Computational Cancer Analysis Laboratory

We are part of the National Cancer Institute’s CTD2 Network comprised of 12 research teams that work independently as well as collaboratively as a “Network”. The UCSD CTD2 Center (NIH U01CA217885) incorporates teams from 7 UCSD laboratories and aims to identify oncogenic cell states, characterize their most salient genomic and immune hallmarks and infer optimal combinations of pharmacological and immunological agents. These studies will lead to the development of novel treatment strategies and provide the foundation for a new generation of more comprehensive, functional-based, precision oncology approaches.

Director and Lead PI.

Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD

Co-Director

William Kim, Ph.D. Assistant Professor of Medicine, Division of Medical Genetics, UCSD

Principal Investigators / Collaborators

Jill Mesirov, Ph.D. Professor of Medicine, Associate Vice-Chancellor, Computational Health Sciences, UCSD
Ezra Cohen, M.D. Professor of Medicine, Co-Director, Center for Precision Immunology, UCSD
Dan Kaufman, M.D. Ph.D. Professor of Medicine, Division of Regenerative Medicine, Director of Cell Therapy, UCSD
Judy Varner, Ph.D. Professor of Pathology, UCSD
Silvio Gutkind, Ph.D. Professor of Pharmacology, UCSD, Associate Director Basic Science (MCC)
Stephen Schoenberger, Ph.D. Professor, Co-Director, Center for Precision Immunology, La Jolla Institute

External Collaborators

William Hahn (Dana Farber), Stuart Schreiber (Broad Institute), Paul Clemons (Broad Institute), Hanlee Ji (Stanford)
Gordon Mills (OHSU), Jeff Tyner (OHSU), and Matt Reyna (Emory)

CCAL Team

Kwat Medetgul-Ernar
Stephanie Ting
Kate Niklason

This project, supported by a CIAPM award, brings together a team of dedicated people across many disciplines to create a powerful, flexible and fully integrated platform for exploring new therapeutic opportunities and precision medicine capabilities. Initially targeting Hispanic TNBC patients, this project will implement a novel collaborative working model for researchers, clinicians, patients, and stakeholders, as well as a research component. The models developed by this effort will be used for novel therapeutic discovery, preclinical validation and to recommend therapeutics strategies for TNBC Hispanic patients.

Lead PI’s

William Kim, Ph.D. Assistant Professor of Medicine, Division of Medical Genetics, UCS
Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD

Principal Investigators

Barbara Parker, M.D. Sr. Deputy Director Cancer Medicine, MCC, and Professor of Medicine, UCSD
Jill Mesirov, Ph.D. Professor of Medicine, Associate Vice-Chancellor, Computational Health Sciences, UCSD
Elena Martinez, Ph.D. Professor of Family Medicine and Public Health, Associate Director, Population Sciences, Community Outreach and Engagement, MCC, UCSD
Rebecca Shatsky, M.D. Assistant Professor of Medicine, UCSD
Warren Paroly, M.D. Medical Oncologist, Tri-City Medical Center
Hasnat Ahmed, M.D. Medical Oncologist, El Centro Regional Medical Center
Jesse Nodora, Ph.D. Associate Professor of Family Medicine and Public Health, UCSD
Alfredo Molinolo, M.D., Ph.D. Director, MCC Biorepository, Professor of Pathology, UCSD
James Murphy, M.D., Ph.D. Associate Professor of Radiation Oncology, UCSD

Key Personnel / Collaborators

Robert Wechsler-Reya, Ph.D. Professor, Director, Tumor Initiation & Maintenance, SBP Medical Institute, Director, Center for Neuro-Oncology and Genomics, Rady’s Children Hospital
Eran Andrechek, Ph.D. Associate Professor, Dept. of Physiology, Michigan State University
Corinne Davidson, Ph.D. Director, Inst. for Public Health, San Diego State Univ.
Adrian Daneri-Navarro, M.D, Ph.D. Professor, Department of Physiology, University of Guadalajara, Mexico
Ludmil Alexandrov, Ph.D. Assistant Professor, Cellular and Molecular Medicine, UCSD
Helen Palomino, LCSW. CEO, Cancer Resource Center of the Desert
Nicole Howard, MPH, Executive Vice President Health, Quality Partners
Bryce Olson, Cancer Patient and Advocate
Sara Fainstein, Cancer Survivor and Advocate
Kay Clark, Health Systems Manager at American Cancer Society

