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Funding Update: NIH Bioinformatics Grants Awarded Aug. 4 — Sept. 4, 2012

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Project Title: Improving Network Analysis and Visualization for Infectious Disease Control
Principal Investigator: Abernethy, Neil Franklin
Organization: University of Washington
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2015
Funding Institute: NLM
FY Total Cost: $334,020


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: $310,688


Project Title: Predicting Prostate Cancer Aggressiveness
Principal Investigator: Anderson, Alexander Robertson Allan
Organization: H. Lee Moffitt Cancer Center and Research Institute
Project Start Date: Sept. 14, 2011
Project End Date: Aug. 31, 2016
Funding Institute: NCI
FY Total Cost: $574,247


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
Funding Institute: NHGRI, NIGMS
FY Total Cost: $6,041,078


Project Title: Informatic Tools for Predicting an Ordinal Response for High-Dimensional Data
Principal Investigator: Archer, Kellie J.
Organization: Virginia Commonwealth University
Project Start Date: Sept. 1, 2012
Project End Date: July 31, 2016
Funding Institute: NLM
FY Total Cost: $233,900


Project Title: Machine Learning Tools for Prognostication in Melanoma
Principal Investigator: Banerjee, Mousumi
Organization: University of Michigan, Ann Arbor
Project Start Date: Sept. 20, 2011
Project End Date: Aug. 31, 2013
Funding Institute: NCI
FY Total Cost: $159,977


Project Title: Computational Biology Resources
Principal Investigator: Bult, Carol J.
Organization: Jackson Laboratory
Project Start Date: March 1, 2005
Project End Date: Aug. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $373,596


Project Title: Continued Development and Maintenance of Appion Software
Principal Investigator: Carragher, Bridget Olivia
Organization: Scripps Research Institute
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2016
Funding Institute: NIGMS
FY Total Cost: $360,050


Project Title: The Epilepsy Bioinformatics Study (EPIBIOS)
Principal Investigator: Engel, Jerome None
Organization: University of California, Los Angeles
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2015
Funding Institute: NINDS
FY Total Cost: $484,652


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
Funding Institute: NIGMS
FY Total Cost: $295,779


Project Title: Development of Bioimage Informatics Tools for Spatial Expression Datasets
Principal Investigator: Frise, Erwin
Organization: Lawrence Berkeley National Laboratory
Project Start Date: Sept. 15, 2011
Project End Date: Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $384,334


Project Title: Semantic LAMHDI: Linking Diseases to Model Organism Resources
Principal Investigator: Haendel, Melissa A.
Organization: Oregon Health and Science University
Project Start Date: Sept. 1, 2012
Project End Date: July 31, 2016
Funding Institute: NIH
FY Total Cost: $1, 303,614


Project Title: Preprocessing and Analysis Tools for Contemporary Microarray Applications
Principal Investigator: Irizarry, Rafael Angel
Organization: Johns Hopkins University
Project Start Date: Sept. 24, 2007
Project End Date: Aug. 31, 2016
Funding Institute: NIGMS
FY Total Cost: $318,559


Project Title: Software for the Statistical Analysis of Microarray Probe Level Data
Principal Investigator: Irizarry, Rafael Angel
Organization: Johns Hopkins University
Project Start Date: July 1, 2005
Project End Date: July 31, 2014
Funding Institute: NIGMS
FY Total Cost: $395,276


Project Title: Cloud-Based Analysis of TCR Repertoire Sequencing Data
Principal Investigator: Johnson, David Scott
Organization: Gigagen
Project Start Date: Aug. 8, 2012
Project End Date: March 31, 2013
Funding Institute: NHGRI
FY Total Cost: $156,450


Project Title: Methods for Genomic Data with Graphical Structures
Principal Investigator: Lee, Hongzhe
Organization: University of Pennsylvania
Project Start Date: July 1, 2007
Project End Date: June 30, 2017
Funding Institute: NCI
FY Total Cost: $304,000


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
Funding Institute: NHGRI
FY Total Cost: $380,794


Project Title: Structure Determination of Proteins and RNA Molecules from NMR SAXS
Principal Investigator: Markley, John
Organization: University of Wisconsin, Madison
Project Start Date: March 1, 1997
Project End Date: Feb. 28, 2015
Funding Institute: NIGMS
FY Total Cost: $62,567


