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    • Funded Project Summary for Fiscal Year: 2011


    Project TitleProject Information
    Bringing BioNetGen Rule-Based Modeling to Virtual Cell Users Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1R01GM095485-01
    Actv: R01
    IC: GM
    PI Name(Contact): BLINOV, MICHAEL
    Institution: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
    Continued Maintenance and Development of Software: Integrated Genome Browser and Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1R01RR032048-01
    Actv: R01
    IC: RR
    PI Name(Contact): LORAINE, ANN E
    Institution: UNIVERSITY OF NORTH CAROLINA CHARLOTTE
    Continued Development and Maintenance of the 3DNA Suite of Programs Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1R01GM096889-01
    Actv: R01
    IC: GM
    PI Name(Contact): LU, XIANG-JUN
    Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE
    MeV: Software for Next Generation Genomic Data Analysis Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1U01CA151118-01A1
    Actv: U01
    IC: CA
    PI Name(Contact): QUACKENBUSH, JOHN
    Institution: DANA-FARBER CANCER INSTITUTE
    Alignment Software for Second-Generation Sequencing Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1R01HG006102-01
    Actv: R01
    IC: HG
    PI Name(Contact): SALZBERG, STEVEN L.
    Institution: JOHNS HOPKINS UNIVERSITY
    AutoDock-FR: A Modular Approach to Flexible Receptor Docking Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1R01GM096888-01
    Actv: R01
    IC: GM
    PI Name(Contact): SANNER, MICHEL F.
    Institution: SCRIPPS RESEARCH INSTITUTE
    Commodity Hardware Acceleration of Popular Modeling Software for Structural Biolo Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1R01GM098243-01
    Actv: R01
    IC: GM
    PI Name(Contact): SCHULTEN, KLAUS
    Institution: UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN
    Interactive software for semiautomated analysis of structural brain images Fiscal Year: 2011
    RFA/PA Number: PAR08-010
    Grant Number: 1R01NS074980-01
    Actv: R01
    IC: NS
    PI Name(Contact): SHATTUCK, DAVID W
    Institution: UNIVERSITY OF CALIFORNIA LOS ANGELES
    A multi-scale model to predict outcomes of immunomodulation and drug therapy duri Fiscal Year: 2011
    RFA/PA Number: PAR08-023
    Grant Number: 2R01EB012579-04A1
    Actv: R01
    IC: EB
    PI Name(Contact): KIRSCHNER, DENISE E
    Institution: UNIVERSITY OF MICHIGAN AT ANN ARBOR
    Multiscale analysis and modeling of spatiotemporal dynamics in human epilepsy Fiscal Year: 2011
    RFA/PA Number: PAR08-023
    Grant Number: 1R01NS072023-01A1
    Actv: R01
    IC: NS
    PI Name(Contact): KRAMER, MARK ALAN
    Institution: BOSTON UNIVERSITY
    Resynchronizing the Failing Heart: Insights from a Multiscale Cardiac Model Fiscal Year: 2011
    RFA/PA Number: PAR08-023
    Grant Number: 1R01HL103428-01A1
    Actv: R01
    IC: HL
    PI Name(Contact): TRAYANOVA, NATALIA A.
    Institution: JOHNS HOPKINS UNIVERSITY
    An Integrative Multi-Scale Model of Extracellular Matrix Mechanics in Vascular Re Fiscal Year: 2011
    RFA/PA Number: PAR08-023
    Grant Number: 1R01HL098028-01A1
    Actv: R01
    IC: HL
    PI Name(Contact): ZHANG, YANHANG
    Institution: BOSTON UNIVERSITY
    Hemodynamics and AAA disease: Uncovering the Hidden Connections Fiscal Year: 2011
    RFA/PA Number: PAR08-183
    Grant Number: 1R21HL108272-01
    Actv: R21
    IC: HL
    PI Name(Contact): SHADDEN, SHAWN C.
    Institution: ILLINOIS INSTITUTE OF TECHNOLOGY
    Computational analysis of Human High Grade Gliomas Fiscal Year: 2011
    RFA/PA Number: PAR08-184
    Grant Number: 5R01NS061776-03
    Actv: R01
    IC: NS
    PI Name(Contact): IAVARONE, ANTONIO
    Institution: COLUMBIA UNIVERSITY HEALTH SCIENCES
    Integrative tools for protozoan parasite research Fiscal Year: 2011
    RFA/PA Number: PAR08-184
    Grant Number: 5R01GM093132-02
    Actv: R01
    IC: GM
    PI Name(Contact): STOECKERT, CHRISTIAN J.
