Abstract

CORE2:BIOINFORMATICSINFRASTRUCTUREANDSERVICES SUMMARY The Bioinformatics Infrastructure and Services Core will support the three CCMI projects at all stages of research and publication. The core will be composed of three major components: Cytoscape and the Cytoscape Cyberinfrastructure (CI)? the Network Data Exchange (NDEx)? and the CCMI Data and Analysis Portal.First,Cytoscapewillprovidearangeoftoolsfortheanalysisandvisualizationofbiologicalnetworks, including the proteinprotein interaction networks from ?Project 1?, the genetic interaction networks from Project2?, and the hierarchical cancer cell ontologies and models from ?Project 3?. The second component, NDEx,willprovidedatabaseinfrastructuretosupportthesharing,reviewanddisseminationofnetworkdata andmodels.ItwillalsoenableconsolidatedaccesstopublicbiologicalnetworkresourcesforusebyCCMI investigators.Finally,theCCMIDataandAnalysisPortalwillprovideacommonaccesspointforsoftwaretools and pipelines and for their associated data. This component will be supported by GenePattern Notebooks, whichwillfacilitatethedevelopmentofworkflowpipelinesandthesharingandreproducibilityofanalyses.The abovethreecomponents?visualnetworkmapsinCytoscape,storageofnetworksandmodelsinNDEx,and softwareandanalysisworkflowsinGenePatte? rnNotebooks?willallbemadeaccessiblethroughtheCCMI?s website(ccmi.org).PublicationsusingCCMIproductswillbeenhancedbytherecentadditionstoCytoscape for dynamically embedding network data in peerreviewed journals. Finally, the Core will draw on an impressivearrayofhardwareinfrastructureforsupercomputing,includinghighperformanceclustersatmultiple sites.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54CA209891-03
Application #
9692266
Study Section
Special Emphasis Panel (ZCA1)
Project Start
Project End
Budget Start
2019-05-01
Budget End
2020-04-30
Support Year
3
Fiscal Year
2019
Total Cost
Indirect Cost

  Institution

Name
University of California San Francisco
Department
Type
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94118

  Publications

Wang, Sheng; Ma, Jianzhu; Zhang, Wei et al. (2018) Typing tumors using pathways selected by somatic evolution. Nat Commun 9:4159
Zhang, Wei; Ma, Jianzhu; Ideker, Trey (2018) Classifying tumors by supervised network propagation. Bioinformatics 34:i484-i493
Zhang, Wei; Bojorquez-Gomez, Ana; Velez, Daniel Ortiz et al. (2018) A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet 50:613-620
Huang, Justin K; Jia, Tongqiu; Carlin, Daniel E et al. (2018) pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinformatics 34:2859-2861
Patrick, Kristin L; Wojcechowskyj, Jason A; Bell, Samantha L et al. (2018) Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. Cell Syst 7:323-338.e6
Bui, Nam; Huang, Justin K; Bojorquez-Gomez, Ana et al. (2018) Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Mol Cancer Ther 17:1585-1594
Huang, Justin K; Carlin, Daniel E; Yu, Michael Ku et al. (2018) Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst 6:484-495.e5
Palovcak, Eugene; Wang, Feng; Zheng, Shawn Q et al. (2018) A simple and robust procedure for preparing graphene-oxide cryo-EM grids. J Struct Biol 204:80-84
Ozturk, Kivilcim; Dow, Michelle; Carlin, Daniel E et al. (2018) The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. J Mol Biol 430:2875-2899
Eckhardt, Manon; Zhang, Wei; Gross, Andrew M et al. (2018) Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov 8:1474-1489

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