STRUCTURAL AND FUNCTIONAL GENOMICS ABSTRACT The goals of the Structural and Functional Genomics Program (SFG) are aligned and integrated with the vision and strategies of Moores Cancer Center (MCC) and the UC San Diego School of Medicine. They use the SFG members? interdisciplinary strength and expertise in computational biology and genomics to employ a full range of both structural and functional genomic data to elucidate complex signaling pathways and identify candidate targets and compounds that can be translated into novel diagnostic and therapeutic targets and clinical interventions. Approved by the NCI in 1997, the Cancer Genetics Program has evolved to SFG to reflect how, during the past project period, members have expanded use of multi-omic data types, moved analysis methods to molecular tumor boards, and elucidated context-dependent molecular states for more targeted treatments. SFG has 36 members from 14 academic departments with $19.2M of peer-reviewed research grant funding (annual direct costs), $6.3M (33%) of which is from the NCI. SFG members published 714 programmatically aligned articles since 2013, 11% were the result of intra-programmatic collaborations, 20% were inter-programmatic, and 34% were inter-NCI Cancer Center. SFG?s specific aims are to: 1) develop innovative, integrative computational genomic methods that synthesize multi-omic patient and clinical data to drive fundamental and translational cancer research and to disseminate them to the broader cancer research community; 2) analyze genetic, transcriptomic, epigenetic, proteomic, immunologic, and metabolomic data to elucidate the underlying biological pathways and mechanisms of cancer development and progression; and 3) characterize context dependent, functional states of tumor cells and understand the dynamics of resistance in order to identify novel diagnostic, prognostic, and therapeutic strategies, including combination therapies. SFG themes are data science and machine learning, signature and network approaches, and precision therapy. SFG is co-led by Joseph Califano, a head and neck surgeon and translational researcher who applies genomics to develop novel prognostic indicators and therapies and Jill Mesirov, a computational biologist who analyzes complex genome-scale cancer datasets to better understand the underlying mechanisms of cancer, stratify patients, and identify candidate therapies. Their complementary expertise and highly integrated efforts foster collaboration among the outstanding SFG investigators who are leaders in their fields with track records of extraordinary productivity and inter- programmatic collaborations among the MCC research programs. As a result, SFG members have conducted paradigm-shifting studies defining the broad role of extrachromosomal DNA in human cancers, developed carcinogen-based mutational signatures across cancer types, demonstrated the role of the microbiome in hepatocellular cancer development, and produced and maintained key computational methods and tools used by hundreds of thousands of scientists worldwide.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
Project #
Application #
Study Section
Special Emphasis Panel (ZCA1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California, San Diego
La Jolla
United States
Zip Code
Nguyen, Vi; Marmor, Rebecca A; Ramamoorthy, Sonia L et al. (2018) The Use of Solicited Publishing by Academic Surgeons. Surgery 164:212-218
Yan, Wei; Wu, Xiwei; Zhou, Weiying et al. (2018) Cancer-cell-secreted exosomal miR-105 promotes tumour growth through the MYC-dependent metabolic reprogramming of stromal cells. Nat Cell Biol 20:597-609
Pandolfi, Erica C; Hoffmann, Hanne M; Schoeller, Erica L et al. (2018) Haploinsufficiency of SIX3 Abolishes Male Reproductive Behavior Through Disrupted Olfactory Development, and Impairs Female Fertility Through Disrupted GnRH Neuron Migration. Mol Neurobiol 55:8709-8727
Galanina, Natalie; Goodman, Aaron M; Cohen, Philip R et al. (2018) Successful Treatment of HIV-Associated Kaposi Sarcoma with Immune Checkpoint Blockade. Cancer Immunol Res 6:1129-1135
Chin, Andrew R; Yan, Wei; Cao, Minghui et al. (2018) Polarized Secretion of Extracellular Vesicles by Mammary Epithelia. J Mammary Gland Biol Neoplasia 23:165-176
Garcia, Daniel A; Baek, Christina; Estrada, M Valeria et al. (2018) USP11 Enhances TGF?-Induced Epithelial-Mesenchymal Plasticity and Human Breast Cancer Metastasis. Mol Cancer Res 16:1172-1184
Jiang, Qingfei; Jamieson, Catriona (2018) BET'ing on Dual JAK/BET Inhibition as a Therapeutic Strategy for Myeloproliferative Neoplasms. Cancer Cell 33:3-5
Ramirez, Oscar; Aristizabal, Paula; Zaidi, Alia et al. (2018) Implementing a Childhood Cancer Outcomes Surveillance System Within a Population-Based Cancer Registry. J Glob Oncol :1-11
Liu, Liang; Yang, Lin; Yan, Wei et al. (2018) Chemotherapy Induces Breast Cancer Stemness in Association with Dysregulated Monocytosis. Clin Cancer Res 24:2370-2382
Lwin, Thinzar M; Murakami, Takashi; Miyake, Kentaro et al. (2018) Tumor-Specific Labeling of Pancreatic Cancer Using a Humanized Anti-CEA Antibody Conjugated to a Near-Infrared Fluorophore. Ann Surg Oncol 25:1079-1085

Showing the most recent 10 out of 862 publications