Help us by acknowledging WormBase in your publications.

We would like to enlist your help in ensuring that WormBase continues to exist and is successful. You can do this by explicitly acknowledging WormBase in each of your papers when you have used it in the planning, design, execution, analysis, or reporting of the research described.

This simple task will help us make the case to administrators at NIH and others for the utility of WormBase. You can do this in two ways:

1. Include in your acknowledgments, a statement thanking WormBase, ‘We thank WormBase’. To save characters, it can be included in a list:  ‘We thank XYZ for reagents, ABC for comments and WormBase’. If this is a problem, just mention the particular WormBase release (WSnnn) in the text.  When you use these methods, the acknowledgements of WormBase are amenable to searching and reporting.

2. As a reviewer or editor, you could check that WormBase is acknowledged, if appropriate.

Thanks for your help!

Another record year for WormBase: over 50 million pages served.

Curious about how many people use WormBase and how often? Me too.

I just finished compiling the access statistics for 2010. Last year, WormBase served 51,606,849 distinct pages. This is a dramatic increase over 2009 (34,106,168) pages and continues the trend seen over the last few years. Note: spiders, web-crawling robots, and programmatic data-mining requests are excluded from these tallies.

We have some great things planned for our user community this year, including a ground up re-design of the site designed in part to meet this growing demand.

Caenorhabditis sp. 3 PS1010 is now Caenorhabditis angaria.

A formal description of C. angaria has been published in the January 2010 issue of Nematology. Analysis of its phylogenetic position within the Caenorhabditis genus has defined a new species group (the Drosophilae group) of equal status, but separate from, the more familiar Elegans group containing C. elegans, C. briggsae, C. remanei, and other elegans look-alikes. Meanwhile, the genome of C. angaria (as determined by next-generation Illumina sequencing and RNA-seq scaffolding) has been published in the December 2010 issue of Genome Research, along with a detailed analysis of its ~23,000 protein-coding genes (available through the WormBase Genome Browser) and ~2,700 elements of conserved non-coding DNA. This is the first genome to be published for a member of the Drosophilae group, with DNA divergence between C. angaria and C. elegans similar to that between mammals and birds.

Full list of modENCODE C. elegans papers

Here’s a quick list of recently published modENCODE C. elegans papers:

Science
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project.
Science 24 December 2010: Vol. 330 no. 6012 pp. 1775-1787
DOI: 10.1126/science.1196914

Genome Research
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.113050.110

A global analysis of C. elegans trans-splicing
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.113811.110

Broad chromosomal domains of histone modification patterns in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.115519.110

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.114587.110

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.115931.110

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.108845.110

Genome-wide analysis of alternative splicing in Caenorhabditis elegans
Genome Res. gr.114645.110 Published in Advance December 22, 2010
doi:10.1101/gr.114645.110

A Spatial and Temporal Map of C. elegans Gene Expression
Genome Res. gr.114595.110 Published in Advance December 22, 2010
doi:10.1101/gr.114595.110

Prediction and characterization of non-coding RNAs in C. elegans by integrating conservation, secondary structure and high throughput sequencing and array data
Genome Res. gr.110189.110 Published in Advance December 22, 2010
doi:10.1101/gr.110189.110