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Funding Update: Oct 8, 2010

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

Project Title: Automated Integration of Biomedical Knowledge
Principal Investigator: Alterovitz, Gil
Organization: Brigham and Women's Hospital
Project Start Date: Sept. 30, 2009
Project End Date: Sept. 29, 2011
RFA/PA: PAR-07-249
Funding Institute: NHGRI
FY Total Cost: $428,079


Project Title: A Holistic Approach to Information Processing for Biomedical Networks
Principal Investigator: Alterovitz, Gil
Organization: Brigham and Women's Hospital
Project Start Date: Sept. 30, 2008
Project End Date: Sept. 29, 2013
RFA/PA: PA-07-297
Funding Institute: NLM
FY Total Cost: $249,000


Project Title: Annotating Functional Sites in 3D Biological Structures
Principal Investigator: Altman, Russ Biagio
Organization: Stanford University
Project Start Date: July 1, 1994
Project End Date: Aug. 31, 2014
RFA/PA: PA-07-070
Funding Institute: NLM
FY Total Cost: $328,016


Project Title: Graduate Training in Biomedical Informatics
Principal Investigator: Altman, Russ Biagio
Organization: Stanford University
Project Start Date: July 1, 1984
Project End Date: June 30, 2012
RFA/PA: RFA-LM-06-001
Funding Institute: NLM
FY Total Cost: $161,004


Project Title: Geisha: a Chicken Embryo Gene Expression Resource
Principal Investigator: Antin, Parker B
Organization: University of Arizona
Project Start Date: Sept. 30, 2010
Project End Date: July 31, 2015
RFA/PA: PA-08-180
Funding Institute: NICHD
FY Total Cost: $735,667


Project Title: Uniprot: a Centralized Protein Sequence and Function Resource
Principal Investigator: Apweiler, Rolf
Organization: European Molecular Biology Laboratory
Project Start Date: Sept. 27, 2010
Project End Date: July 31, 2013
RFA/PA: RFA-HG-10-004
Funding Institute: NHGRI
FY Total Cost: $5,000,000


Project Title: Uniprot: a Centralized Protein Sequence and Function Resource
Principal Investigator: Apweiler, Rolf
Organization: European Molecular Biology Laboratory
Project Start Date: Sept. 27, 2010
Project End Date: July 31, 2013
RFA/PA: RFA-HG-10-004
Funding Institute: NIGMS
FY Total Cost: $1,000,000


Project Title: National Center for Integrative Biomedical Informatics (RMI)
Principal Investigator: Athey, Brian David
Organization: University of Michigan at Ann Arbor
Project Start Date: Sept. 25, 2005
Project End Date: July 31, 2011
RFA/PA: RFA-RM-04-022
Funding Institute: NIGMS
FY Total Cost: $2,776,008


Project Title: Development of Software for Comparative/Quantitative Clinical Proteomics
Principal Investigator: Atwood, James Alexander
Organization: Bioinquire
Project Start Date: Jan. 18, 2008
Project End Date: Aug. 31, 2011
RFA/PA: PA-07-452
Funding Institute: NIGMS
FY Total Cost: $368,001


Project Title: Conceptual Prediction of Drug Bioactivities in Cell-Based Assays: Cell-QSAR
Principal Investigator: Balaz, Stefan
Organization: Albany College of Pharmacy
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2014
RFA/PA: PA-07-070
Funding Institute: NIGMS
FY Total Cost: $266,805


Project Title: Efficient Data Structures and Algorithms for Genomics Sequence Data
Principal Investigator: Baldi, Pierre Baldi
Organization: University of California Irvine
Project Start Date: Sept. 30, 2010
Project End Date: Sept. 29, 2013
RFA/PA: PA-07-070
Funding Institute: NLM
FY Total Cost: $176,932


Project Title: Biomedical Informatics Training Program
Principal Investigator: Baldi, Pierre Baldi
Organization: University of California Irvine
Project Start Date: July 1, 2002
Project End Date: June 30, 2012
RFA/PA: RFA-LM-06-001
Funding Institute: NLM
FY Total Cost: $216,000


Project Title: Prediction of Molecular Regulatory Networks in Dental and Craniofacial Disease
Principal Investigator: Bastian, Caleb D
Organization: Princeton University
Project Start Date: Sept. 3, 2010
Project End Date: Aug. 31, 2015
RFA/PA: PA-10-059
Funding Institute: NIDCR
FY Total Cost: $119,279


Project Title: RESTMD-CHARMM Simulation of the Chk2/Pp2a Interaction in DNA Repair
Principal Investigator: Begay, Shanadeen C
Organization: Boston University
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2012
RFA/PA: PA-07-106
Funding Institute: NIGMS
FY Total Cost: $36,860


