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Funding Update: Oct 15, 2010

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NIH bioinformatics grants awarded Aug. 26 — Oct. 6, 2010 (Part two of two. Part one is available here.)

Project Title: Training in Biomedical Informatics at Columbia University
Principal Investigator: Hripcsak, George M.
Organization: Columbia University Health Sciences
Project Start Date: July 1, 1992
Project End Date: June 30, 2012
RFA/PA: RFA-LM-06-001
Funding Institute: NLM
FY Total Cost: $216,000


Project Title: Integrated Human Genome Annotation: Generation of a Reference Gene Set
Principal Investigator: Hubbard, Timothy John
Organization: Sanger Institute
Project Start Date: Sept. 27, 2007
Project End Date: June 30, 2011
RFA/PA: RFA-HG-07-030
Funding Institute: NHGRI
FY Total Cost: $2,338,425


Project Title: Computational Analysis of Human High Grade Gliomas
Principal Investigator: Iavarone, Antonio
Organization: Columbia University Health Sciences
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2014
RFA/PA: PAR-08-184
Funding Institute: NINDS
FY Total Cost: $476,618


Project Title: Resource for Analysis, Vizualization, and Integration of Networks (Ravin)
Principal Investigator: Ideker, Trey
Organization: University of California, San Diego
Project Start Date: Sept. 13, 2010
Project End Date: June 30, 2015
RFA/PA: PAR-08-259
Funding Institute: NCRR
FY Total Cost: $1,604,021


Project Title: Center for Integrative Biomedical Computing
Principal Investigator: Johnson, Christopher R.
Organization: University of Utah
Project Start Date: Sept. 1, 2000
Project End Date: July 31, 2015
RFA/PA: PAR-08-259
Funding Institute: NCRR
FY Total Cost: $1,158,691


Project Title: Multiscale Models for Synthetic Biology
Principal Investigator: Kaznessis, Yiannis
Organization: University of Minnesota Twin Cities
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PA-07-070
Funding Institute: NIGMS
FY Total Cost: $247,072


Project Title: The UCSC Encode Data Coordination Center
Principal Investigator: Kent, William James
Organization: University of California, Santa Cruz
Project Start Date: Sept. 28, 2007
Project End Date: June 30, 2011
RFA/PA: RFA-HG-07-031
Funding Institute: NHGRI
FY Total Cost: $1,262,547


Project Title: Model-Based Clustering of Genomic Data Using Complex Covariance Structures
Principal Investigator: Koestler, Devin Charles
Organization: Brown University
Project Start Date: March 17, 2010
Project End Date: Jan. 15, 2012
RFA/PA: PA-10-108
Funding Institute: NIA
FY Total Cost: $27,397


Project Title: Rosetta: An Integrated Macromolecular Modeling Suite
Principal Investigator: Kuhlman, Brian A
Organization: University of North Carolina, Chapel Hill
Project Start Date: March 1, 2005
Project End Date: Aug. 31, 2013
RFA/PA: PAR-08-010
Funding Institute: NIGMS
FY Total Cost: $573,047


Project Title: Evolutionary Bioinformatics of Human Mutations
Principal Investigator: Kumar, Sudhir
Organization: Arizona State University, Tempe Campus
Project Start Date: Sept. 30, 2010
Project End Date: Sept. 29, 2013
RFA/PA: PAR-08-080
Funding Institute: NLM
FY Total Cost: $381,250


Project Title: Developing Statistical Methods for Disease Gene Discovery
Principal Investigator: Li, Chun
Organization: Vanderbilt University
Project Start Date: Sept. 19, 2008
Project End Date: July 31, 2013
RFA/PA: PA-07-070
Funding Institute: NHGRI
FY Total Cost: $384,328


Project Title: Statistical Methods for Gene Mapping Studies in Admixed Populations
Principal Investigator: Li, Mingyao
Organization: University of Pennsylvania
Project Start Date: Sept. 9, 2010
Project End Date: June 30, 2013
RFA/PA: PA-07-070
Funding Institute: NHGRI
FY Total Cost: $330,930


Project Title: Novel Methods for Effective Analysis Assembly and Comparison of HMP Sequences
Principal Investigator: Li, Weizhong
Organization: University of California, San Diego
Project Start Date: Sept. 27, 2010
Project End Date: June 30, 2013
RFA/PA: RFA-RM-09-020
Funding Institute: OD
FY Total Cost: $394,784


Project Title: Computational Models for Mechanisms of Global Transcription Regulation
Principal Investigator: Liu, Xiaole Shirley
Organization: Dana-Farber Cancer Institute
Project Start Date: Sept. 27, 2006
Project End Date: Aug. 31, 2011
RFA/PA: PAR-03-106
Funding Institute: NHGRI
FY Total Cost: $396,072


