Oct 29th, 2013. UCSF, Cold Spring Harbor Laboratory, MIT, and Davidson College receive $400,000 from Dr. David Botstein to further advanced technology courses for graduate education. Dr. Botstein is the recent recipient of the Breakthrough Prize in Life Science, and has pledged a portion of that prize to these four institutions in recognition of their efforts to further advanced teaching, especially at the graduate school level. At UCSF, the award recognizes the recently built Teaching Lab at Mission Bay together with the Integrated Program in Complex Biological Systems, an NIBIB T32 supported program that promotes a project-based curriculum for students in biophysics and bioinformatics. The Teaching Lab was opened in 2011 and was funded by QB3.
Read the CSHL Press Release here


We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of pre-assembled contigs. It was designed to address the challenge of assembling viral genomes that constituted a small minority of the reads within ultra-deep, short-read, metagenomic, shotgun datasets. PRICE has already enabled the discovery of several novel virus genomes from such complex datasets.
The early online edition of the PRICE paper, published in G3, is here.
Download PRICE


For many years, a mysterious disease in boa constrictors and pythons called Inclusion Body Disease (IBD) has been the scourge of aquariums, breeders, and pet snake owners. The disease is ultimately fatal, and until now, its cause was unknown. Using the latest methods in ultra deep sequencing and de novo sequence assembly, the DeRisi lab, in collaboration with the California Academy of Science and local veterinarians, has identified a novel snake arenavirus that is closely linked to the disease. The paper describing this discovery is published in ASM's new open-access journal mBio, to be released August 14th.

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