on C. elegans chromosome V”
Buoyed by the ...
Source: WormBase - December 21, 2021 Category: Genetics & Stem Cells Authors: Magdalena Zarowiecki Tags: brief communication news Uncategorized new gene WS283 Source Type: news
