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    • Funded Project Summary for Fiscal Year: 2012


    Project TitleProject Information
    Combining systems biology and structural biology to find new therapeutics Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM102365-01
    Actv: R01
    IC: GM
    PI Name(Contact): ALTMAN, RUSS BIAGIO
    Institution: STANFORD UNIVERSITY
    Computational design of specific binding proteins using Leave-One-Out Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM099827-01A1
    Actv: R01
    IC: GM
    PI Name(Contact): BYSTROFF, CHRISTOPHER
    Institution: RENSSELAER POLYTECHNIC INSTITUTE
    RepServer: Antigen Receptor Repertoire Analysis Pipelines via the WWW Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01AI097403-01
    Actv: R01
    IC: AI
    PI Name(Contact): COWELL, LINDSAY G
    Institution: UNIVERSITY OF TEXAS SW MED CTR/DALLAS
    Internet-scale discovery of RNA bioengineering rules Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM100953-01
    Actv: R01
    IC: GM
    PI Name(Contact): DAS, RHIJU
    Institution: STANFORD UNIVERSITY
    Application of Machine Learning Algorithms to Thiopurine Monitoring in IBD Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM097117-01A1
    Actv: R01
    IC: GM
    PI Name(Contact): HIGGINS, PETER D.R.
    Institution: UNIVERSITY OF MICHIGAN AT ANN ARBOR
    Computational Tools for Mining Large Amounts of ChIP and Gene Expression Data Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01HG006282-01A1
    Actv: R01
    IC: HG
    PI Name(Contact): JI, HONGKAI
    Institution: JOHNS HOPKINS UNIVERSITY
    Statistical and Computational Tools for Next-generation ChIP-seq Applications Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01HG006841-01
    Actv: R01
    IC: HG
    PI Name(Contact): JI, HONGKAI
    Institution: JOHNS HOPKINS UNIVERSITY
    Expression2Kinases: mRNA Profiling Linked to Multiple Upstream Regulatory Layers Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM098316-01A1
    Actv: R01
    IC: GM
    PI Name(Contact): MA'AYAN, AVI
    Institution: MOUNT SINAI SCHOOL OF MEDICINE
    WikiPathways Project: At the Intersection of Big Data and Researcher Knowledge Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM100039-01
    Actv: R01
    IC: GM
    PI Name(Contact): PICO, ALEXANDER R
    Institution: J. DAVID GLADSTONE INSTITUTES
    Unlocking Transcript Diversity via Differential Analyses of Splice Graphs Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01HG006272-01A1
    Actv: R01
    IC: HG
    PI Name(Contact): PRINS, JAN F
    Institution: UNIVERSITY OF NORTH CAROLINA CHAPEL HILL
    A Multi-Scale Finite Element Musculoskeletal Modeling Framework Applied to Curren Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01EB015497-01
    Actv: R01
    IC: EB
    PI Name(Contact): SHELBURNE, KEVIN B
    Institution: UNIVERSITY OF DENVER (COLORADO SEMINARY)
    Quantifying Brain Abnormality by Multimodality Neuroimage Analysis Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01AG041721-01A1
    Actv: R01
    IC: GM
    PI Name(Contact): SHEN, DINGGANG
    Institution: UNIVERSITY OF NORTH CAROLINA CHAPEL HILL
    Apollo: Increasing Access and Use of Epidemic Models Through the Development and Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM101151-01
    Actv: R01
    IC: GM
    PI Name(Contact): WAGNER, MICHAEL MATTHEW
    Institution: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
    Improved Quantitative Assessment of the Fetal Brain from 3D Volumetric MRI Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01EB013248-01A1
    Actv: R01
    IC: EB
    PI Name(Contact): WARFIELD, SIMON K
    Institution: CHILDREN'S HOSPITAL BOSTON
    Computational Framework for Multiscale Mechanics of Connective Tissues Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01EB015133-01A1
    Actv: R01
    IC: EB
    PI Name(Contact): WEISS, JEFFREY A.