Project Title: Modeling In Vivo Protein-DNA Interactions from High-Throughput Data Mp1/1
Principal Investigator: Benos, Panagiotis V
Organization: University of Pittsburgh at Pittsburgh
Project Start Date: Sept. 15, 2007
Project End Date: Sept. 14, 2012
RFA/PA: PA-06-094
Funding Institute: NLM
FY Total Cost: $470,983


Project Title: EDAC: Encode Data Analysis Center
Principal Investigator: Birney, Ewan
Organization: European Molecular Biology Laboratory
Project Start Date: May 15, 2008
Project End Date: March 31, 2012
RFA/PA: RFA-HG-07-010
Funding Institute: NHGRI
FY Total Cost: $151,816


Project Title: EDAC: Encode Data Analysis Center
Principal Investigator: Birney, Ewan
Organization: European Molecular Biology Laboratory
Project Start Date: May 15, 2008
Project End Date: March 31, 2012
RFA/PA: RFA-HG-07-010
Funding Institute: OD
FY Total Cost: $113,520


Project Title: EDAC: Encode Data Analysis Center
Principal Investigator: Birney, Ewan
Organization: European Molecular Biology Laboratory
Project Start Date: May 15, 2008
Project End Date: March 31, 2012
RFA/PA: RFA-HG-07-010
Funding Institute: NHGRI
FY Total Cost: $300,000


Project Title: Development of a Software Pipeline for Sequence Data
Principal Investigator: Bloom, Toby
Organization: Broad Institute
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: RFA-OD-09-004
Funding Institute: NHGRI
FY Total Cost: $597,624


Project Title: Development of Trans Proteomics Pipeline, an Analysis Suite for Mass Spectrometry
Principal Investigator: Boyle, John
Organization: Institute for Systems Biology
Project Start Date: Sept. 1, 2010
Project End Date: Aug. 31, 2013
RFA/PA: PAR-08-010
Funding Institute: NIGMS
FY Total Cost: $589,424


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Project Title: A Systems Biology Platform for the Assessment of Substance Abuse
Principal Investigator: Brennan, Richard John
Organization: GeneGo
Project Start Date: Sept. 15, 2010
Project End Date: March 31, 2011
RFA/PA: PA-09-080
Funding Institute: NIDA
FY Total Cost: $119,166


Project Title: Data Coordinating Center for Systems Biology Approach to the Mechanisms of TB
Principal Investigator: Bennett, Siiri
Organization: University of Washington
Project Start Date: Sept. 17, 2010
Project End Date: Aug. 31, 2014
RFA/PA: RFA-HL-10-022
Funding Institute: NHLBI
FY Total Cost: $580,245


Project Title: Improving Genotype Accuracy and Haplotypic Analysis for Genome-Wide Studies
Principal Investigator: Browning, Brian Lee
Organization: University of Washington
Project Start Date: Aug. 7, 2009
Project End Date: June 30, 2012
RFA/PA: PA-07-070
Funding Institute: NHGRI
FY Total Cost: $110,570


Project Title: Population Structure Admixture and Selection Across the 1000 Genomes Data Set
Principal Investigator: Bustamante, Carlos Daniel
Organization: Stanford University
Project Start Date: Sept. 9, 2010
Project End Date: June 30, 2012
RFA/PA: RFA-HG-09-002
Funding Institute: NHGRI
FY Total Cost: $441,922


Project Title: Integrating Microarray and Proteomic Data by Ontology-Based Annotation
Principal Investigator: Butte, Atul J
Organization: Stanford University
Project Start Date: Sept. 30, 2008
Project End Date: Sept. 29, 2012
RFA/PA: PA-07-070
Funding Institute: NLM
FY Total Cost: $277,200


Project Title: MU Biomedical Informatics Research Training Program
Principal Investigator: Caldwell, Charles W
Organization: University of Missouri-Columbia
Project Start Date: July 1, 1997
Project End Date: June 30, 2012
RFA/PA: RFA-LM-06-001
Funding Institute: NLM
FY Total Cost: $185,503


Project Title: Statistical Algorithms for Valid Inferences in Genomic Data
Principal Investigator: Casella, George
Organization: University of Florida
Project Start Date: Sept. 1, 2008
Project End Date: Aug. 31, 2011
RFA/PA: PA-07-070
Funding Institute: NIGMS
FY Total Cost: $168,864


Project Title: Novel Bioinformatics Tools for Gene Regulatory Network Inference
Principal Investigator: Chang, Li-Wei
Organization: Washington University
Project Start Date: Sept. 30, 2010
Project End Date: Sept. 29, 2012
RFA/PA: PA-09-036
Funding Institute: NLM
FY Total Cost: $90,000


Project Title: Data Structures, Algorithms and Tools for Ontological Discovery
Principal Investigator: Chesler, Elissa J
Organization: Jackson Laboratory
Project Start Date: Sept. 25, 2010
Project End Date: Aug. 31, 2014
RFA/PA: PAR-09-218
Funding Institute: NIAAA
FY Total Cost: $297,640