Project Title: Technologies to Enable Privacy in Biomedical Databanks
Principal Investigator: Malin, Bradley A
Organization: Vanderbilt University
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2013
RFA/PA: PA-07-070
Funding Institute: NLM
FY Total Cost: $1,860


Project Title: Technologies to Enable Privacy in Biomedical Databanks
Principal Investigator: Malin, Bradley A
Organization: Vanderbilt University
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2013
RFA/PA: PA-07-070
Funding Institute: NLM
FY Total Cost: $272,423


Project Title: Computational Methods for NMR Structure Determination of Proteins in Membranes
Principal Investigator: Marassi, Francesca M
Organization: Burnham Institute for Medical Research
Project Start Date: Sept. 30, 2010
Project End Date: Aug. 31, 2012
RFA/PA: PAR-09-219
Funding Institute: NIGMS
FY Total Cost: $291,050


Project Title: VESPA: Vanderbilt Electronic Systems for Pharmacogenomic Assessment
Principal Investigator: Masys, Daniel R
Organization: Vanderbilt University
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: RFA-OD-09-004
Funding Institute: NIGMS
FY Total Cost: $610,795


Project Title: VESPA: Vanderbilt Electronic Systems for Pharmacogenomic Assessment
Principal Investigator: Masys, Daniel R
Organization: Vanderbilt University
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: RFA-OD-09-004
Funding Institute: OD
FY Total Cost: $610,796


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Project Title: Supporting RNAstructure: Software for RNA Analysis
Principal Investigator: Mathews, David H
Organization: University of Rochester
Project Start Date: Dec. 1, 2005
Project End Date: Aug. 31, 2014
RFA/PA: PAR-08-010
Funding Institute: NIGMS
FY Total Cost: $267,627


Project Title: Copasi: Biochemical Network Modeling and Simulation Software
Principal Investigator: Mendes, Pedro
Organization: Virginia Polytechnic Institute and St University
Project Start Date: Sept. 1, 2007
Project End Date: Aug. 31, 2011
RFA/PA: PAR-05-057
Funding Institute: NIGMS
FY Total Cost: $509,951


Project Title: Biomedical Informatics Research Training at Yale
Principal Investigator: Miller, Perry L
Organization: Yale University
Project Start Date: July 1, 1987
Project End Date: June 30, 2012
RFA/PA: RFA-LM-06-001
Funding Institute: NLM
FY Total Cost: $216,000


Project Title: Bioinformatics Strategies for Genome-Wide Association Studies
Principal Investigator: Asselbergs, Folkert Wouter
Organization: Dartmouth College
Project Start Date: Sept. 30, 2009
Project End Date: Sept. 29, 2013
RFA/PA: PAR-08-080
Funding Institute: NLM
FY Total Cost: $296,179


Project Title: Building and Validating Location Proteomics Databases
Principal Investigator: Murphy, Robert F.
Organization: Carnegie-Mellon University
Project Start Date: June 15, 2007
Project End Date: May 31, 2011
RFA/PA: NA
Funding Institute: NIGMS
FY Total Cost: $33,678


Project Title: National Center for Biomedical Ontology
Principal Investigator: Musen, Mark A
Organization: Stanford University
Project Start Date: Sept. 23, 2005
Project End Date: July 31, 2015
RFA/PA: RFA-RM-09-002
Funding Institute: OD
FY Total Cost: $3,698,211


Project Title: Computational Tools for Mass Spectrometry-Based Interactome Data
Principal Investigator: Nesvizhskii, Alexey I
Organization: University of Michigan at Ann Arbor
Project Start Date: Sept. 1, 2010
Project End Date: Aug. 31, 2014
RFA/PA: PAR-09-218
Funding Institute: NIGMS
FY Total Cost: $292,264


Project Title: DNA Polymerase Database
Principal Investigator: Jack, William E
Organization: New England BioLabs
Project Start Date: March 1, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PA-08-050
Funding Institute: NIGMS
FY Total Cost: $251,329


Project Title: Integrative Analysis of Multiple Genomic Data Sets
Principal Investigator: Park, Peter J
Organization: New England BioLabs
Project Start Date: Sept. 25, 2007
Project End Date: Aug. 31, 2012
RFA/PA: PAR-06-410
Funding Institute: NIGMS
FY Total Cost: $293,659


Project Title: Research Training for Computation and Informatics in Biology and Medicine
Principal Investigator: Phillips, George Neal
Organization: University of Wisconsin Madison
Project Start Date: July 1, 2002
Project End Date: June 30, 2012
RFA/PA: RFA-LM-06-001
Funding Institute: NLM
FY Total Cost: $94,834


