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NSF Bioinformatics Awards, Feb. 5 -- March 4, 2006

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BioLit: Open Source Tools for Integrating Biological Literature and Databases. Start date: April 1. Expires: March 31, 2007. Estimated total amount: $953,466. Principal investigator: Philip Bourne. Sponsor: University of California, San Diego.

Supports a grant to develop tools for integrating biological literature and databases. These open source software tools, collectively called BioLit, include "authoring tools to facilitate biologists in employing existing ontologies, post manuscript submission tools to extract relevant facts from the manuscript which are stored as metadata, a database of journal content and tools for the visualization and further analysis of data and knowledge presented in this database of on-line published papers," according to the grant abstract. Development and testing will be performed using the complete corpus of Public Library of Science journals integrated with the Protein Data Bank.


Identification of Genetic Networks in Neurospora Crassa: A Systems Biology Approach. Start date: March 1. Expires: Feb. 29, 2008. Expected total amount: $157,115. Principal investigator: David Logan. Sponsor: Clark Atlanta University.

Proposal to study the metabolism of quinic acid in the bread mold Neurospora crassa. The metabolic response will be monitored by measuring the organism's messenger ribonucleic acid levels by using molecular and computational biology methods.


Computing Infrastructure for the UConn Health-Grid Initiatives. Start date: March 1. Expires: Feb. 28, 2007. Expected total amount: $50,000. Principal investigator: Chun-Hsi Huang. Sponsor: University of Connecticut.

Supports planning activities for the UConn Health-Grid Initiative, which will apply information technology to various disciplines of life science research and practice. The computing infrastructure will be based on a campus-wide computational and data grid, an effort that began in 2004. The current grant supports development of general-purpose middleware support for secure transfer of data over computing infrastructure. The grant also supports an annual scientific meeting called the international BioGrid Workshop.


Statistically Predicting Hotspots and Coldspots in Caenorhabditis Elegans. Start date: Aug. 1. Expires: July 31, 2007. Expected total amount: $100,000. Principal investigator: Eleanne Solorzano. Sponsor: University of New Hampshire.

Supports comparative genomics analysis for the model nematode, Caenorhabditis elegans, and the development of statistical models for predicting the types of mutations that will occur. This analysis will be based on the comparison of the laboratory strain of C. elegans with other strains and closely related species. The statistical models will initially focus on the prediction of cold spots, which are DNA sequences in the genome with low rates of mutation, and hot spots, which are sequences with high mutation rates.

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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.