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Funding Update: NSF Bioinformatics Grants Awarded Oct. 22 — Nov. 14, 2012

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Computing regulatory DNA for comparing genomes
Start Date: Nov. 1, 2012
Expires: Oct. 31, 2014
Awarded Amount to Date: $882,032
Principal Investigator: Michael Freeling
Sponsor: University of California, Berkeley

The funds will support the development of a new application for the Accelerating Comparative Genomics, or CoGe, toolbox — used for visualizing and comparing sequences — that will let users view motifs and transcription factor binding sites when comparing chromosomal sequences. The investigator will also look for genes with new regulatory capabilities by finding rare cases of new sequence that correspond to new patterns of expression; and explore how plant regulatory DNA evolves into non-detectability without losing its function, among other research activities.


Monte Carlo simulations in exploring non-equilibrium systems
Start Date: June 5, 2012
Expires: Nov. 30, 2014
Awarded Amount to Date: $78,347
Principal Investigator: Jiajia Dong
Sponsor: Bucknell University

The funds will support efforts to use Monte Carlo simulations to explore more than 4,000 gene sequences in Escherichia coli and the limits on their protein production rates, to better understand the “existence of non-optimal sequences; effects of quenched randomness on the totally asymmetric simple exclusion process; and [provide] guidance to experimentalists on ‘fine-tuning’ mRNA sequences for optimal protein production.” The investigator will also use the simulations approach to study host-parasite dynamics.


Theoretical and experimental study of functional association of proteins
Start Date: Jan. 1, 2013
Expires: Dec. 31, 2015
Awarded Amount to Date: $258,731
Principal Investigators: Eugene Shakhnovich, Gerhard Wagner
Sponsor: Harvard University

The investigators will use the funds to develop computational tools that can predict possible structures and the thermodynamic stabilities of oligomers formed by mutant forms of the dihydrofolate reductase enzyme. They will also “formulate hypotheses of domain swap mechanisms” and test them in mutagenesis experiments, according to the grant abstract.


Creating gene network prediction tools applicable to plants and animals
Start Date: Dec. 1, 2012
Expires: Nov. 30, 2014
Awarded Amount to Date: $119,378
Principal Investigators: Cassandra Extavour
Sponsor: Harvard University

The investigators will use the funds to develop computational tools that will enable gene function predictions based on sequence data from organisms that lack fully sequenced genomes without relying on previously generated data about the biochemical or genetic function of their genes. The team plans to test the tools on gene transcript data from insects, crustaceans, and spiders.


Implementation of genetic algorithms for personalized chemosensitivity testing for cancer patients
Start Date: Oct. 1, 2012
Expires: March 31, 2013
Awarded Amount to Date: $119,378
Principal Investigators: Cassandra Extavour
Sponsor: Harvard University

The funds will support efforts to develop a high-throughput real-time assay that determines the efficacy of cancer treatments directly from living biopsied tissue and uses genetic algorithms for automated data capture.


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