Project Title: Software for the Analysis of Large-Scale Genotyping and Sequencing Studies
Principal Investigator: Purcell, Shaun M
Organization: Massachusetts General Hospital
Project Start Date: Sept. 27, 2010
Project End Date: June 30, 2013
RFA/PA: PAR-08-010
Funding Institute: NHGRI
FY Total Cost: $319,350


Project Title: Model-Based Methods for Analyzing Chip Sequencing Data
Principal Investigator: Qin, Zhaohui Steve
Organization: Emory University
Project Start Date: July 22, 2009
Project End Date: June 30, 2013
RFA/PA: PA-07-070
Funding Institute: NHGRI
FY Total Cost: $292,421


Project Title: Statistical Methods to Analyze Resequencing Data
Principal Investigator: Qin, Zhaohui Steve
Organization: Emory University
Project Start Date: Sept. 27, 2010
Project End Date: July 31, 2012
RFA/PA: PA-09-164
Funding Institute: NHGRI
FY Total Cost: $192,719


Project Title: Efficient Algorithms for Motif Search
Principal Investigator: Rajasekaran, Sanguthevar
Organization: University of Connecticut Storrs
Project Start Date: Sept. 30, 2010
Project End Date: Sept. 29, 2014
RFA/PA: PAR-08-080
Funding Institute: NLM
FY Total Cost: $397,043


Project Title: Predicting and Engineering Molecular Structures for Biomedical Applications
Principal Investigator: Randall, Arlo Zan
Organization: University of California Irvine
Project Start Date: Sept. 30, 2010
Project End Date: Sept. 29, 2012
RFA/PA: PA-09-036
Funding Institute: NLM
FY Total Cost: $101,874


Project Title: Computational System to Predict Novel Genetic Disease Associations
Principal Investigator: Reese, Martin G
Organization: Omicia
Project Start Date: May 3, 2005
Project End Date: June 30, 2011
RFA/PA: PA-08-050
Funding Institute: NHGRI
FY Total Cost: $262,867


Project Title: Vanderbilt Genome-Electronic Records Project
Principal Investigator: Roden, Dan M
Organization: Vanderbilt University
Project Start Date: Sept. 28, 2007
Project End Date: July 31, 2011
RFA/PA: RFA-HG-07-005
Funding Institute: NHGRI
FY Total Cost: $1,512,082


Project Title: Vanderbilt Genome-Electronic Records Project
Principal Investigator: Roden, Dan M
Organization: Vanderbilt University
Project Start Date: Sept. 28, 2007
Project End Date: July 31, 2011
RFA/PA: RFA-HG-07-005
Funding Institute: NIGMS
FY Total Cost: $205,892


Project Title: Advanced Strategies for Genotype Imputation
Principal Investigator: Rosenberg, Noah
Organization: University of Michigan at Ann Arbor
Project Start Date: Sept. 13, 2010
Project End Date: June 30, 2015
RFA/PA: PA-07-070
Funding Institute: NHGRI
FY Total Cost: $377,783


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Project Title: Visual Programming Tool for Integrated Gene/Protein Networks in Cancer Research
Principal Investigator: Sasinowski, Maciek
Organization: Incogen
Project Start Date: Jan. 1, 2007
Project End Date: Aug. 31, 2012
RFA/PA: PAR-07-160
Funding Institute: NCI
FY Total Cost: $738,301


Project Title: Modeling the Effect of Drugs in Integromics by Linking Drug Ontology and Pathways
Principal Investigator: Schadow, Gunther
Organization: Indiana University/Purdue University at Indianapolis
Project Start Date: Sept. 26, 2008
Project End Date: Aug. 31, 2011
RFA/PA: PAR-07-425
Funding Institute: NIGMS
FY Total Cost: $232,566


Project Title: Computational Studies of in Vitro Selection of RNAs
Principal Investigator: Schlick, Tamar
Organization: New York University
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2013
RFA/PA: PA-07-070
Funding Institute: NIGMS
FY Total Cost: $309,559


Project Title: Software for the Accurate De Novo 3D Structure Prediction of RNA
Principal Investigator: Santalucia, John
Organization: DNA Software
Project Start Date: Sept. 1, 2010
Project End Date: Feb. 28, 2011
RFA/PA: PA-09-080
Funding Institute: NIGMS
FY Total Cost: $99,586


Project Title: Innovative Supercomputing for Breakthrough Molecular Dynamics
Principal Investigator: Stiles, Joel R.
Organization: Carnegie-Mellon University
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: RFA-OD-09-004
Funding Institute: NIGMS
FY Total Cost: $1,346,550


Project Title: Dynamically Scalable Accessible Analysis for Next Generation Sequence Data
Principal Investigator: Nekrutenko, Anton
Organization: Emory University
Project Start Date: Sept. 25, 2009
Project End Date: July 31, 2011
RFA/PA: RFA-OD-09-004
Funding Institute: NHGRI
FY Total Cost: $734,945


