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NSF Bioinformatics Grants Nov. 25 — Dec. 30, 2006

Toward Boltzmann-Weighted Protein Ensembles Using Novel Computations. Start date: Jan. 1, 2007. Expires: Dec. 31, 2007. Awarded amount to date: $168,010. Principal investigator: Daniel Zuckerman. Sponsor: University of Pittsburgh.
Proposal to continue the development of computational approaches for equilibrium sampling of biomacromolecules, especially proteins. The goal of the project is to generate ensembles of canonically sampled protein structures, exhibiting full fluctuations. According to the grant abstract, the Resolution Exchange algorithm and its variants, developed by the PI and his colleagues “represent a particularly promising class of algorithms for employing coarse-grained models to greatly accelerate rigorous statistical sampling … of standard atomically detailed representations of proteins.”

Data Analysis Environment for Microbial Proteome Studies. Start date: Dec. 1, 2006.
Expires: May 31, 2008. Awarded amount to date: $200,000. Principal investigator: Eugene Kolker. Sponsor: Biatech.
Supports development of a prototype of a database and software environment for analyzing microbial proteomes. According to the grant abstract, the investigators will work with multiple microorganisms, “enabling a rapid development and testing cycle that is robust to differences across species, resulting in tools that are readily available to the broader scientific community.”

A Direct Modeling Approach for Phylogenetic Comparative Analysis. Start date: Aug. 1, 2006. Expires: Aug. 31, 2008. Awarded amount to date: $178,893. Principal investigator: Marguerite Butler. Sponsor: University of Hawaii.
Supports development of a modeling method for phylogenetic comparative analysis that simultaneously accounts for random evolutionary fluctuations (such as genetic drift), common ancestry, and natural selection (under multiple adaptive regimes). The method is able to formulate scientific hypotheses as explicit mathematical models, each of which can then be fit to the data, the grant abstract states. Scientists should be able to use the approach to identify “which aspects of the evolutionary process are most important, describe the relative strengths and directions of these evolutionary forces, and understand how they have influenced the tempo and mode of evolution,” the abstract states.

BioPortal — An Informatics Infrastructure for Infectious Disease and Biosecurity Information Sharing, Analysis, and Visualization. Start date: Jan. 1, 2007. Expires: June 30, 2007. Awarded amount to date: $99,989. Principal investigator: Hua Su. Sponsor: International BioComputing.
Phase I SBIR funds development of an information management system to monitor infectious disease outbreaks. The project will build upon the ongoing BioPortal effort to develop “an integrated infrastructure for infectious disease information collection, sharing, analysis, and visualization and to demonstrate its feasibility in real-world public health management settings,” according to the grant abstract.

Improving RNA Pseudoknot Models and Algorithms. Start date: Feb. 1, 2007. Expires: Jan. 31, 2010. Awarded amount to date: $260,819. Principal investigator: Daniel Aalberts.
Proposal to extend and improve the Aalberts and Hodas statistical-mechanical theory to consider rarer types of RNA pseudoknots, to study temperature and base-composition dependences of pseudoknots, to estimate theoretically the abundance of pseudoknot folds, and to test predictions against known structures. An additional goal is to develop an efficient algorithm for predicting the most abundant class of pseudoknots.

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The Scan

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.