NSF Bioinformatics Grants Awarded May 26 — June 29, 2011
Algorithms for Genetics: Epistatic Interactions, Haplotype Assembly, and Selection Signatures
Start Date: Oct. 1, 2011
Expires: Sept. 30, 2014
Awarded Amount to Date: $445,000
Principal Investigators: Vineet Bafna
Sponsor: University of California, San Diego
Supports the development of combinatorial and machine learning techniques to detect epistasis based on the development of a "metric embedding that maps the genotypes at a locus to a point in a high dimensional Euclidean metric, such that interacting pairs have small Euclidean distances." The project also aims to expand the length of achievable haplotypes; and identify regions under genetic selection using pooled and partially sampled DNA.
Ontology-enabled Reasoning Across Phenotypes from Evolution and Model Organisms
Start Date: July 1, 2011
Expires: June 30, 2012
This grant was awarded to two investigative teams:
$351,409, Todd Vision, University of North Carolina, Chapel Hill
$490,399, Paul Mabee, Paul Sereno, Monte Westerfield, University of South Dakota
The funds will support the development of ontology-driven tools for machine reasoning over large volumes of phenotype data.
Specifically, the investigators will develop ontologically aware software that lets users "discover similar sets of phenotypes for different taxa or mutant genes within large and diverse datasets." They intend to develop a semantic similarity engine that will allow users to search for "evolutionary transitions and mutant genes that are characterized by similar phenotypic profiles." Furthermore, they hope to develop an ontological framework "for reasoning over homology ... [that will] allow rigorous reasoning over evolutionary diverse lineages" as well as natural language processing tools to mine phenotype data from the literature.