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NSF Bioinformatics Grants Awarded Nov. 9, 2007 — Jan. 17, 2008

Comparative Genomics and Biological Signal Discovery in the Human Genome. Start date: Dec. 1, 2007. Expires: Nov. 30, 2008. Awarded amount to date: $200,637. Principal investigator: Manolis Kellis. Sponsor: Massachusetts Institute of Technology.
Supports development of comparative genomics methods that use mammalian sequences to discover biological signals. One aim of the project is to develop comparative methods for ortholog identification that can scale to dozens of complete mammals and account for the phylogenies relating them, gene duplication and loss, varying rates of divergence across gene families, and across species. A second aim is to create a classification framework for gene identification.

Maximizing the Utility of Orthologs and Phylogenetic Profiles for Systems-Scale Comparative Genomics. Start date: Dec. 1, 2007. Expires: Nov. 30, 2008. Awarded amount to date: $230,604. Principal investigator: Dennis Wall. Sponsor: Harvard University.
Supports development of “the largest ortholog repository to date using an improved algorithm for identifying orthologs, based on appropriate evolutionary metrics of similarity,” according to the grant abstract. The investigators plan to aggregate whole-genome orthology data into matrices of phylogenetic profiles, “enabling a series of meta-analyses including the reconstruction of genome phylogenies, and analysis of protein function and network organization.” The resource will be a web-based, freely available system that will allow researchers to conduct large-scale comparative genomics investigations to study the functional relationships among genes or phylogenetic relationships among genomes.

Biochemical Pathways Workbench. Start date: Dec. 1, 2007. Expires: Nov. 30, 2008. Awarded amount to date: $321,402. Principal investigator: Shankar Subramaniam. Sponsor: University of California-San Diego.
Supports development of “a comprehensive pathways database, query/analysis toolkit, interface infrastructure, and an authoring toolkit” for biological networks called the Biochemical Pathways Workbench. The project will add the capability for biological modeling, algorithm design, analytical modeling, and statistical validation to the existing Biology Workbench.

Stochastic Modeling, Analysis and Simulation of Gene Networks. Start date: Jan. 1, 2008. Expires: Dec. 31, 2009. Awarded amount to date: $160,472. Principal investigator: Xiaodong Cai. Sponsor: University of Miami.
Funds development of a module-based approach for modeling large gene networks, “similar to that used in analyzing electronic circuits,” according to the grant abstract. The investigator plans to derive a general stochastic model for gene expression and statistical methods for estimating model parameters based on experimental results, characterize some common modules in gene networks and develop a module-based approach to analyzing gene networks, and devise efficient stochastic simulation methods for large gene networks.

Arabidopsis 2010: Constructing and Analyzing a Model Gene Regulatory Network. Start date: Jan. 15, 2008. Expires: Dec. 31, 2008. Awarded amount to date: $315,777. Principal investigator: John Schiefelbein. Sponsor: University of Michigan Ann Arbor.
Funds development of a systems-based approach to construct and analyze a “relatively simple” gene network that controls root epidermal cell differentiation in Arabidopsis. According to the grant abstract, the investigators will use a cell-specific transcript profiling method to define a set of root epidermis genes, which will be assembled into a probabilistic network by systematically perturbing specific genes and defining relationships from gene expression data using Bayesian network analysis. “The project is expected to provide new computational and experimental tools for gene network construction in Arabidopsis and to uncover fundamental features of plant gene network structure and circuitry,” the grant abstract states. The data will be made available through the Arabidopsis Biological Resource Center, the Arabidopsis Information Resource (TAIR), and the Gene Expression Omnibus.

Integrating Bioinformatics into the Life Sciences. Start date: Jan. 15, 2008. Expires: Dec. 31, 2009. Awarded amount to date: $149,807. Principal investigator: Mark Pauley.
Sponsor: University of Nebraska at Omaha.
Funds a project to integrate bioinformatics concepts into the undergraduate curriculum in the life sciences. The project investigators plan to disseminate a set of bioinformatics modules that can be integrated into curricula in the biological sciences, computer science, and other disciplines. Each module includes around five hours of instruction and addresses a “fundamental concept” in bioinformatics. The investigators note that around 300 biology and computer science undergraduates currently use these modules at the University of Nebraska at Omaha, and a goal of the project is to expand the initiative “throughout the state and nation.”

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