Project Title: Computational Method to Improve Signal Detection in NIRS Instruments
Principal Investigator: Medvedev, Andrei V.
Organization: Georgetown University
Project Start Date: Sept. 1, 2010
Project End Date: Aug. 31, 2013
Funding Institute: NIGMS
FY Total Cost: $188,897


Project Title: CG-GRID: Computational Genetics Grid Resource for Interaction Discovery
Principal Investigator: Moore, Jason H.
Organization: Parabon Computation
Project Start Date: Sept. 19, 2011
Project End Date: Aug. 31, 2013
Funding Institute: NIGMS
FY Total Cost: $184,522


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: $3,029,255


Project Title: IDASH: Integrating Data for Analysis, Anonymization, and Sharing
Principal Investigator: Ohno-Machado, Lucila
Organization: University of California, San Diego
Project Start Date: Sept. 20, 2010
Project End Date: June 30, 2015
Funding Institute: NHGRI
FY Total Cost: $150,000


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Project Title: AutoDock Software Development and Maintenance
Principal Investigator: Olson, Arthur J.
Organization: Scripps Research Institute
Project Start Date: Jan. 1, 2004
Project End Date: July 31, 2016
Funding Institute: NIGMS
FY Total Cost: $509,643


Project Title: System Genetics of Alcoholism: Network-Based Approaches for Genetic Association
Principal Investigator: Palmer, Rohan H.C.
Organization: Rhode Island Hospital
Project Start Date: Aug. 20, 2012
Project End Date: July 31, 2017
Funding Institute: NIAAA
FY Total Cost: $171,104


Project Title: WikiPathways Project: At the Intersection of Big Data and Researcher Knowledge
Principal Investigator: Pico, Alexander R.
Organization: J. David Gladstone Institutes
Project Start Date: Sept. 1, 2012
Project End Date: May 31, 2017
Funding Institute: NIGMS
FY Total Cost: $368,384


Project Title: Incorporating MicroRNA Data and Analyses into the Leading Cancer Genomics Portal
Principal Investigator: Rhodes, Daniel R.
Organization: Compendia Bioscience
Project Start Date: Aug. 1, 2010
Project End Date: July 31, 2013
Funding Institute: NCI
FY Total Cost: $571,234


Project Title: Chemical Address Tags: A Cheminformatics & Image Data Management and Analysis Platform
Principal Investigator: Rosania, Gus R.
Organization: University of Michigan, Ann Arbor
Project Start Date: July 1, 2006
Project End Date: July 31, 2016
Funding Institute: NIGMS
FY Total Cost: $462,719


Project Title: Conte Center for Computational Systems Genomics of Neuropsychiatric Phenotypes
Principal Investigator: Rzhetsky, Andrey
Organization: University of Chicago
Project Start Date: Sept. 22, 2011
Project End Date: July 31, 2016
Funding Institute: NIMH
FY Total Cost: $2,078,313


Project Title: Computational Gene Modeling and Genome Sequence Assembly
Principal Investigator: Salzberg, Steven
Organization: Johns Hopkins University
Project Start Date: Sept. 1, 1999
Project End Date: Aug. 31, 2014
Funding Institute: NHGRI, NIGMS
FY Total Cost: $595,227


Project Title: Legacy Informatics Resources for Glycomics
Principal Investigator: Sasisekharan, Ram
Organization: Massachusetts Institute of Technology
Project Start Date: Sept. 15, 2011
Project End Date: Aug. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $635,580


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
Funding Institute: NIGMS
FY Total Cost: $312,654


Project Title: Structural Alignment of RNA Sequences with Applications
Principal Investigator: Sharma, Gaurav
Organization: University of Rochester
Project Start Date: Sept. 15, 2011
Project End Date: Aug. 31, 2016
Funding Institute: NIGMS
FY Total Cost: $293,550


Project Title: Predicting and Analyzing Protein Interaction Networks
Principal Investigator: Singh, Mona
Organization: Princeton University
Project Start Date: Feb. 18, 2006
Project End Date: March 31, 2016
Funding Institute: NIGMS
FY Total Cost: $307,117