Project Title: Ecolihub2.0: a Next-Generation E. Coli Model Organism Resource
Principal Investigator: Ball, Catherine A
Organization: University of Southern California
Project Start Date: Aug. 1, 2009
Project End Date: July 31, 2013
RFA/PA: RFA-GM-09-010
Funding Institute: NIGMS
FY Total Cost: $1,122,304


Project Title: Gneimo: Generalized Internal Coordinate Molecular Dynamics Methods
Principal Investigator: Vaidehi, Nagarajan
Organization: City of Hope/Beckman Research Institute
Project Start Date: Sept. 1, 2008
Project End Date: Aug. 31, 2012
RFA/PA: PA-07-070
Funding Institute: NIGMS
FY Total Cost: $298,287


Project Title: Automated Literature Mining for Validation of High-Throughput Function Prediction
Principal Investigator: Verspoor, Karin Maria
Organization: University of Colorado Denver
Project Start Date: July 1, 2009
Project End Date: June 30, 2011
RFA/PA: RFA-GM-09-008
Funding Institute: NLM
FY Total Cost: $80,113


Project Title: A New Method for Biomembrane Simulations
Principal Investigator: Voth, Gregory A.
Organization: University of Chicago
Project Start Date: June 1, 2001
Project End Date: Aug. 31, 2013
RFA/PA: PA-07-070
Funding Institute: NIGMS
FY Total Cost: $87,360


Project Title: Machine Learning to Identify Predictive SNPs and Complex Interaction Effects
Principal Investigator: Wang, Yue
Organization: Virginia Polytechnic Institute and St University
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PAR-06-411
Funding Institute: NIGMS
FY Total Cost: $226,422


Project Title: Visual Analytics Software Environment for Proteomics Data Integration
Principal Investigator: Webb-Robertson, Bobbie-Jo Mary
Organization: Battelle Pacific Northwest Laboratories
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PAR-07-235
Funding Institute: NIGMS
FY Total Cost: $474,570


Project Title: Integrative Pipeline for Analysis & Translational Application of TCGA Data (GDAC)
Principal Investigator: Mills, Gordon B.
Organization: University of Texas MD Anderson Cancer Center
Project Start Date: Sept. 29, 2009
Project End Date: Nov. 30, 2011
RFA/PA: RFA-CA-09-010
Funding Institute: NCI
FY Total Cost: $841,344


Project Title: Integrative Pipeline for Analysis & Translational Application of TCGA Data (GDAC)
Principal Investigator: Mills, Gordon B.
Organization: University of Texas MD Anderson Cancer Center
Project Start Date: Sept. 29, 2009
Project End Date: Aug. 31, 2011
RFA/PA: RFA-CA-09-010
Funding Institute: NCI
FY Total Cost: $900,000


Project Title: Zfin: the Zebrafish Model Organism Database
Principal Investigator: Westerfield, Monte
Organization: University of Oregon
Project Start Date: July 11, 2003
Project End Date: Feb. 28, 2011
RFA/PA: NA
Funding Institute: NHGRI
FY Total Cost: $2,651,206


Project Title: Zfin: the Zebrafish Model Organism Database
Principal Investigator: Westerfield, Monte
Organization: University of Oregon
Project Start Date: July 11, 2003
Project End Date: Feb. 28, 2011
RFA/PA: NA
Funding Institute: NICHD
FY Total Cost: $235,757


Project Title: Statistical Analysis of Exon Arrays
Principal Investigator: Wong, Wing H.
Organization: Stanford University
Project Start Date: Sept. 18, 2008
Project End Date: June 30, 2012
RFA/PA: PA-07-070
Funding Institute: NHGRI
FY Total Cost: $348,319


Project Title: Tool for Annotation and Analyses of Human Whole-Genome Sequence Variation Data
Principal Investigator: Reese, Martin G
Organization: University of Utah
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: RFA-OD-09-004
Funding Institute: NHGRI
FY Total Cost: $384,738


Project Title: A New Informatics Paradigm for Reconstructing Signaling Pathways in Human Disease
Principal Investigator: Zhu, Dongxiao
Organization: Louisiana State University/University of New Orleans
Project Start Date: Sept. 30, 2009
Project End Date: Sept. 29, 2011
RFA/PA: PA-06-181
Funding Institute: NLM
FY Total Cost: $200,506


Project Title: A New Scoring Framework for Selecting Structural Models
Principal Investigator: Zou, Xiaoqin
Organization: University of Missouri, Columbia
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PAR-06-411
Funding Institute: NIGMS
FY Total Cost: $227,250

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