Project Title: Data Structures, Algorithms and Tools for Ontological Discovery
Principal Investigator: Chesler, Elissa J
Organization: Jackson Laboratory
Project Start Date: Sept. 25, 2010
Project End Date: Aug. 31, 2014
RFA/PA: PAR-09-218
Funding Institute: NIDA
FY Total Cost: $268,290


Project Title: The Cancer Genome Atlas Data Analysis Center
Principal Investigator: Chin, Lynda
Organization: Broad Institute
Project Start Date: Sept. 1, 2010
Project End Date: Aug. 31, 2011
RFA/PA: RFA-CA-09-010
Funding Institute: NCI
FY Total Cost: $693,768


Project Title: IBD Genetics Consortium Data Coordinating Center
Principal Investigator: Cho, Judy H
Organization: Yale University
Project Start Date: Sept. 30, 2002
Project End Date: Aug. 31, 2012
RFA/PA: RFA-DK-06-504
Funding Institute: NIDDK
FY Total Cost: $1,051,196


Project Title: IBD Genetics Consortium Data Coordinating Center
Principal Investigator: Cho, Judy H
Organization: Yale University
Project Start Date: Sept. 30, 2002
Project End Date: Aug. 31, 2012
RFA/PA: RFA-DK-06-504
Funding Institute: NIDDK
FY Total Cost: $349,711


Project Title: Encoding Semantic Knowledge in Vector Space for Biomedical Information
Principal Investigator: Cohen, Trevor
Organization: University of Texas Health Science Center Houston
Project Start Date: Sept. 30, 2010
Project End Date: Sept. 29, 2012
RFA/PA: PA-09-164
Funding Institute: NLM
FY Total Cost: $221,500


Project Title: Predicting Patient Outcomes From Clinical and Genome-Wide Data
Principal Investigator:Cooper, Gregory F
Organization: University of Pittsburgh at Pittsburgh
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PA-07-070
Funding Institute: NLM
FY Total Cost: $582,590


Project Title: Using the Transcriptome for SNP and Gene Annotation
Principal Investigator: Cox, Nancy J.
Organization: University of Chicago
Project Start Date: Sept. 17, 2010
Project End Date: July 31, 2012
RFA/PA: RFA-RM-09-006
Funding Institute: NHGRI
FY Total Cost: $51,930


Project Title: Using the Transcriptome for SNP and Gene Annotation
Principal Investigator: Cox, Nancy J.
Organization: University of Chicago
Project Start Date: Sept. 17, 2010
Project End Date: July 31, 2012
RFA/PA: RFA-RM-09-006
Funding Institute: NHLBI
FY Total Cost: $150,000


Project Title: Using the Transcriptome for SNP and Gene Annotation
Principal Investigator: Cox, Nancy J.
Organization: University of Chicago
Project Start Date: Sept. 17, 2010
Project End Date: July 31, 2012
RFA/PA: RFA-RM-09-006
Funding Institute: OD
FY Total Cost: $119,082


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Project Title: Beyond Information Extraction: Identifying Gene Ontology Concepts in Text
Principal Investigator: Crangle, Colleen Elizabeth
Organization: Converspeech
Project Start Date: Sept. 1, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PA-06-180
Funding Institute: NLM
FY Total Cost: $50,000


Project Title: Pittsburgh Biomedical Informatics Training Program
Principal Investigator: Crowley, Rebecca S
Organization: University of Pittsburgh at Pittsburgh
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: Joint SNP and CNV Calling in 1000 Genomes Sequence Data
Principal Investigator: Daly, Mark J
Organization: Broad Institute
Project Start Date: Sept. 23, 2010
Project End Date: Aug. 31, 2011
RFA/PA: RFA-HG-09-001
Funding Institute: NHGRI
FY Total Cost: $804,338


Project Title: Joint SNP and CNV Calling in 1000 Genomes Sequence Data
Principal Investigator: Daly, Mark J
Organization: Broad Institute
Project Start Date: Sept. 16, 2009
Project End Date: June 30, 2011
RFA/PA: RFA-HG-09-001
Funding Institute: NHGRI
FY Total Cost: $735,210


Project Title: Anchor: a PDB-Wide and Web-Based Discovery Resource of Small Molecular Weight Pro[teins]
Principal Investigator: Camacho, Carlos J.
Organization: University of Pittsburgh at Pittsburgh
Project Start Date: Sept. 8, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PAR-06-411
Funding Institute: NIGMS
FY Total Cost: $143,326


Project Title: Computational Methods for Functional Genomic Discovery from Gene Knockout Studies
Principal Investigator: Drake, Kenneth L
Organization: Seralogix
Project Start Date: July 1, 2007
Project End Date: June 30, 2012
RFA/PA: PA-09-080
Funding Institute: NHGRI
FY Total Cost: $537,957