    Institution: UNIVERSITY OF UTAH
    Functional Genetic Variations in Splicing Regulation Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01HG006264-01A1
    Actv: R01
    IC: GM
    PI Name(Contact): XIAO, XINSHU GRACE
    Institution: UNIVERSITY OF CALIFORNIA LOS ANGELES
    Machine Learning Methods to Increase Genomic Accessibility by Next-gen Sequencing Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01HG006870-01
    Actv: R01
    IC: HG
    PI Name(Contact): XIE, XIAOHUI
    Institution: UNIVERSITY OF CALIFORNIA IRVINE
    Cloud-computer-aided Diagnostic Imaging Decision Support System Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01CA166816-01
    Actv: R01
    IC: CA
    PI Name(Contact): YOSHIDA, HIROYUKI
    Institution: MASSACHUSETTS GENERAL HOSPITAL
    Identification, Discovery, and Public Archiving of RNA Structural Motifs Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM102515-01
    Actv: R01
    IC: GM
    PI Name(Contact): ZHANG, SHAOJIE
    Institution: UNIVERSITY OF CENTRAL FLORIDA
    A Novel Co-Expression Network Approach that is Robust to Genetic Heterogeneity An Fiscal Year: 2012
    RFA/PA Number: PAR09-218
    Grant Number: 1R01GM100364-01
    Actv: R01
    IC: GM
    PI Name(Contact): ZHANG, WEIXIONG
    Institution: WASHINGTON UNIVERSITY
    Probabilistic White and Gray Matter Atlas of the Adult Human Brain Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21NS076827-01A1
    Actv: R21
    IC: NS
    PI Name(Contact): ARFANAKIS, KONSTANTINOS
    Institution: ILLINOIS INSTITUTE OF TECHNOLOGY
    Understanding pH-Dependent Protein Behavior Using Advanced Continuum Theory Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM102642-01
    Actv: R21
    IC: GM
    PI Name(Contact): BARDHAN, JAYDEEP PORTER
    Institution: NORTHEASTERN UNIVERSITY
    Correcting Pervasive Errors in RNA Crystallography with Rosetta Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM102716-01
    Actv: R21
    IC: GM
    PI Name(Contact): DAS, RHIJU
    Institution: STANFORD UNIVERSITY
    OncoCL: A Cancer Cell Ontology Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM096156-01A1
    Actv: R21
    IC: CA
    PI Name(Contact): DOLAN, MARY E
    Institution: JACKSON LABORATORY
    Detecting Adaptive Evolution in the Context of Linked Deleterious Mutations Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM098896-01
    Actv: R21
    IC: GM
    PI Name(Contact): FAY, JUSTIN C
    Institution: WASHINGTON UNIVERSITY
    Computational Modeling and Analysis of Kinetochore Dynamics during Mitosis Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM100122-01
    Actv: R21
    IC: GM
    PI Name(Contact): GARDNER, MELISSA KLEIN
    Institution: UNIVERSITY OF MINNESOTA TWIN CITIES
    In Silico and in Vitro Investigation of Non-Conserved Interaction Characteristics Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM100303-01
    Actv: R21
    IC: GM
    PI Name(Contact): GERLOFF, DIETLIND L
    Institution: UNIVERSITY OF CALIFORNIA SANTA CRUZ
    Computer Simulations of Lysosomal and Osteoclast Microphysiology Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM100224-01
    Actv: R21
    IC: GM
    PI Name(Contact): GRABE, MICHAEL
    Institution: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
    Mapping and Functional Analysis of RNA:DNA Hybrid-Forming Loci Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM096156-01A1
    Actv: R21
    IC: GM
    PI Name(Contact): GREALLY, JOHN
    Institution: ALBERT EINSTEIN COL OF MED YESHIVA UNIV
    Fast k-mer Counting to Quantify Gene Expression and Improve Genome Assembly Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21HG006913-01
    Actv: R21
    IC: HG
    PI Name(Contact): KINGSFORD, CARLETON LEE
    Institution: UNIVERSITY OF MARYLAND COLLEGE PK CAMPUS
    Improve Genome Annotation Using Multiple Sequence Alignment Reliability Scores Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21HG006464-01
    Actv: R21
    IC: HG
    PI Name(Contact): MA, JIAN
    Institution: UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN
    Computational and Experimental Studies of the Amyloid Fibril Formation by PAPf39 Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM101134-01
    Actv: R21
    IC: GM
    PI Name(Contact): MAKHATADZE, GEORGE I
    Institution: RENSSELAER POLYTECHNIC INSTITUTE
    Quantum Nuclear Dynamics and Enzyme Chemistry Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM102226-01
    Actv: R21
    IC: GM
    PI Name(Contact): SCHWARTZ, STEVEN D
    Institution: ALBERT EINSTEIN COL OF MED YESHIVA UNIV
    A Translational Model of Evolution of Myeloma Adhesion-Mediated Drug Resistance Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21CA164322-01
    Actv: R21
    IC: GM
    PI Name(Contact): SILVA, ARIOSTO S
    Institution: H. LEE MOFFITT CANCER CTR & RES INST
    Integrative Modeling of Regulatory Processes Using High-Throughput Genetic Data Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM094649-01A1
    Actv: R21
    IC: GM
    PI Name(Contact): SINGH, AMBUJ K
    Institution: UNIVERSITY OF CALIFORNIA SANTA BARBARA
    Elastic Shape Analysis for Protein Structure Alignment-New Advancement in an Old Fiscal Year: 2012
    RFA/PA Number: PAR09-219
    Grant Number: 1R21GM101552-01
    Actv: R21
    IC: GM
    PI Name(Contact): ZHANG, JINFENG
    Institution: FLORIDA STATE UNIVERSITY
    Structural bioinformatics software for epitope selection and antibody engineering Fiscal Year: 2012
    RFA/PA Number: PAR09-220
    Grant Number: 1R43GM100520-01
    Actv: R43
    IC: GM
    PI Name(Contact): DARNELL, STEVEN JOSEPH
    Institution: DNASTAR, INC.
