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Funding Update: NSF Bioinformatics Grants Awarded Dec. 20, 2012 — Jan. 23, 2013

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Statistical Methods and Algorithms for Genomic Data
Start Date: Aug. 31, 2012
Expires: July. 31, 2013
Awarded Amount to Date: $48,444
Principal Investigator: Shu-Chuan Chen
Sponsor: Idaho State University

According to the abstract, the funds will support three aims. The first aim will focus on extending a method for constructing hierarchical trees from sequence data using maximum likelihood and modal inference. The second project aim will “enhance the biological realism of the ancestral mixture model to include multi-state characters; advanced models of sequence evolution; and recombination.” Finally, the investigators will work on a method for reconstructing haplotype sequences from genotype data “without knowing the parental information.” In addition, the team plans to extend the method to longer sequences “by sliding a window along longer genotype sequences, then using the information from the overlapping estimates to construct longer haplotype estimates.”


US-India Catalyzing New International Collaboration with Anna University for Computational Enzyme Design Research: Sirt 1 and Sirt 3
Start Date: Aug. 1, 2012
Expires: May 31, 2013
Awarded Amount to Date: $33,828
Principal Investigator: Raj Chakrabarti
Sponsor: Carnegie-Mellon University

According to the abstract, the funds will support an international research collaboration that will study the evolutionary dynamics of sirtuin enzymes as it relates to the binding of small molecules. The project will use computer-aided sequence and binding-site analysis of enzymes; and it will experimentally verify the predicted activities of computer-generated sequences and structures.


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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.