WormBase curators have published a new paper describing a controlled vocabulary for worm phenotypes. The paper is now available at BMC Bioinformatics in provisional form.
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.
modENCODE papers published
Results from the modENCODE project have now been published. Integrative Analysis of the C. elegans Genome in Science provides an in-depth overview accompanied by multiple companion papers in Genome Biology and Genome Research. See the full list of papers on M9: The WormBase Blog.
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