Project Title: Computer Simulation Theory of Globular Protein Dynamics
Principal Investigator: Skolnick, Jeffrey
Organization: Georgia Institute of Technology
Project Start Date: Dec. 1, 1986
Project End Date:Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $293,871


Project Title: Genomics GPUs and Next Generation Computational Statistics
Principal Investigator: Sobel, Eric
Organization: University of California, Los Angeles
Project Start Date: Aug. 26, 2011
Project End Date:June 30, 2015
Funding Institute: NHGRI
FY Total Cost: $359,174


Project Title: Methods for Accurate and Efficient Discovery of Local Pathways
Principal Investigator: Statnikov, Alexander
Organization: New York University School of Medicine
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2016
Funding Institute: NLM
FY Total Cost: $218,771


Project Title: Model and Methods for Population Genomics
Principal Investigator: Storey, John D.
Organization: Princeton University
Project Start Date: Aug. 25, 2012
Project End Date: June 30, 2015
Funding Institute: NHGRI
FY Total Cost: $300,004


Project Title: ChemBench: The Integrated Web Portal to Accelerate Cheminformatics and Chemical Genomics Research
Principal Investigator: Tropsha, Alexander
Organization: University of North Carolina, Chapel Hill
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2016
Funding Institute: NIGMS
FY Total Cost: $288,800


Project Title: Stochastic Models of Cell Cycle Regulation in Eukaryotes
Principal Investigator: Tyson, John J.
Organization: Virginia Polytechnic Institute
Project Start Date: June 6, 2006
Project End Date: Aug. 31, 2014
Funding Institute: NIGMS
FY Total Cost: $482,160


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
Funding Institute: NIGMS
FY Total Cost: $311,907


Project Title: Protein Design Using Physical Scoring Functions Integrated with Site Couplings
Principal Investigator: Wang, Junmei
Organization: University of Texas Southwestern Medical Center
Project Start Date: Sept. 1, 2011
Project End Date: Aug. 31, 2013
Funding Institute: NIGMS
FY Total Cost: $198,750


Project Title: High-Dimensional Unsupervised Learning with Applications to Genomics
Principal Investigator: Witten, Daniela
Organization: University of Washington
Project Start Date: Sept. 20, 2011
Project End Date: Aug. 31, 2016
Funding Institute: NIH
FY Total Cost: $377,315


Project Title: PRO: A Protein Ontology in OBO Foundry for Integration of Biomedical Knowledge
Principal Investigator: Wu, Cathy H.
Organization: University of Delaware
Project Start Date: May 1, 2007
Project End Date: June 30, 2015
Funding Institute: NIGMS
FY Total Cost: $82,863


Project Title: Bridging Sustainable Distribution of TRBD Bioinformatics Resources
Principal Investigator: Xiao, Wenzhong
Organization: Massachusetts General Hospital
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $579,394


Project Title: Time/Space-Varying Networks of Molecular Interactions: A New Paradigm
Principal Investigator: Xing, Poe E.
Organization: Carnegie-Mellon University
Project Start Date: July 1, 2010
Project End Date: June 30, 2015
Funding Institute: NIGMS
FY Total Cost: $442,016


Project Title: Identification, Discovery, and Public Archiving of RNA Structural Motifs
Principal Investigator: Zhang, Shaojie
Organization: University of Central Florida
Project Start Date: Sept. 1, 2012
Project End Date: Aug. 31, 2015
Funding Institute: NIGMS
FY Total Cost: $169,158


Project Title: A Novel Co-expression Network Approach that is Robust to Genetic Heterogeneity
Principal Investigator: Zhang, Weixiong
Organization: Washington University
Project Start Date: Sept. 1, 2012
Project End Date: July 31, 2016
Funding Institute: NIGMS
FY Total Cost: $296,400


Project Title: New Bayesian Algorithms for Genome-Wide Association Mapping
Principal Investigator: Zhang, Yu
Organization: Pennsylvania State University, University Park
Project Start Date: Aug. 15, 2008
Project End Date: June 30, 2015
Funding Institute: NHGRI
FY Total Cost: $178,651


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