    Institution: UNIVERSITY OF PENNSYLVANIA
    Automated Web-Based Behavioral Diagnostics of Cognitive Impairment Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01EB014266-01A1
    Actv: R01
    IC: EB
    PI Name(Contact): AGICHTEIN, YEVGENY EUGENE
    Institution: EMORY UNIVERSITY
    An Observational Acute Stroke Model for Decision Support and Comparing Outcomes Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01NS076534-01
    Actv: R01
    IC: NS
    PI Name(Contact): BUI, ALEX
    Institution: UNIVERSITY OF CALIFORNIA LOS ANGELES
    Statistical methods for the study of alternative splicing using deep sequencing Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM097230-01
    Actv: R01
    IC: GM
    PI Name(Contact): CHEN, LIANG
    Institution: UNIVERSITY OF SOUTHERN CALIFORNIA
    Analyzing Neural Stem Cell Clonal Development Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01NS076709-01
    Actv: R01
    IC: NS
    PI Name(Contact): COHEN, ANDREW ROBERT
    Institution: UNIVERSITY OF WISCONSIN MILWAUKEE
    Developing Physics-Based Virtual Simulation Technology for Natural Orifice Transl Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01EB009362-01A2
    Actv: R01
    IC: EB
    PI Name(Contact): DE, SUVRANU
    Institution: RENSSELAER POLYTECHNIC INSTITUTE
    Software Tools for Automated Modeling of White Matter Fascicles from Diffusion MR Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01NS070963-01A1
    Actv: R01
    IC: NS
    PI Name(Contact): FISCHL, BRUCE
    Institution: MASSACHUSETTS GENERAL HOSPITAL
    Development of Bioimage Informatics Tools for Spatial Expression Datasets Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM097231-01
    Actv: R01
    IC: GM
    PI Name(Contact): FRISE, ERWIN
    Institution: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
    Clinically Relevant Use of Partial Roc Curves in Performance Comparison Studies Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM098253-01
    Actv: R01
    IC: GM
    PI Name(Contact): GUR, DAVID
    Institution: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
    Comparative Molecular Sequence Analysis Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 2R01HG002096-10A1
    Actv: R01
    IC: HG
    PI Name(Contact): KUMAR, SUDHIR
    Institution: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
    Computational Analysis of Gene Expression Pattern Images Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 2R01HG002516-07
    Actv: R01
    IC: HG
    PI Name(Contact): KUMAR, SUDHIR
    Institution: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
    Prosthesis Control by Forward Dynamic Simulation of the Intact Biomedical system Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01EB011615-01A1
    Actv: R01
    IC: EB
    PI Name(Contact): MURRAY, WENDY M
    Institution: REHABILITATION INSTITUTE OF CHICAGO
    Tools for Linking and Mining image and Genomic Data in Non-Small Cell Lung Cancer Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01CA160251-01
    Actv: R01
    IC: CA
    PI Name(Contact): NAPEL, SANDY A
    Institution: STANFORD UNIVERSITY
    Machine learning analysis of tandem mass spectra Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 9R01GM096306-05
    Actv: R01
    IC: GM
    PI Name(Contact): NOBLE, WILLIAM STAFFORD
    Institution: UNIVERSITY OF WASHINGTON
    A New Model of Peptide Fragmentation for Improved Protein Identification and Targ Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01CA155453-01
    Actv: R01
    IC: CA
    PI Name(Contact): OLD, WILLIAM MARLAND
    Institution: UNIVERSITY OF COLORADO AT BOULDER
    High Content Representation and Association of 3D Cell Culture Models Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01CA140663-01A2
    Actv: R01
    IC: CA
    PI Name(Contact): PARVIN, BAHRAM
    Institution: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
    Structural Alignment of RNA Sequences with Applications Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM097334-01
    Actv: R01
    IC: GM
    PI Name(Contact): SHARMA, GAURAV
    Institution: UNIVERSITY OF ROCHESTER
    Multi-scale modeling of asymmetric cell division Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM095990-01
    Actv: R01
    IC: GM
    PI Name(Contact): SHEN, XILING
    Institution: CORNELL UNIVERSITY ITHACA
    Molecular Signatures to Characterize the Oncogenic State of Individual Tumors Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01CA154480-01A1
    Actv: R01
    IC: CA
    PI Name(Contact): TAMAYO, PABLO
    Institution: BROAD INSTITUTE, INC.
