Brown CS News

Sorin Istrail, Julie Nguyen Brown Professor of Computational and Mathematical Sciences and Professor of Computer Science, has just received a NSF grant, “The cisGRN Browser and Database: cis-Regulatory Information Behind the Network.” Funding in the expected amount of $850,000 will be used by Istrail and his students — Ryan Tarpine and a few others to be added to the team — to develop algorithms and software tools for building genomic maps of the regulatory circuitry of cells. The work will focus on solutions to three major problems in the developmental biology community: building genomics libraries of software tools to reveal the logical principles and gene-network architecture of the “genomic computer,” building a lexicon of experimentally validated cis-regulatory modules to improve predictive algorithms for cis-regulatory modules and networks, and designing a next-generation regulatory genomics logic map browser. This work builds on Istrail’s extensive collaboration with Caltech’s Eric Davidson towards a unified concept of “regulatory information” and the unveiling of the principles of information processing of cell regulation. This collaboration has already been instrumental in: (1) constructing the first sea-urchin genome assembly, (2) identifying a first repertoire of logic functions of the genomic cis-regulatory code, (3) building the first high-resolution transcriptome map of the sea-urchin embryo, and (4) providing the first comprehensive analysis of the principles of the regulatory genome vis-à-vis those of the computer. The goals of this research also build on Istrail’s extensive experience, with his group at Celera Genomics, in developing software libraries for genome assembly, whole-genome alignment, and automatic annotation of genomes.