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Funding Update: NIH Bioinformatics Grants Awarded Aug. 20 — Sept. 26, 2013: Sep 27, 2013

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Part 1 of 3

Project Title: Quant. Methods for Systems-level Analyses of Regulation & Signaling Dynamics
Principal Investigator: Airoldi, Edoardo
Organization: Harvard University
Project Start Date: Aug. 1, 2010
Project End Date: July 31, 2015
Funding Institute: NIGMS
FY Total Cost: $210,022


Project Title: Computational Methods Towards the Spatio-temporal Organization of the Proteome
Principal Investigator: Alber, Frank
Organization: University of Southern California
Project Start Date: Sept. 30, 2011
Project End Date: Aug. 31, 2016
Funding Institute: NIGMS
FY Total Cost: $299,929


Project Title: Biomedical Computation Research
Principal Investigator: Altman, Russ
Organization: Stanford University
Project Start Date: Not Listed
Project End Date: Not Listed
Funding Institute: NIGMS
FY Total Cost: $ 1,217,437


Project Title: Physics-based Simulation of Biological Structures
Principal Investigator: Altman, Russ
Organization: Stanford University
Project Start Date: Sept. 15, 2004
Project End Date: Aug. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $2,334,788


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: April 30, 2014
Funding Institute: NHGRI
FY Total Cost: $3,945,000


Project Title: The Virtual Physiological Rat Project
Principal Investigator: Beard, Daniel
Organization: Medical College of Wisconsin
Project Start Date: Aug. 11, 2011
Project End Date: July 31, 2016
Funding Institute: NIGMS
FY Total Cost: $2,437,686


Project Title: SVM-based Analysis of the Fine Scale Structure of Regulatory Elements
Principal Investigator: Beer, Michael
Organization: Johns Hopkins University
Project Start Date: Sept. 13, 2013
Project End Date: June 30, 2018
Funding Institute: NHGRI
FY Total Cost: $460,570


Project Title: Compressive Genomics for Large Omics Datasets: Algorithms, Applications, & Tools
Principal Investigator: Berger, Bonnie
Organization: Massachusetts Institute of Technology
Project Start Date: Sept. 5, 2013
Project End Date: May 31, 2016
Funding Institute: NIGMS
FY Total Cost: $217,893


Project Title: Informatics to Enable Routine Personalized Cancer Therapy
Principal Investigator: Bernstam, Elmer
Organization: University of Texas, Houston
Project Start Date: Sept. 1, 2013
Project End Date: Aug. 31, 2016
Funding Institute: NCI
FY Total Cost: $335,040


Project Title: Predicting Protein-DNA Interactions with Structural Models
Principal Investigator: Bradley, Philip
Organization: Fred Hutchinson Cancer Research Center
Project Start Date: Aug. 10, 2009
Project End Date: July. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $314,611


Project Title: New Tools for the Characterization of Gene Prediction in Prokaryote Genomes
Principal Investigator: Brocchieri, Luciano
Organization: University of Florida
Project Start Date: Aug. 5, 2010
Project End Date: July 31, 2015
Funding Institute: NIGMS
FY Total Cost: $268,647


Project Title: Analyzing Next-Generation Sequencing Data
Principal Investigator: Brown, Charles
Organization: Michigan State University
Project Start Date: Aug. 23, 2011
Project End Date: July 31, 2014
Funding Institute: NHGRI
FY Total Cost: $54,000


Project Title: National Center: Multiscale Analysis of Genomic and Cellular Networks (MAGNET)
Principal Investigator: Califano, Andrea
Organization: Columbia University
Project Start Date: Sept. 26, 2005
Project End Date: July 31, 2015
Funding Institute: NCI
FY Total Cost: $99,887


Project Title: The EM Open Connectome Project
Principal Investigator: Burns, Randal
Organization: Johns Hopkins University
Project Start Date: Sept. 10, 2012
Project End Date: Aug. 31, 2015
Funding Institute: NIBIB
FY Total Cost: $99,887

Project Title: A Data Coordinating Center for ENCODE
Principal Investigator: Cherry, Joe
Organization: Stanford University
Project Start Date: Sept. 21, 2012
Project End Date: July 31, 2016
Funding Institute: NHGRI
FY Total Cost: $2,499,949


Project Title: A Data Coordinating Center for ENCODE
Principal Investigator: Cherry, Joe
Organization: Stanford University
Project Start Date: Sept. 21, 2012
Project End Date: July 31, 2016
Funding Institute: NHGRI
FY Total Cost: $660,000


Project Title: Proteolysis In Silico: Statistics, Structural Chemistry, and Biology
Principal Investigator: Cieplak, Piotr
Organization: Sanford-Burnham Medical Research Institute
Project Start Date: Sept. 30, 2011
Project End Date: Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $357,533


