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Funding Update: Jul 1, 2011 (rev. 1)


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.

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.