Finding variations in canine tumors may provide insight into common pathways for human cancer

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Bioinformatics Core analyst/programmer Nikhil Joshi was co-author on a paper recently published in The Journal of Neuropathology & Experimental Neurology: Chromosomal Aberrations in Canine Gliomas Define Candidate Genes and Common Pathways in Dogs and Humans Nikhil was involved with quality assurance and alignment of data, visualization and calculating statistics about the alignments, as well as… Read more »

New paper involving assembly of PacBio reads from a tricky part of the dog genome, published in Immunogenetics

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Bioinformatics data analyst Joe Fass was involved in work that was published recently in Immunogenetics: Refinement of the canine CD1 locus topology and investigation of antibody binding to recombinant canine CD1 isoforms The Bioinformatics Core’s role was to assembly bacterial artifitial chromosomes (BACs) tiling across a region of the canFam3 genome assembly. The assembled BACs… Read more »

New RNA-Seq paper published in Parasites & Vectors journal

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Two Bioinformatics Core members (Monica Britton and Joseph Fass) have been involved in some work that has just been published in Parasites & Vectors journal: RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs The Bioinformatics Core was involved in analyzing and… Read more »

The Bioinformatics Core helps understand the effects of ibuprofen contamination on the transcriptome of an inland fish

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Monica Britton was involved in some recent work that has just been published in the Environmental Science and Pollution journal: Chronic exposures to low and high concentrations of ibuprofen elicit different gene response patterns in a euryhaline fish. Monica was involved generating a transcriptome assembly and subsequently annotating it from comparisons of all contigs with a custom subset of the nr… Read more »

Announcing the 2015 Bioinformatics Core Pilot Grant Program

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Overview The Bioinformatics Core at the UC Davis Genome Center is pleased to announce the Pilot Grant Program (for UC Davis customers) for 2015. The Bioinformatics Core provides data analysis for a variety of experiments, including RNA-Seq, Exome Sequencing, Variant Discovery, Genome and Transcriptome Assembly, and more (here are some examples of the varied projects… Read more »

The Assemblathon 2 paper features contributions from the UC Davis Bioinformatics Core

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The Assemblathon project is intended to be an ongoing set of contests between developers of genome assembly software to determine how good different assemblers are at tackling different problems relating to this growing field. Results from the second competition (Assemblathon 2) have just been published in the journal Gigascience:   Assemblathon 2: evaluating de novo… Read more »

Assemblathon 1 paper published, featuring work of Bioinformatics Core members

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The Assemblathon, an international consortium of researchers interested in advancing the field of genome assembly, have published their first set of findings as to the current state of genome assembler performance:   Assemblathon 1: A competitive assessment of de novo short read assembly methods   The paper, published in the journal Genome Research, features the… Read more »