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, 2019
Registration Deadline:  December 5, 2019
Early Discount:  December 5, 2019
Submit a Workshop Proposal: by November 1, 2019
Travel Award Deadline:  December 5, 2019

We will have C. elegans Community Scientific Sessions, and social events, with the opportunity to interact with 6 other Communities (Drosophila, Mammalian, PEQG, Xenopus, Yeast and Zebrafish).

* Abstracts will be considered for both the C. elegans Community Sessions, and for the Thematic Sessions, that include all 7 Communities.

~ 5 C. elegans Sessions, Invited Speakers, and Chairs ~

Development and Cell Biology

Invited Speaker: James Priess – Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Chair: Jessica Feldman – Stanford University, Stanford, CA, USA

New Technology and Resources in Development

Invited Speaker: Sander van den Heuvel – Utrecht University, Utrecht, The Netherlands
Chair: Jordan Ward – University of California, Santa Cruz, CA, USA

Genomics, Gene Regulation, and Systems Biology

Invited Speaker: Susan M. Gasser – Friedrich Miescher Institute, Basil, Switzerland
Chair: Florian Steiner – University of Geneva, Geneva, Switzerland

Neuronal Development

Invited Speaker: Oliver Hobert – Columbia University, New York, USA
Chair: Richard Poole – University College London, London, United Kingdom

Germ Line

Invited Speaker: Diane Shakes – College of William & Mary, Williamsburg, VA, USA
Chair: Diana Chu – San Francisco State University, San Francisco, CA, USA


Scientific Organizing Committee

Needhi Bhalla – U.C. Santa Cruz, Santa Cruz, USAMichalis Barkoulas – Imperial College London, London, UK
Olivia Casanueva – Babraham Institute, Cambridge, UK
Julie Claycomb – University of Toronto, Toronto, Canada
Luisa Cochella – Research Institute of Molecular Pathology (IMP), Vienna, Austria
Brent Derry – The Hospital for Sick Children, Toronto, Canada
Denis Dupuy – Inserm/University of Bordeaux, Bordeaux, France
Max Heiman – Harvard Medical School and Boston Children’s Hospital, Boston, USA
Diana Libuda – University of Oregon, Eugene, USA
Matt Marcello – Pace University, New York, USA
Alicia Melendez – Queens College, City University of New York, New York, USA
Fumio Motegi – National University of Singapore, Singapore, Singapore
Sara Olson – Pomona College, Claremont, USA
Yonathan Tzur – The Hebrew University of Jerusalem, Jerusalem, Israel
Natascia Ventura – Heinrich Heine University, Düsseldorf, Germany
Anne Wehmann – University of Würzburg, Würzburg, Germany
Itai Yanai – NYU School of Medicine, New York, USA

C. elegans workshops coordinator Coleen Murphy – Princeton University, Princeton, NJ, USA

GSA representative on Allied Program Committee for TAGC2020 Piali Sengupta – Brandeis University, Waltham, MA, USA


We ask for your help spreading the word about this exciting and unique scientific conference.  We welcome your ideas to make it a well–attended, interactive event.

Help us encourage broad participation from all members of our Community.


Your C. elegans Community Program Organizers

Martha and Mike

Mike Boxem – Utrecht University, Utrecht, The Netherlands   m.boxem@uu.nl
Martha Soto – Rutgers University, Piscataway, NJ, USA  sotomc@rutgers.edu

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.

WS267 release of WormBase

Please note that the WS267 release of WormBase is now live.  The complete release notes for WS267 can be viewed here.  Some of the highlights include–

Trichuris muris update
Trinity assembled RNASeq reads from publicly available short read data at SRA have been added to Trichuris muris as additional track and alignments. In addition IsoSeq data from long-range PacBio data (provided by the Berriman lab), corrected by genome alignment has been used as additional source to build transcript models.

In addition the Trichuris muris ncRNA gene set has increased from 26 to 759 following the integration of data produced by the WormBase Parasite ncRNA prediction pipeline. These transcripts have been fully integrated with stable IDs and associated naming and meta data.

Gene descriptions for T. muris will be coming in the WS268 release of WormBase.

Brugia malayi update
New gene models provided by the Beech lab for Parasitology at the McGill University have been merged into the official gene set.

WS266 release

Please note that the WS266 version of WormBase has been released! The release notes for this release describe the data types and their numbers. A list of all files available on our FTP site can also be viewed.  Changes in this release include the following:

Physical Interaction data curation

We have added over 5000 manually curated physical interactions which include binary protein-protein interactions as well as protein interactions that occur in a protein complex. Protein-protein interaction data can be found as a part of physical interaction data in the Interactions widget on the gene page. The Interactions widget provides different types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions.


Protein Identifiers

We have made a change to our internal identifiers for nematode protein sequences. Previously, we prefixed each identifier with *two* prefixes to denote which  species the protein is from, e.g. WP:CE00001. We have removed the first prefix (the “WP:”) from these identifiers.

Since these prefixes are almost entirely invisible on the site and have never been used by external resources hosting worm data (e.g. UniProt), this change should not affect most users.

WS265 release

loci with two different protein products

There are a small number of loci which code for two very different protein products. These include dicistronic mRNA operons and loci which have a few small exons in common then have alternate splicing leading to many different exons being used.

The details of some of these can be found in the WormBook chapter “Operon and non-operon gene clusters in the C. elegans genome”.

Previously, these have been curated as isoforms of a single gene. This was causing problems because the description of gene
function would be based on one isoform, leaving the other isoform undescribed or described incorrectly, based on the first isoform.
There are 42 C. elegans and 47 C. briggsae known loci that have now been split to have different Gene IDs.