About

Investigators

 

Leadership


Trey Ideker, Director

Professor of Medicine and Bioengineering, University of California San Diego
Co-Director, Cancer Genomes and Networks Program, UC San Diego Moores Cancer Center
Director, National Resource for Network Biology
Director, San Diego Center for Systems Biology

Nevan Krogan, Director

Professor of Cellular and Molecular Pharmacology, University of California San Francisco
Director, Quantitative Biosciences Institute, UCSF

Senior Investigator, The Gladstone Institutes

Joint Faculty, Sanford Burnham Prebys Medical Discovery Institute

Jason Kreisberg, Assistant Director

Assistant Research Scientist, UC San Diego
Assistant Director, San Diego Center for Systems Biology 

 

Investigators


David Agard

David AgardProfessor, Departments of Biochemistry/Biophysics and Pharmaceutical Chemistry, UCSF; Scientific Director, Institute for Bioengineering, Biotechnology, and Quantitative Biomedical Research, University of California, San Francisco, Berkeley, Santa Cruz; HHMI Investigator

My research is focused on elucidating the mechanism of Hsp90 chaperone function and its role in human disease. My group has solved the full length crystal structures of the apo and ADP states of the E. coli Hsp90, revealing potential client protein binding sites in each domain. By a combination of single particle EM and small angle x-ray scattering (SAXS), we demonstrated that bacterial, yeast and human Hsp90s share a conserved three-state nucleotide cycle, yet have very different probabilities of reaching each state. A new structure of the mitochondrial Hsp90 TRAP1 that we discovered reveals a new asymmetric closed state, suggesting a sequential ATP hydrolysis mechanism. Using model human client proteins, NMR, SAXS and EM, and FRET, we are working out how Hsp90 influences client structure as well as the impact of clients on the Hsp90 structure. visit website »


Alan Ashworth

Alan AshworthPresident, UCSF Helen Diller Family Comprehensive Cancer Center, UCSF; Senior Vice President for Cancer Services, UCSF Health; Professor of Medicine, Division of Hematology/Oncology, Department of Medicine, E. Dixon Heise Distinguished Professor in Oncology, UCSF

My current research reflects my passion for the development of personalized cancer medicine, translating laboratory studies into improvements in patient care. I was a key part of the team that in 1995 discovered the gene BRCA2, which is linked to an increased risk of some types of cancers. Ten years later, I identified a way to exploit genetic weaknesses in cancer cells including mutated BRCA2, leading to a new approach to cancer treatment. This approach is now being tested in numerous clinical trials. I am also joint leader, with Professor Tony Swerdlow, of one of the world’s most comprehensive and largest (>100,000 participants), studies of breast cancer causation, the Breakthrough Generations Study. visit website »


Laura Esserman

Professor, Departments of Surgery and Radiology, and Affiliate Faculty, Institute for Health Policy Studies, UCSF
Director, Carol Franc Buck Breast Care Center; Co-Leader, Breast Oncology Program, UCSF Helen Diller Family Comprehensive Cancer Center

My work in breast cancer spans the spectrum from public policy issues to basic science and the impact of both on the delivery of clinical care. In addition to being the Director of the Breast Care Center and the Clinical Leader of the NCI-designated Breast Oncology Program, I direct (as Principal Investigator) two large multicenter collaborations in breast cancer: the I-SPY TRIAL (Investigating Serial Studies to Predict Your Therapeutic Response using Imaging And molecular analysis) and the I-SPY 2 Trial. A distinctive feature of the trial is that it will screen multiple drugs from multiple companies—up to 12 different cancer drugs over the course of the trial. visit website »


Jennifer Grandis

Director, Clinical and Translational Science Institute (CTSI), UCSF
Associate Vice Chancellor of Clinical and Translational Research, UCSF
Professor, Otolaryngology – Head and Neck Surgery, UCSF

My research focuses on the signal transduction in head and neck squamous cell carcinoma (HNSCC) development and progression with the ultimate goal of targeting key pathways for therapeutic benefit. By taking key findings from the clinic and investigating mechanisms in a series of preclinical models, as well as developing novel therapeutic approaches in the laboratory and carrying out innovative clinical trials that employ these treatment strategies. We have developed translational resources including patient-derived xenografts (PDXs) and tissue microarrays of over 500 human HNSCCs which are linked to a professionally curated clinical and pathologic database that includes information on treatment and survival. Our ongoing studies are aimed at identifying the targetable genetic alterations in cancers with the goal of designing precision medicine approaches.  visit website »


Silvio Gutkind

Silvio GutkindProfessor and Associate Director of Basic Science
UC San Diego, Moores Cancer Center

In my research group, we exploit the emerging information on dysregulated signaling circuitries and individual genomic and molecular alterations to identify new therapeutic options to prevent and treat cancer. We have focused on the study of the oncogenic activity of G proteins and G protein coupled receptors (GPCRs), including virally-encoded GPCRs, to dissect the signaling pathways regulating normal and aberrant cell growth, tumor-induced angiogenesis, and metastasis. We are now investigating the mechanisms by which genetic mutations in Gaq proteins initiate uveal and cutaneous melanoma, the role of Gas and its target, PKA, in cancer, and how mutations and autocrine activation of GPCRs contribute to tumor progression, immune evasion, and therapy resistance. In parallel, we are exploring the role of the mTOR pathway in cancers of the oral cavity. From our multi-institutional clinical trial targeting mTOR in oral cancer, we are now investigating the effectiveness and mechanism of action of PI3K/mTOR inhibitors for oral cancer prevention and treatment. visit website »