    Automated Delineation, Parcellation and Analysis of the Cerebellum from MR Images Fiscal Year: 2012
    RFA/PA Number: PAR09-220
    Grant Number: 1R43AA021945-01A1
    Actv: R43
    IC: AA
    PI Name(Contact): FEIN, GEORGE
    Institution: NEUROBEHAVIORAL RESEARCH, INC.
    Parsimonious Models for Survival Data Fiscal Year: 2012
    RFA/PA Number: PAR09-220
    Grant Number: 1R43GM101729-01A1
    Actv: R43
    IC: GM
    PI Name(Contact): FRALEY, CHRIS
    Institution: INSILICOS
    3D Single Fiber Endoscope for Minimally Invasive Surgeries Fiscal Year: 2012
    RFA/PA Number: PAR09-220
    Grant Number: 1R43EB014598-01
    Actv: R43
    IC: EB
    PI Name(Contact): GENG, JASON
    Institution: XIGEN, LLC
    Ontology-Based Knowledge and Belief Management System Fiscal Year: 2012
    RFA/PA Number: PAR09-220
    Grant Number: 1R44GM097851-01A1
    Actv: R44
    IC: GM
    PI Name(Contact): KABUKA, MANSUR R.
    Institution: INFOTECH SOFT, INC.
    XCMS-Online: An Integrated Platform for Metabolic Profile Analysis and Metabolite Fiscal Year: 2012
    RFA/PA Number: PAR09-220
    Grant Number: 1R43GM103689-01
    Actv: R43
    IC: GM
    PI Name(Contact): RINEHART, DUANE
    Institution: METABOSCIENTIA, LLC
    Continued Development of Protein Dynamics Software ProDy Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM099738-01
    Actv: R01
    IC: GM
    PI Name(Contact): BAHAR, IVET
    Institution: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
    Continued Development and Maintenance of Appion Software Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM099678-01
    Actv: R01
    IC: GM
    PI Name(Contact): CARRAGHER, BRIDGET OLIVIA
    Institution: SCRIPPS RESEARCH INSTITUTE
    Statistical Tools for Whole-Genome Prediction of Complex Traits and Diseases Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM101219-01
    Actv: R01
    IC: GM
    PI Name(Contact): DE LOS CAMPOS, GUSTAVO A
    Institution: UNIVERSITY OF ALABAMA AT BIRMINGHAM
    Continued Development and Maintenance of GLYCAM-Web Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM100058-01
    Actv: R01
    IC: GM
    PI Name(Contact): FOLEY, B. LACHELE
    Institution: UNIVERSITY OF GEORGIA
    Maintenance and Development of the IMa Program Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM096872-01A1
    Actv: R01
    IC: GM
    PI Name(Contact): HEY, EMANUEL
    Institution: RUTGERS THE ST UNIV OF NJ NEW BRUNSWICK
    Enabling Long Timestep Molecular Dynamics on Parallel CPU and GPU Environments Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM101935-01
    Actv: R01
    IC: GM
    PI Name(Contact): IZAGUIRRE, JESUS ANTONIO
    Institution: UNIVERSITY OF NOTRE DAME
    Development and Support of the Pathway Tools Software [SRI Proposal ECU 11-614] Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 2R01GM075742-09A1
    Actv: R01
    IC: GM
    PI Name(Contact): KARP, PETER D
    Institution: SRI INTERNATIONAL
    A Next-generation Integrative Genomics Viewer for Biomedical and Cancer Research Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01CA157304-01A1
    Actv: R01
    IC: CA
    PI Name(Contact): MESIROV, JILL P
    Institution: BROAD INSTITUTE, INC.
    Stochastic Simulation Service: A Cloud Computing Framework for Modeling and Simul Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01EB014877-01
    Actv: R01
    IC: EB
    PI Name(Contact): PETZOLD, LINDA R.
    Institution: UNIVERSITY OF CALIFORNIA SANTA BARBARA
    New Algorithms and Tools for Large-scale Genomic Analyses Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01HG006693-01
    Actv: R01
    IC: HG
    PI Name(Contact): QUINLAN, AARON R
    Institution: UNIVERSITY OF VIRGINIA CHARLOTTESVILLE
    Towards Real-time XFEL Data Reduction with CCTBX Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM102520-01
    Actv: R01
    IC: GM
    PI Name(Contact): SAUTER, NICHOLAS K
    Institution: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
    Chembench: the Integrated Web Portal to Accelerate Cheminformatics and Chemical G Fiscal Year: 2012
    RFA/PA Number: PAR11-028
    Grant Number: 1R01GM096967-01A1
    Actv: R01
    IC: GM
    PI Name(Contact): TROPSHA, ALEXANDER
    Institution: UNIVERSITY OF NORTH CAROLINA CHAPEL HILL
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