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Funding Update: NIH Bioinformatics Grants Awarded Aug. 20 — Sept. 26, 2013: Oct 4, 2013

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Part 2 of 3

Project Title: Rosetta: An Integrated Macromolecular Modeling Suite
Principal Investigator: Kuhlman, Brian
Organization: University of North Carolina, Chapel Hill
Project Start Date: March 1, 2005
Project End Date: April 30, 2017
Funding Institute: NIGMS
FY Total Cost: $581,848


Project Title: Statistical Informatics for Cancer Research
Principal Investigator: Lin, Xihong
Organization: Harvard University School of Public Health
Project Start Date: Sept. 10, 2008
Project End Date: June 30, 2018
Funding Institute: NCI
FY Total Cost: $682,166


Project Title: Developing Informatics Technologies to Model Cancer Gene Regulation
Principal Investigator: Liu, Xiaole
Organization: Dana Farber Cancer Institute
Project Start Date: Sept. 17, 2013
Project End Date: Aug. 31, 2016
Funding Institute: NCI
FY Total Cost: $363,125


Project Title: Inferring Mammalian Transcriptional Regulatory Networks from Epigenomics
Principal Investigator: Liu, Xiaole
Organization: Dana Farber Cancer Institute
Project Start Date: Sept. 10, 2011
Project End Date: Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $329,306


Project Title: Novel Analysis of Gene-gene and Gene-environment Interactions in Alcoholism
Principal Investigator: Lobach, Iryna
Organization: University of California, San Francisco
Project Start Date: Sept. 1, 2013
Project End Date: Aug. 31, 2015
Funding Institute: NIAAA
FY Total Cost: $186,635


Project Title: Supporting RNA Structure: Software for RNA Analysis
Principal Investigator: Matthews, David
Organization: University of Rochester
Project Start Date: Dec. 1, 2005
Project End Date: Aug. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $265,683


Project Title: Statistical Methods for Estimation of Gene Regulatory Networks
Principal Investigator: McCall, Matthew
Organization: University of Rochester
Project Start Date: Sept. 10, 2013
Project End Date: Aug. 31, 2015
Funding Institute: NHGRI
FY Total Cost: $79,893


Project Title: Integrative Statistical Methods and Tools for Analysis of Perturbation Signatures
Principal Investigator: Medvedovic, Mario
Organization: University of Cincinnati
Project Start Date: Sept. 24, 2011
Project End Date: June 30, 2014
Funding Institute: NHLBI
FY Total Cost: $343,462


Project Title: Discovery and Analysis of Structural Variation in Whole Genome Sequences
Principal Investigator: Mills, Ryan
Organization: University of Michigan
Project Start Date: Sept. 13, 2013
Project End Date: July 31, 2017
Funding Institute: NHGRI
FY Total Cost: $382,699


Project Title: Bioconductor: An Open Computing Resource for Genomics
Principal Investigator: Morgan, Martin
Organization: Fred Hutchinson Cancer Research Center
Project Start Date: Sept. 28, 2006
Project End Date: Feb. 29, 2016
Funding Institute: NHGRI
FY Total Cost: $199,999


Project Title: H3ABioNet: A Sustainable African Bioinformatics Network for H3Africa
Principal Investigator: Mulder, Nicola
Organization: University of Cape Town
Project Start Date: Aug. 15, 2012
Project End Date: July 31, 2017
Funding Institute: NHGRI
FY Total Cost: $2,150,374


Project Title: HYPHY: Molecular Evolutionary Analyses
Principal Investigator: Muse, Spencer
Organization: North Carolina State University, Raleigh
Project Start Date: Sept. 15, 2010
Project End Date: Aug. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $265,099


Project Title: A Computational Approach to Developing Heterchiral Peptide Therapeutics
Principal Investigator: Nanda, Vikas
Organization: Robert Wood Johnson Medical School
Project Start Date: Sept. 1, 2010
Project End Date: Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $303,801


Project Title: Computational Tools for Mass Spectrometry-based Interactome Data
Principal Investigator: Nesvizhskii, Alexey
Organization: University of Michigan
Project Start Date: Sept. 1, 2010
Project End Date: Aug. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $377,586


Project Title: Develop New Mathematical and Computational Tools for Modeling
Principal Investigator: Nie, Qing
Organization: University of California, Irvine
Project Start Date: Not Listed
Project End Date: Not Listed
Funding Institute: NIGMS
FY Total Cost: $311,942


Project Title: Methods for the Analysis of RNA-seq and Related Sequence Census-based Experiments
Principal Investigator: Pachter, Lior
Organization: University of California, Berkeley
Project Start Date: Aug. 19, 2011
Project End Date: May 31, 2014
Funding Institute: NHGRI
FY Total Cost: $353,656


Project Title: Computational Approaches to Protein Identification and Quantification using MS/MS
Principal Investigator: Radivojac, Pedrag
Organization: Indiana University
Project Start Date: May 1, 2007
Project End Date: July 31, 2016
Funding Institute: NIGMS
FY Total Cost: $396,933


Project Title: Clinical Genome Inference System: Variant Prioritization for Clinical Diagnostics
Principal Investigator: Reese, Martin
Organization: Omicia
Project Start Date: June 6, 2012
Project End Date: Aug. 31, 2014
Funding Institute: NHGRI
FY Total Cost: $781,754


Project Title: Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer
Principal Investigator: Regev, Aviv
Organization: Broad Institute
Project Start Date: Sept. 17, 2013
Project End Date: Aug. 31, 2018
Funding Institute: NCI
FY Total Cost: $678,887


Project Title: The Cancer Bioinformatics Initiative
Principal Investigator: Robbins, Kay
Organization: University of Texas, San Antonio
Project Start Date: Sept. 11, 2012
Project End Date: Aug. 31, 2016
Funding Institute: NCI
FY Total Cost: $134,686

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The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.