Advisors / Supporters

Christian Tomaszweski, M.D., MBA. Chief Medical Officer, El Centro Regional Medical Center
Scott Lippman, M.D. Director, Moores Cancer Center. Associate Dean for Cancer Research and Care
Geoff Wahl, Ph.D. Professor, Salk Institute
Jing Yang, Ph.D. Associate Professor of Pharmacology and Pediatrics, UCSD
Judy Varner, Ph.D. Professor of Pathology, UCSD
Jadwiga Bienkowska, Ph.D. Head of Computational Biology, Pfizer Oncology
Silvio Gutkind, Ph.D. Professor of Pharmacology, UCSD, Associate Director Basic Science (MCC)
Trey Ideker, Ph.D. Professor of Medicine, UCSD. Director, San Diego Center for Systems Biology
Ezra Cohen, M.D. Professor of Medicine, Co-Director, Center for Precision Immunology, UCSD
Stephen Schoenberger, Ph.D. Professor, Co-Director, Center for Precision Immunology, La Jolla Institute
Hanlee Ji, M.D. Associate Professor of Medicine, Stanford University
Razelle Kurzrock, M.D. Professor of Medicine, Director, Center for Personalized Medicine, UCSD
Paul Clemons, Ph.D. Director, Computational Chemical Biology, Broad Institute
Kun Zhang, Ph.D. Professor of Bioengineering, UCSD
Manuela Gago, M.D., Ph.D. Galician Foundation of Genomic Medicine, Santiago de Compostela, Spain

CCAL Team

Xiaojun Max Xu
Kwat Medetgul-Ernar

GenePattern Notebooks for Cancer Research (NIH U24CA194107)
The goal of this project is to build on GenePattern’s foundation to provide GenePattern Notebook, a beginning-to-end computational electronic lab notebook environment for combining analysis and text.

Supporting and evolving Gene Set Enrichment Analysis and the Molecular Signatures Database for cancer research
(NIH U24CA220341).The goal of this proposal is to continue to evolve and add value to the GSEA/MSigDB resource to best address the needs of the cancer research community.

Decomposing Molecular Signatures DataBase (MSigDB) Gene Sets to Extract More Coherent and Specific Cellular Signatures and Hallmarks
The goal of this project is to develop the next generation of hallmark gene sets. This new collection will add value by providing more coherent and better representation of the biological processes and subprocesses that are often inherent in MSigDB gene sets.

Principal Investigators

Jill Mesirov, Ph.D. Professor of Medicine, Associate Vice-Chancellor, Computational Health Sciences, UCSD
Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD

Project Manager

Helga Thorvaldsdóttir (Mesirov Lab)

CCAL Team

Jack Niklason
Kwat Medetgul-Ernar
Kate Niklason
Xiaojun (Max) Xu

Gene Pattern Team

Peter Carr
Michael Reich
David Eby
Thorin Tabor
Barabara Hill
Ted Liefeld
Edwin Juarez

The Moores Cancer Center component of the GCBSR, supported by an NIH CCSG grant, provides no cost support to MCC investigators with a variety of cancer genomics downstream analyses and training including: cancer variant analysis, gene expression profiling, biomarker discovery, epigenomic analyses, systems biology, gene set enrichment analysis, matrix decomposition, and many other advanced cancer genomics analysis tools.

Co-Director (MCC GCBSR)

Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD

CCAL Team

Kwat Medetgul-Ernar
Stephanie Ting
Kate Niklason
Xiaojun (Max) Xu

This project brings together a team of dedicated people across many disciplines to create a powerful, flexible and fully integrated platform for exploring new therapeutic opportunities and precision medicine capabilities for Prostate Cancer. nitially targeting Hispanic TNBC patients, this project will implement a novel collaborative working model for researchers, clinicians, patients, and stakeholders, as well as a research component. The models developed by this effort will be used for novel therapeutic discovery, preclinical validation and to recommend therapeutics strategies for prostate patients.