    Collaborative Integration of HCV Molecular Virology and Mathematical Modeling Fiscal Year: 2011
    RFA/PA Number: PAR09-218
    Grant Number: 1R01AI078881-01A2
    Actv: R01
    IC: AI
    PI Name(Contact): UPRICHARD, SUSAN L
    Institution: UNIVERSITY OF ILLINOIS AT CHICAGO
    Dynamic Structures of Large and Flexible RNAs Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM096156-01A1
    Actv: R21
    IC: GM
    PI Name(Contact): AL-HASHIMI, HASHIM M
    Institution: UNIVERSITY OF MICHIGAN AT ANN ARBOR
    Reverse Engineering of Direct versus Indirect Effects in Biological Pathways Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM098984-01
    Actv: R21
    IC: GM
    PI Name(Contact): BLERIS, LEONIDAS
    Institution: UNIVERSITY OF TEXAS DALLAS
    Multiscale modeling of blood flow and clotting in cardiovascular devices Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21HL096930-01A2
    Actv: R21
    IC: HL
    PI Name(Contact): BLUESTEIN, DANNY
    Institution: STATE UNIVERSITY NEW YORK STONY BROOK
    UV Photodissociation for Acidic and Basic Proteome Characterization Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM099028-01
    Actv: R21
    IC: GM
    PI Name(Contact): BRODBELT, JENNIFER S
    Institution: UNIVERSITY OF TEXAS AUSTIN
    Semiparametric Methods for Efficiency-Adjusted Relative qRT-PCR Quantification Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21CA159816-01A1
    Actv: R21
    IC: CA
    PI Name(Contact): CHERVONEVA, INNA
    Institution: THOMAS JEFFERSON UNIVERSITY
    A phylogenetic approach to metagenomic analysis Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21HG006039-01
    Actv: R21
    IC: HG
    PI Name(Contact): FILIPSKI, ALAN
    Institution: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
    Bayesian hierarchical nonlinear models for pharmacogenomic cytotoxicity studies Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM086689-01A2
    Actv: R21
    IC: GM
    PI Name(Contact): FRIDLEY, BROOKE L.
    Institution: MAYO CLINIC
    Tools for detecting biologically important sequence variation in cancer Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21CA152432-01A1
    Actv: R21
    IC: CA
    PI Name(Contact): KARCHIN, RACHEL
    Institution: JOHNS HOPKINS UNIVERSITY
    A Systems Approach To Iron Metabolism In Cancer Cells Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21CA156133-01A1
    Actv: R21
    IC: CA
    PI Name(Contact): LAUBENBACHER, REINHARD
    Institution: VIRGINIA POLYTECHNIC INST AND ST UNIV
    Multivariate Dynamical Systems Methods for Identifying Causal Interactions in fMR Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21NS071221-01A1
    Actv: R21
    IC: NS
    PI Name(Contact): MENON, VINOD
    Institution: STANFORD UNIVERSITY
    Fusion of Electromagnetic Brain Imaging and fMRI Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21NS076171-01A1
    Actv: R21
    IC: NS
    PI Name(Contact): NAGARAJAN, SRIKANTAN S
    Institution: UNIVERSITY OF CALIFORNIA SAN FRANCISCO
    Automatic Quantitative Analysis of MR Images of the Knee in Osteoarthritis Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21AR059890-01A1
    Actv: R21
    IC: AR
    PI Name(Contact): NIETHAMMER, MARC
    Institution: UNIVERSITY OF NORTH CAROLINA CHAPEL HILL
    Chemical Pattern Detection and Visualization in Biological Networks Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM095952-01
    Actv: R21
    IC: IC
    PI Name(Contact): OPREA, TUDOR I
    Institution: UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR
    Hemodynamics in Intracranial Aneurysm Pathogenesis Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21NS075341-01
    Actv: R21
    IC: NS
    PI Name(Contact): SFORZA, DANIEL MARCELO
    Institution: GEORGE MASON UNIVERSITY
    Protein Design Using Physical Scoring Functions integrated with Site Couplings Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM097617-01
    Actv: R21
    IC: GM
    PI Name(Contact): WANG, JUNMEI
    Institution: UNIVERSITY OF TEXAS SW MED CTR/DALLAS
    Empirical-Bayesian Testing for Family Genome-wide Association Data Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21HG006150-01
    Actv: R21
    IC: HG
    PI Name(Contact): WANG, TAO
    Institution: ALBERT EINSTEIN COL OF MED YESHIVA UNIV
    Force field development for zinc metalloproteins Fiscal Year: 2011
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM097530-01
    Actv: R21
    IC: GM
    PI Name(Contact): ZHANG, YINGKAI
    Institution: NEW YORK UNIVERSITY
    Biocomputation across distributed private datasets to enhance drug discovery Fiscal Year: 2011
    RFA/PA Number: PAR09-220
    Grant Number: 1R43LM011152-01
    Actv: R43
    IC: LM
    PI Name(Contact): BUNIN, BARRY
    Institution: COLLABORATIVE DRUG DISCOVERY, INC.