Trey Ideker

Professor of Medicine and Bioengineering, UC San Diego; Co-Director, Cancer Genomes and Networks Program, UC San Diego Moores Cancer Center; Director, Cancer Cell Map Initiative; Director, National Resource for Network Biology;  Director, San Diego Center for Systems Biology

Our laboratory’s long-range goal is to develop infrastructure to map and model molecular networks and to insert these models at key decision points in health care. We advance this goal along two general aims, seeking to build better network representations of the cell and seeking to use these networks to translate genotype to phenotype in cancer. With Dr. Mesirov, we have introduced a series of widely-used computational methods and tools for bioinformatic analysis of cancer data sets, including the Integrated Genomics Viewer (IGV); Cytoscape; GenomeSpace; Non-negative Matrix Factorization (NMF); Gene Set Enrichment Analysis (GSEA); network-guided clustering of gene expression profiles and stratification of genomes, and automated construction of gene ontologies using network data (NeXO). We argue that recent progress in computer science (embodied by intelligent agents such as Siri and Watson), inspires an approach for moving from networks and gene ontologies to predictive models – able to integrate with patient data to predict disease outcomes in response to specific therapies. visit website »


Nevan Krogan

Professor of Cellular and Molecular Pharmacology, UCSF; Director, Quantitative Biosciences Institute, UCSF; Director, Cancer Cell Map Initiative;  Senior Investigator, The Gladstone Institutes; Joint Faculty, Sanford Burnham Preby Medical Discovery Institute

In my lab we generate and analyze proteomics and genomics data and develop models based on these datasets to further understand and predict the systems and pathways under study. We have pioneered two technological approaches: (1) quantitative genetic interaction (GI) mapping, termed E-MAP, and (2) innovative mass spectrometry-based strategies for studying protein-protein interactions (PPIs) and post-translational modifications (PTMs). By bridging the gap between systems biology and more detailed mechanistic studies, we are able to extract deep physiological insights from these data. We are using these and other systems approaches to cut through the noise of tumor variability to elucidate commonly shared underlying cellular networks. If cancer is a pathway-based disease, our ability to query multiple cancer genomes is going to be critical to understanding cancer development and response to treatment. visit website »


Prashant Mali

Prashant MaliAssistant Professor of Bioengineering, UC San Diego

My research lies at the interface of technology development and basic science, with a long-term interest in studying and eventually programming the processes of organogenesis for personalized regenerative medicine applications. I use human pluripotent stem cells as a core model system, and take an integrated genome engineering and tissue engineering approach to systematically study the interplay of gene regulatory networks and cellular niche on normal and aberrant cell fate specification. Given the parallels in phenotypes (such as self renewal and tumor forming ability) between pluripotent stem cells and cancer cells, a key research thrust is also in dissecting aberrant cellular transformation processes such as during tumorigenesis. Taken together these approaches and experiences are particularly relevant to defining and analyzing the physical and genetic networks underlying tumorigenesis. visit website »


Jill Mesirov

Jill MesirovAssociate Vice Chancellor for Computational Health Sciences, UC San Diego; Senior Institute Fellow, The Broad Institute, MIT/Harvard; Professor, Department of Medicine, UC San Diego

My group’s research expertise is computational biology with a focus on algorithms and analytic methodologies for pattern recognition and discovery, with applications to cancer genomics and infectious disease. In addition, my lab has a history of developing biologists-friendly analysis tools, and disseminating the resulting software. We have also developed numerous portals for the public distribution of genomic data from scientific projects. I have collaborated with Dr. Tamayo since the late 1990’s on numerous statistical and machine learning methods for the analysis of genomic data to better understand the underlying mechanisms of different tumor types and to better model the oncogenic landscape. We have also developed integrative predictive models for patient stratification from clinical, expression, and copy number data with a view towards translation to the clinic. visit website »


Laura van ‘t Veer

Leader, Breast Oncology Program, and Director, Applied Genomics, UCSF Helen Diller Family Comprehensive Cancer Center
Angela and Shu Kai Chan Endowed Chair in Cancer Research

My research focuses on personalized medicine and aims to advance patient management based on knowledge of the genetic makeup of the tumor as well as the genetic makeup of the patient. My laboratory has a strong research line investigating human kinases and studies how kinase inhibitors elicit response and resistance. I am the UCSF Precision Medicine Platform convener for cancer. I chair the Biomolecular Committee of the I-SPY 2 trial ensuring CLIA compliant companion diagnostics. I am the Principal Investigator of the Athena Breast Health Network at UCSF, a 150,000-women cohort study evaluating new paradigms to enhance breast health for which I lead the targeted genome testing for 65,000 women for nine breast cancer susceptibility genes and a selection of ~100 known susceptibility Single Nucleotide Polymorphisms (SNPs). visit website »