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

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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

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.