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Chemical Genomics, Next-Gen Sequencing, mpiBlast, Atul Butte, and ISB


Five years ago, Genome Technology's cover story examined the rise of chemical genomics and profiled Chris Austin, who was kicking off a new small molecule screening initiative at NIH. Today, Austin is director of the NIH Chemical Genomics Center, which has established a successful track record through a model of partnering with experts in the community and designing assays critical for screening compounds. The center has built up a production-scale facility and capacity including some 400,000 compounds. Austin has also been instrumental in getting the Molecular Libraries Initiative up and running, which has established a network of centers to help researchers with production of small molecule probes.

Also in the January/February 2005 issue, GT reported on the winners of NHGRI's first round of awards for the $1,000 and $100,000 genome sequencing grants. Some of the near-term winners included Gina Costa for Agencourt, which turned into the sequencing technology scooped up by Applied Biosystems in 2006; researchers at 454 Life Sciences, acquired in 2007 by Roche; and Steve Quake, whose technology concept became the foundation for Helicos' platform.

Another story in 2005 updated readers on mpiBlast, the highly parallelized version of Blast developed by Wu-chun Feng at Los Alamos. In the time since, Feng has moved to Virginia Tech, where he and his colleagues continue to improve the popular algorithm — last fall, that led to a new version aimed at petascale parallel computers.

In news a year ago, we reported on work from Atul Butte at Stanford, who described 'fitSNPs,' or functionally interpolating polymorphisms that help prioritize SNPs in disease studies. In December, Butte and colleagues published a new paper in PLoS Genetics demonstrating a meta-analysis of genome-wide association studies previously performed on autoimmune diseases. The findings suggest that the variants that increase someone's risk for one type of autoimmune disease might actually make that person less likely to have other types of autoimmune problems.

Another article last February profiled the Institute for Systems Biology, launched in 2000 by Alan Aderem, Ruedi Aebersold, and Lee Hood. In the year since, ISB scientists became early users of Complete Genomics' sequencing service. After a pilot program sequencing the genomes of a four-member family, the ISB scientists and collaborators signed on with the company to have 100 human genomes sequenced for a study of Huntington's disease.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.