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Funding Update: NSF Bioinformatics Grants Awarded March 1 — April 2, 2014

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Statistical Ensembles for the Identification of Bacterial Genomes
Start Date: Aug. 1, 2013
Expires: July 31, 2014
Awarded Amount to Date: $495,318
Principal Investigator: Jennifer Clarke
Sponsor: University of Nebraska

According to the abstract, investigators involved in this project, which is focused on reducing bioterrorism threats, will develop statistical and computational tools for detecting pathogens using NGS. As part of their efforts, they plan to develop methods that enable "classification by sequence enrichment; comparison of empirical clusterings and reference genomes; and shrinkage estimation and model selection in hierarchical log-linear models," the abstract states.


New Methods for Genomic Analysis of Noninvasive Species
Start Date: March 1, 2014
Expires: Feb. 29, 2016
Awarded Amount to Date: $292,778
Principal Investigators: Jenny Tung, Susan Alberts
Sponsor: Duke University

These funds will support efforts to develop novel methods for generating analyzing genome-scale data from biological samples collected by noninvasive means, the abstract states. Specifically, the investigators plan to develop "new lab protocols for increasing and purifying the DNA yield from noninvasive samples to a level appropriate for genomic analysis" and to develop new software to analyze the resulting data.


Phylogenetic Tools for Studying Phenotypic Diversification in the Tree of Life
Start Date: April 1, 2014
Expires: March 31, 2019
Awarded Amount to Date: $169,802
Principal Investigator: Liam Revell
Sponsor: University of Massachusetts

These funds will support research efforts to develop a new computational toolkit for phylogentic studies that will include tools for " visualizing trait evolution on trees; new methods to integrate tree estimation and comparative inference; and new approaches to link micro-scale processes and macro-scale patterns on a tree," according to the abstract.


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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.