The National Resource for Network Biology (NRNB) administration is led by Dr. Trey Ideker, Director of NRNB and Professor of Genetics in the Department of Medicine at UC San Diego. He is assisted in day-to-day operations by Dr. Alex Pico at the Gladstone Institutes in San Francisco, who serves as NRNB Executive Director. Ideker and Pico are joined by the other project leads Dr. Gary Bader (Toronto) and Dr. Chris Sander (Memorial Sloan Kettering) to form the NRNB Internal Executive Committee (IEC). The three Technology Research and Development (TRD) projects are led by Trey Ideker (TRD: Multi-Scale Networks), Gary Bader (TRD: Predictive Networks), and Dr. Chris Sander (TRD: Differential Networks). Close integration of TRD projects with Driving Biomedical Projects is overseen directly by Ideker with support from the IEC. Other components of the resource are administered by an extended NRNB management team, which coordinates both internal functions (e.g., infrastructure, meetings, project tracking and reporting across performance sites) as well as external functions (e.g., dissemination, collaboration, training and outreach) of the resource center. NRNB Bioinformatics Infrastructure and Dissemination components are led by Dr. Barry Demchak (UCSD), an expert in computer systems architecture and design. Demchak's team is responsible for the overall architectural design and development plan for NRNB hardware and software, including the NRNB high-performance computing environment and Cytoscape Cyberinfrastructure. Under Dissemination, he oversees the timely release of new software tools, creating and maintaining NRNB web portals, and tracking usage and website statistics. NRNB Collaboration and Service is coordinated by Dr. Aaron Chang (UCSD), a former VP of Informatics who runs the collaborative Center for Computational Biology, a bioinformatics outreach core facility at UCSD supported by matching and in-kind resources from the University of California. Training, Outreach, and Communications are overseen by NRNB Executive Director, Alex Pico. He oversees a Training Coordinator, Dr. Scooter Morris (UCSF), who is vital for outreach to new users, app developers and strategic partnerships. Pico also manages an Outreach Coordinator, Ms. Kristina Hanspers (Gladstone), who is responsible for tracking and coordinating NRNB collaborations, running the NRNB Academy training program, managing the Cytoscape and NetBio Publication Tumblr feeds, and creating and organizing documentation for the NRNB suite of software tools. External oversight is provided by an External Advisory Committee (EAC), which meets approximately once a year. The chief role of the EAC is to advise resource personnel on new research and development priorities, to help select new opportunities and requests for collaboration and service, and to ensure the quality and sufficiency of our infrastructure and training efforts. The EAC was very engaged during the past performance period and has been extremely valuable in establishing NRNB as a successful resource over the past four years. We expect that this body will continue to contribute enormously to the vision and strategic plan for the NRNB.
| 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 |
| Ma, Jianzhu; Yu, Michael Ku; Fong, Samson et al. (2018) Using deep learning to model the hierarchical structure and function of a cell. Nat Methods 15:290-298 |
| Buckley, Alexandra R; Ideker, Trey; Carter, Hannah et al. (2018) Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. Genome Med 10:69 |
| 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 |
| Nikolayeva, Iryna; Guitart Pla, Oriol; Schwikowski, Benno (2018) Network module identification-A widespread theoretical bias and best practices. Methods 132:19-25 |
| 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 |
| Reznik, Ed; Luna, Augustin; Aksoy, Bülent Arman et al. (2018) A Landscape of Metabolic Variation across Tumor Types. Cell Syst 6:301-313.e3 |
| 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 |
| MacParland, Sonya A; Liu, Jeff C; Ma, Xue-Zhong et al. (2018) Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun 9:4383 |
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