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Funding Update: Apr 16, 2010

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NSF Bioinformatics Grants Awarded March 18 — April 15, 2010

Efficient and Accurate Computation for High Throughput Sequencing Related Problems in Population Genomics
Start date: July 1, 2010
Expires: June 30, 2011
Awarded amount to date: $78,716
Principal investigator: Yufeng Wu
Sponsor: University of Connecticut

The investigators propose to develop computational methods capable of analyzing "large-scale high-throughput sequencing data for several population genomics problems," according to the grant abstract. The project will focus on inferring genotypes, correcting sequencing errors, detecting meiotic recombination, and searching for disease-causing rare gene variants "and other emerging applications of high-throughput sequencing." According to the grantees, "a key difference between the proposed research and many existing methods is that the proposed approaches are explicitly designed for processing large amount of high-throughput sequencing data." In particular, the project will focus on applying combinatorial optimization techniques such as integer linear programming, as well as probabilistic models, which will be integrated with optimization approaches.


SBIR Phase I: De Novo Design of Unnatural Peptides — Affordable Drug Discovery Platform
Start date: July 1, 2010
Expires: Dec. 31, 2010
Awarded amount to date: $150,000
Principal investigator: Przemyslaw Czyryca
Sponsor: Allosterix Pharmaceuticals

This grant funds the testing and validation of a drug discovery platform based on an algorithm that designs "previously unknown peptides that are capable of modulating selected macromolecules of therapeutic importance," according to the abstract. After the design phase, these "designer peptides" are "routinely and inexpensively synthesized." In particular, the project will focus on the design of compounds that disrupt the function of selected viral envelope proteins.


Evolutionary Computation and Bioinformatics
Start date: June 1, 2010
Expires: May 31, 2012
Awarded amount to date: $200,000
Principal investigator: Clare Congdon
Sponsor: University of Southern Maine

This project aims to develop an evolutionary computation-based approach for identifying "candidate modules" in non-coding DNA that respond to environmental toxins and alter gene expression. The modules are protein-binding sites and their interactions "are believed to contribute to the inducibility and specificity of environmentally responsive genes," according to the grant abstract. Since each gene has an "enormous" number of possible modules, "the development of artificial intelligence techniques is called for," the abstract states. While there are tools available that can search the thousand-base-pair region immediately upstream of the gene, this project intends to search "significantly longer sections, 1 million base pairs and longer in length."


QuasiNovo: An Information Theoretic Approach to De Novo Peptide Sequencing
Start date: April 15, 2010
Expires: March 31, 2013
Awarded amount to date: $643,747
Principal investigator: John Rose
Sponsor: University of South Carolina Research Foundation

This grant funds a project that will systematically study amino acid usage models in fragmentation and cross-correlation peptide scoring functions with the aim of improving scoring functions for de novo peptide sequencing. "Preliminary results strongly support the hypothesis that a scoring function that considers amino acid usage patterns will be better able to distinguish between candidate peptides. This in turn will lead to much higher accuracy in peptide prediction," according to the grant abstract. The investigators also propose to develop a Bayesian model for exploring the uncertainty of candidate peptides produced by de novo sequencing. "A major difference between this model with that developed by other groups is that the proposed approach will incorporate the concept of proteome signature as a prior," the abstract states. "Existing models for de novo sequencing do not expressly indicate amino acid usage, and thus implicitly assume flat priors for amino acid usage."


Computational and Experimental Studies of Microtubule Dynamics and Regulation by Binding Proteins
Start date: March 15, 2010
Expires: Feb. 28, 2011
Awarded amount to date: $211,082
Principal investigator: Holly Goodson
Sponsor: University of Notre Dame

This project aims to develop two computational models of microtubule dynamics and then use these models to investigate the function and mechanism of microtubule-binding proteins. These models will be built at two scales, according to the abstract: a medium-scale model that will be used to investigate the intrinsic properties of a system of dynamic microtubules in a cell-like environment; and a molecular-scale model that will be used to develop hypotheses about the mechanisms of dynamic instability and its alteration by microtubule-binding proteins.


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.