Project Title: Software to Facilitate Adoption of the Sequence Ontology for Genome Management
Principal Investigator: Eilbeck, Karen Louise
Organization: University of Utah
Project Start Date: Aug. 15, 2007
Project End Date: June 30, 2011
RFA/PA: PAR-05-057
Funding Institute: NHGRI
FY Total Cost: $181,517


Project Title: Mouse Genome Informatics
Principal Investigator: Eppig, Janan T.
Organization: Jackson Laboratory
Project Start Date: July 1, 1997
Project End Date: July 31, 2011
RFA/PA: NA
Funding Institute: NHGRI
FY Total Cost: $6,946,287


Project Title: Novel Statistical Methods for Human Gene Mapping
Principal Investigator: Epstein, Michael Philip
Organization: Emory University
Project Start Date: Sept. 27, 2006
Project End Date: Aug. 31, 2011
RFA/PA: NA
Funding Institute: NHGRI
FY Total Cost: $288,566


Project Title: Commercial Software for Modeling of G Protein-Coupled Receptors
Principal Investigator: Farid, Ramy
Organization: Schrodinger
Project Start Date: Jan. 1, 2007
Project End Date: Aug. 31, 2013
RFA/PA: PAR-09-220
Funding Institute: NIGMS
FY Total Cost: $374,255


Project Title: Collaborative Systems for Analyzing Tissue Microarrays
Principal Investigator: Foran, David J
Project Start Date: University of Medicine and Dentistry of NJ/Robert Wood Johnson Medical School
Project Start Date: April 1, 2004
Project End Date: July 31, 2015
RFA/PA: PA-07-070
Funding Institute: NCI
FY Total Cost: $347,098


Project Title: Image Mining for Comparative Analysis of Expression Patterns in Tissue Microarray
Principal Investigator: Foran, David J
Organization: University of Medicine and Dentistry of NJ/Robert Wood Johnson Medical School
Project Start Date: Sept. 30, 2007
Project End Date: Sept. 29, 2011
RFA/PA: NA
Funding Institute: NLM
FY Total Cost: $568,927


Project Title: Novel Computational Tools for Studying the Human Microbiome
Principal Investigator: Fredricks, David Neal
Organization: Fred Hutchinson Cancer Research Center
Project Start Date: Sept. 27, 2010
Project End Date: June 30, 2013
RFA/PA: RFA-RM-09-020
Funding Institute: OD
FY Total Cost: $533,722


Project Title: Vanderbilt Biomedical Informatics Training Program
Principal Investigator: Gadd, Cynthia S
Organization: Vanderbilt University
Project Start Date: July 1, 2002
Project End Date: June 30, 2012
RFA/PA: RFA-LM-06-001
Funding Institute: NLM
FY Total Cost: $214,796


Project Title: A New Paradigm for Biomolecular Simulations
Principal Investigator: Gao, Jiali
Organization: University of Minnesota Twin Cities
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: RFA-OD-09-003
Funding Institute: NIGMS
FY Total Cost: $449,558


Project Title: Development of a Comprehensive System for Distant Homology Analysis
Principal Investigator: Godzik, Adam
Organization: Burnham Institute for Medical Research
Project Start Date: Sept. 30, 2009
Project End Date: Aug. 31, 2011
RFA/PA: PAR-08-010
Funding Institute: NIGMS
FY Total Cost: $477,500


Project Title: Connectivity Map 100K
Principal Investigator: Golub, Todd R.
Organization: Broad Institute
Project Start Date: Sept. 29, 2009
Project End Date: July 31, 2011
RFA/PA: RFA-OD-09-004
Funding Institute: NHGRI
FY Total Cost: $968,711


Project Title: Adapting Phred/Phrap/Consed for Nextgen Sequencing
Principal Investigator: Green, Philip P
Organization: University of Washington
Project Start Date: Sept. 18, 2010
Project End Date: June 30, 2013
RFA/PA: PAR-08-010
Funding Institute: NHGRI
FY Total Cost: $591,336


Project Title: Algorithmically-Tuned Protein Families, Rule_Base and Characterized Proteins
Principal Investigator: Haft, Daniel H.
Organization: J. Craig Venter Institute
Project Start Date: Sept. 26, 2008
Project End Date: July 31, 2011
RFA/PA: RFA-RM-08-008
Funding Institute: OD
FY Total Cost: $534,170


Project Title: Enhancement of the GBrowse Genome Annotation Browser
Principal Investigator: Holmes, Ian H
Organization: University of California Berkeley
Project Start Date: Sept. 1, 2007
Project End Date: Aug. 31, 2011
RFA/PA: PAR-05-057
Funding Institute: NHGRI
FY Total Cost: $288,719


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