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Research Programs

Structural and Functional Genomics

 

Leadership

Jill Mesirov, PhD

Jill P. Mesirov, PhD

Professor of Medicine
Associate Vice Chancellor, Computational Health Sciences

Phone: 858-534-5096
Email: jmesirov@ucsd.edu
Research Summary

 
Joseph Califano, MD

Joseph Califano, MD

Physician-in-Chief, Moores Cancer Center
Director, Head & Neck Cancer Center
Professor of Surgery

Phone: 858-534-5400
Email: jcalifano@ucsd.edu
Research Summary

 

About the Program

Overview

Over the last decade, there has been a significant rise in the use of high throughput structural genomic data to guide cancer scientific discovery and its clinical translation. Investigators and molecular tumor boards leverage these genetic data (DNA variants, copy number variants, translocations and fusions) to define patient eligibility and to target patient specific therapeutic interventions. Despite this progress, the number of actionable genetic lesions remains small (a few hundred) and our knowledge of how such variants influence cell function and therapeutic sensitivity remains limited. Moreover, each patient and each tumor environment represents a different context in which the cancer cell develops and survives, with effects on cellular molecular states and profiles. Integrating a wider range of data types (e.g., gene and protein expression, metabolic, epigenetic) provides a depth of functional information to better elucidate what drives cancer etiology and progression, how to detect it, and importantly how to most effectively treat it.

The SFG program has 36 members drawn from 12 departments across UCSD schools. Members of the SFG program provide international leadership in defining novel approaches to the characterization of targetable alterations, molecular signatures, and networks. The increasing breadth of expertise and interdisciplinary nature of SFG (experimental, computational, and translational) position it well to continue to lead the field: SFG will continue pursuing innovative solutions to the challenge of integrating large scale datasets to define candidate clinical tools and therapeutic targets for direct benefit to patients in the MCC catchment area, and beyond.

Program Goals

SFG seeks to acquire and use the full range of structural and functional genomics data and to relate them to biological and cancer phenotypes with the overall goal of leveraging new knowledge and data to generate hypotheses for validation and translation to support the diagnosis and treatment of cancer.

The specific aims of the SFG program are as follows:

  1. Computational Discovery Sciences: Develop innovative, integrative computational genomic methods that synthesize multi-omic patient and clinical data to drive fundamental and translational cancer research and to disseminate these tools and methods to the cancer research community.
  2. Analyze and integrate genetic, transcriptomic, epigenetic, proteomic, immunologic, and metabolomic data to elucidate the underlying biological pathways and mechanisms of cancer development and progression.
  3. Define context dependent, functional states of tumor cells and understand the dynamics of response or resistance in order to identify novel diagnostic, prognostic, and therapeutic strategies.

Meetings & Events

The following list includes events and seminars of notable interest to the Structural and Functional Genomics Program and its members. Please look for the Upcoming SFG Events list on the right edge of this page; this list is updated automatically and may be added to your Outlook or Google calendars.

SFG Program Events

Seminars and other programmatic meetings led by the Structural and Functional Genomics Program:

Multi-program Events

Intra- and inter-programmatic activities, lectures and symposia, external collaborations, and program development:



 

Collaborations

Please contact us if you are interested in developing a collaboration or in joining our research program. To see recent cross-program collaboration highlights with the SFG group, please click here.

Click on the link below to see a list of all current SFG members.

For a full list of all program membership affiliations, please click here.


Upcoming SFG Events


Click on an event headline to add it to your calendar. To view all Research Program events, click the link below:

View All Events

October 2020

MCC Scientific Retreat 2020

Now accepting submissions until September 10

We look forward to seeing your presentation and poster proposals.

Please contact Raluca Ciochina for more information.


SFG Scientific Highlights

Recent Scientific Highlights from Structual & Functional Genomics Research Program members. Please contact us if you have a highlight to share.

An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia

Jeevisha Bajaj, Michael Hamilton, Yutaka Shima, Kendall Chambers, Kyle Spinler, Eric L. Van Nostrand, Brian A. Yee, Steven M. Blue, Michael Chen, David Rizzeri, Charles Chuah, Vivian G. Oehler, H. Elizabeth Broome, Roman Sasik, James Scott-Browne, Anjana RaoSTTGene W. YeoSFGTannishtha ReyaSFG

Nature Communications | 1, 410–422(2020) | https://doi.org/10.1038/s43018-020-0054-2
Read the paper


The repertoire of mutational signatures in human cancer

Ludmil B. AlexandrovSFG, Jaegil Kim, Nicholas J. Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R. Covington, Dmitry A. Gordenin, Erik N. Bergstrom, S. M. Ashiqul Islam, Nuria Lopez-Bigas, Leszek J. Klimczak, John R. McPherson, Sandro Morganella, Radhakrishnan Sabarinathan, David A. Wheeler, Ville Mustonen, PCAWG Mutational Signatures Working Group, Gad Getz, Steven G. Rozen, Michael R. Stratton & PCAWG Consortium

Nature 578, 94–101 (2020). https://doi.org/10.1038/s41586-020-1943-3
Read the paper


Research Programs at Moores Cancer Center

Our scientific achievements are made possible through collaborations with colleagues across all other research programs at Moores Cancer Center. To learn more about these programs follow the links below:



SFG Leadership & Research Summary

Jill P. Mesirov, PhD

As associate vice chancellor, Dr. Mesirov is responsible for the overarching strategy for computational health sciences and research computing at UC San Diego School of Medicine. Before moving to UCSD in 2015, Mesirov was associate director and chief informatics officer at the Broad Institute of MIT and Harvard, formerly the Whitehead Institute/MIT Center for Genome Research, where she directed the Computational Biology and Bioinformatics Program. Dr. Mesirov has more than twenty years of progressive leadership in computational biology and analysis of complex genome-scale cancer datasets to determine the underlying biological mechanisms of specific tumor subtypes, stratify patients according to their relative risks of relapse, and identify candidate compounds for new treatments.. Her laboratory also develops software (GenePattern and GenePattern Notebook, Gene Set Enrichment Analysis and the Integrative Genomics Viewer) that brings advanced computational methods to the non-programming cancer biologist. These tools have almost 500,000 registered users worldwide and over 20,000 citations in the literature. Dr. Mesirov, a former president of the Association for Women in Mathematics, is a fellow of the American Association for the Advancement of Science (AAAS), the American Mathematical Society (AMS), the Association for Women in Mathematics (AWM), and the International Society for Computational Biology (ISCB).

Academic Profile

Lab Website

Joseph Califano, MD/PhD

Dr. Califano is an internationally recognized physician scientist who has translated multiple discoveries from his own laboratory into the clinic, including detection of HPV-related and other head and neck cancers. Before joining UCSD, Dr. Califano was at John Hopkins where he was Professor in the Head and Neck Division and the Division of Head and Neck Cancer Research at John Hopkins Department of Otolaryngology-Head and Neck Surgery. Dr. Califano Dr. Califano is Physician in Chief of the Moores Cancer Center as well as Director of the Head and Neck Cancer Center. His major focus is the clinical practice of head and neck surgical oncology and the integration of basic, molecular biologic research in that practice by using integrative computational techniques to define novel therapeutic and diagnostic strategies for cancers. Dr. Califano also currently directs an NIH funded laboratory investigating the molecular biologic basis of head and neck cancer. He has published over 300 articles related to both the clinical and basic scientific aspects of cancer, and currently serves as a member of the NCI Head and Neck Steering Committee and Council Member of the American Head and Neck Society, NCCN Board of Directors, as well as other professional organizations and editorial boards.

Academic Profile

Director's Office Biography