Project Title: SimTK.org: A Resource to Enable Collaboration & Reproducibility of Biosimulations
Principal Investigator: Delp, Scott
Organization: Stanford University
Project Start Date: Sept. 1, 2013
Project End Date: April 30, 2017
Funding Institute: NIGMS
FY Total Cost: $463,367


Project Title: Association Analysis Software for Mining Clinical Next-gen Sequencing Data
Principal Investigator: Durfee, Timothy
Organization: DNAStar
Project Start Date: Sept. 25, 2012
Project End Date: June 30, 2015
Funding Institute: NHGRI
FY Total Cost: $150,000


Project Title: The Epilepsy Bioinformatics Study
Principal Investigator: Engel, Jerome
Organization: University of California, Los Angeles
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2015
Funding Institute: NINDS
FY Total Cost: $152,000


Project Title: The Epilepsy Bioinformatics Study
Principal Investigator: Engel, Jerome
Organization: University of California, Los Angeles
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2015
Funding Institute: NINDS
FY Total Cost: $446,019


Project Title: Enhanced Gene Identification in Complex Traits Using Kernel Machines
Principal Investigator: Epstein, Michael
Organization: Emory University
Project Start Date: Sept. 4, 2013
Project End Date: June 30, 2016
Funding Institute: NHGRI
FY Total Cost: $350,000


Project Title: Development of a Web-based Database and Research Engine for Genetic Discovery
Principal Investigator: Eriksson, Nicholas
Organization: 23andMe
Project Start Date: Sept. 4, 2013
Project End Date: June 30, 2016
Funding Institute: NHGRI
FY Total Cost: $350,000


Project Title: Software for Modeling and Optimization of Protein Therapeutics
Principal Investigator: Hall, David
Organization: Acpharis
Project Start Date: Sept. 10, 2013
Project End Date: Sept. 9, 2014
Funding Institute: NIGMS
FY Total Cost: $149,999


Project Title: Pathway Analysis Tools for Personalized Medicine and Drug Repositioning
Principal Investigator: Hartman, John
Organization: Advaita
Project Start Date: Sept. 10, 2013
Project End Date: April 9, 2014
Funding Institute: NIGMS
FY Total Cost: $148,487


Project Title: Cloud-based Resource for Data Hosting, Visualization, and Analysis Using UCSC Cancer Genomics Browser
Principal Investigator: Haussler, David
Organization: University of California, Santa Cruz
Project Start Date: Sept. 17, 2013
Project End Date: Aug. 31, 2018
Funding Institute: NCI
FY Total Cost: $621,154


Project Title: Continued Support of Essential SBML Software and Community Resources
Principal Investigator: Hucka, Michael
Organization: California Institute of Technology
Project Start Date: Feb. 1, 2004
Project End Date: April 30, 2016
Funding Institute: NIGMS
FY Total Cost: $553,166


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
Funding Institute: NINDS
FY Total Cost: $457,788


Project Title: Bayesian Approaches to Model Selection for Survival Data
Principal Investigator: Ibrahim, Joseph
Organization: University of North Carolina, Chapel Hill
Project Start Date: March 1,1996
Project End Date: Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $272,896


Project Title: Cytoscape: A Modeling Platform for Biomolecular Networks
Principal Investigator: Idekker, Trey
Organization: University of California
Project Start Date: June 1, 2004
Project End Date: April 30, 2017
Funding Institute: NIGMS
FY Total Cost: $495,855


Project Title: Preprocessing and Analysis Tools for Contemporary Microarray Applications
Principal Investigator: Irizarry, Rafael
Organization: Johns Hopkins University
Project Start Date: Sept. 24, 2007
Project End Date: Aug. 31, 2016
Funding Institute: NIGMS
FY Total Cost: $295,461


Project Title: Software for the Statistical Analysis for Microarray Probe Level Data
Principal Investigator: Irizarry, Rafael
Organization: Johns Hopkins University
Project Start Date: July 1, 2005
Project End Date: July 31, 2014
Funding Institute: NIGMS
FY Total Cost: $377,281


Project Title: Informatics Tools for High-throughput Analysis of Cancer Mutations
Principal Investigator: Karchin, Rachel
Organization: Johns Hopkins University
Project Start Date: Sept. 17, 2013
Project End Date: Aug. 31, 2016
Funding Institute: NCI
FY Total Cost: $289,971


Project Title: The UCSC Genome Browser
Principal Investigator: Kent, William
Organization: University of California, Santa Cruz
Project Start Date: July 12, 2001
Project End Date: June 30, 2017
Funding Institute: NHGRI
FY Total Cost: $160,326


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