Politics, Information Technology, and Genomics

Sequencing AML with paired-end reads

When The Genome Center performed the sequencing of the first whole cancer genome, the state of the art for next-generation sequencing was single-end, or fragment, reads. While these data allowed the discovery of single nucleotide variants and small indels, they do not allow discovery of structural variation, e.g., indels larger than a few bases, inversions, and translocations. With the advent of pair-end sequencing on the next-generation sequencing platforms, i.e., two reads sequenced from each end... Full Post

AAAS Fellows in our midst

It somehow escaped my attention last November when it was announced and earlier this year in February when the ceremony was held that Richard K. Wilson and George M. Weinstock, Director and Associate Director, respectively, of The Genome Center, were elected as Fellows of the American Association for the Advancement of Science. Congratulations to both! Full Post

CSHL Biology of Genomes 2009

I should have posted this earlier, but things have been pretty busy. In any event, I will be presenting a poster next week at the Biology of Genomes meeting at Cold Spring Harbor. The poster is entitled "Maximizing utility of genome sequence data". Here is the abstract. Advances in DNA sequencing technologies over the past few years have led to data generation and processing rates that far outpace Moore's Law and storage capacity improvements. As... Full Post

Sequencing — the past, present, and future

Science Magazine has a nice article, Sanger Who? Sequencing the Next Generation, describing past sequencing technology, the current "next-generation" sequencing instruments and their capabilities, and several of the companies working to become the next big thing in sequencing. If you are interested in learning, at a high level, how each of the technologies work and how they compare to each other, it is worth a read. Full Post

OSCON 2009

I will be speaking at OSCON 2009 in San Jose, CA. My talk, entitled The Freedom to Cure Cancer: Open Source Software in Genomics, will be at 10:45 a.m. PDT on Friday 24 July 2009. If you are planning to attend OSCON this year, let me know (and be sure to attend my talk). Full Post