    Web Software for Drug Targeting Signaling Networks in Primary Cell Subsets Fiscal Year: 2011
    RFA/PA Number: PAR09-220
    Grant Number: 1R43GM096579-01
    Actv: R43
    IC: GM
    PI Name(Contact): KOTECHA, NIKESH
    Institution: CYTOBANK, INC.
    An Open Source Digital Pathology System Supporting Multi-Touch Interaction Fiscal Year: 2011
    RFA/PA Number: PAR09-220
    Grant Number: 1R43EB013518-01A1
    Actv: R43
    IC: EB
    PI Name(Contact): LAW, CHRISTOPHER CHARLES
    Institution: KITWARE, INC.
    Large-Scale Time Lapse Imaging to Monitor Neuroplasticity and Circuit Function Fiscal Year: 2011
    RFA/PA Number: PAR09-220
    Grant Number: 1R43MH096669-01A1
    Actv: R43
    IC: MH
    PI Name(Contact): LAW, CHRISTOPHER CHARLES
    Institution: KITWARE, INC.
    DiseaseNet Finder: A Systems Medicine Toolkit for Clinical and Translational Rese Fiscal Year: 2011
    RFA/PA Number: PAR09-220
    Grant Number: 1R43RR031932-01
    Actv: R43
    IC: RR
    PI Name(Contact): NIBBE, ROD K
    Institution: NEOPROTEOMICS, INC.
    NITRC Image Repository: A Commercial Solution to Advancing Data Sharing in Neuros Fiscal Year: 2011
    RFA/PA Number: PAR09-220
    Grant Number: 1R43NS074540-01
    Actv: R43
    IC: NS
    PI Name(Contact): PREUSS, NINA
    Institution: TURNER CONSULTING GROUP, INC.
    Novel WEB Decision Support System for cardiac image interpretation and reporting Fiscal Year: 2011
    RFA/PA Number: PAR09-221
    Grant Number: 1R42HL106818-01
    Actv: R42
    IC: HL
    PI Name(Contact): GARCIA, ERNEST V
    Institution: SYNTERMED, INC
    CG-GRID: Computational Genetics Grid Resource for Interaction Discovery Fiscal Year: 2011
    RFA/PA Number: PAR09-221
    Grant Number: 1R41GM097765-01
    Actv: R41
    IC: GM
    PI Name(Contact): MOORE, JASON H
    Institution: PARABON COMPUTATION, INC.
    Skyline Targeted Proteomics Environment Fiscal Year: 2011
    RFA/PA Number: PAR11-028
    Grant Number: 1R01RR032708-01
    Actv: R01
    IC: RR
    PI Name(Contact): MACCOSS, MICHAEL J
    Institution: UNIVERSITY OF WASHINGTON
    Continued Development and Maintenance of ITK-SNAP 3D Image Segmentation Software Fiscal Year: 2011
    RFA/PA Number: PAR11-028
    Grant Number: 1R01EB014346-01
    Actv: R01
    IC: EB
    PI Name(Contact): YUSHKEVICH, PAUL A.
    Institution: UNIVERSITY OF PENNSYLVANIA
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