Project Leaders

William Kim, Ph.D. Assistant Professor of Medicine, Division of Medical Genetics, UCS
Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD
Ludmil Alexandrov, Ph.D. Assistant Professor, Cellular and Molecular Medicine, UCSD
Rana McKay, MD Medical Oncologist, Assistant Professor of Medicine, UCSD
Ida Deichaite, PhD Director, Industry Relations, Moores Cancer Center, UCSD
Katie Vaughan, Research Analyst, Translational Oncology, Moores Cancer Center, UCSD
Gordon Mills, M.D., Ph.D. Director of Precision Oncology, OHSU Knight Cancer Institute
Professor, Cell, Developmental and Cancer Biology OHSU

CCAL Team

Xiaojun (Max) Xu
Kwat Medetgul-Ernar

EMT oncogenic states and metastasis (Yang Lab)
Oncogenesis and the CNA Signature of Cyclin E1 (Reed Lab)
GPCR-driven cellular states (Gurkind Lab)
The PKA-MET cellular state (Gutkind Lab)
KIT resistance states in GIST (Sicklick Lab)
Platinum-based drug resistance states (Harismendy and Howell Labs)
SDH- driven cancers (Sicklick Lab)
An AR/EGFR driven State in desmoplastic small round cell tumors (DSRCT) sarcomas (Husain Lab)
Cellular states in glioma and meningiomas (Rich Lab)
The GNAQ activation state in uveal melanoma (Gutkind Lab)
Liver Cancer Cellular States and NRF2 (Burgoyne, Hui and Durden Labs)
Methylation-based oncogenic states in myelodysplasia (Bejar Lab)
Molecular portfolios across hematologic malignancies (Galanina Lab)
HPV+ oncogenic states (Califano, Cohen and Gutkind Labs)
Metformin sensitivity state (Gutkind)
Oncogenic states in TNBC (Harismendy Lab)

Project Leaders

William Kim, Ph.D. Assistant Professor of Medicine, Division of Medical Genetics, UCS
Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD
Ludmil Alexandrov, Ph.D. Assistant Professor, Cellular and Molecular Medicine, UCSD
Rana McKay, MD Medical Oncologist, Assistant Professor of Medicine, UCSD
Ida Deichaite, PhD Director, Industry Relations, Moores Cancer Center, UCSD
Katie Vaughan, Research Analyst, Translational Oncology, Moores Cancer Center, UCSD
Gordon Mills, M.D., Ph.D. Director of Precision Oncology, OHSU Knight Cancer Institute
Professor, Cell, Developmental and Cancer Biology OHSU

CCAL Team

Kwat Medetgul-Ernar
Stephanie Ting
Xiaojun (Max) Xu
Kate Niklason

Signatures of Immune Suppressive Macrophages (Varner Lab)
Precision Immunotherapy (Cohen and Schoenberger Labs)
Stimulation Neo-Antigen Specific T Cell Responses in Head and Neck Cancers (Cohen and Schoenberger Labs, NIH 1U01DE028227)
Novel Tumor Targets that Mediate NK Cell Activity (Kaufman Lab)
The immunosuppressive environment of the PKA-MET Oncogenic state (Gutkind Lab)
Macrophage Differentiation (Kaufman Lab)
Targeting the immunosuppressive Syk-PI3Kγ-HIF axis (Durden Lab)
Tumor innate immunity and endogenous retroviruses (Barbie Lab)
Signatures of PD-L1 immune response (Bhanot Lab)
APOBEC-related mutagenesis and neo-peptide hydrophobicity (Kurzrock Lab)

Principal Investigators

William Kim, Ph.D. Assistant Professor of Medicine, Division of Medical Genetics, UCS
Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD
Ezra Cohen, M.D. Professor of Medicine, Co-Director, Center for Precision Immunology, UCSD
Dan Kaufman, M.D. Ph.D. Professor of Medicine, Division of Regenerative Medicine, Director of Cell Therapy, UCSD
Judy Varner, Ph.D. Professor of Pathology, UCSD
Razelle Kurzrock, M.D. Professor of Medicine, Director, Center for Personalized Medicine, UCSD
Don Durden, MD, Ph.D. Professor, Division of Pediatric Hematology/Oncology, University of Nebraska and UCSD
Silvio Gutkind, Ph.D. Professor of Pharmacology, UCSD, Associate Director Basic Science (MCC)
Stephen Schoenberger, Ph.D. Professor, Co-Director, Center for Precision Immunology, La Jolla Institute
David Barbie, MD, Assistant Professor, Harvard Medical School and Dana Farber Cancer Institute
Gyan Bhanot, Ph.D. Professor of Molecular Biology and Biochemistry; and Department of Physics School of Arts and Sciences Rutgers, The State University of New Jersey

CCAL Team

Kwat Medetgul-Ernar

Similarity Weighted Non-Negative Embedding (Zhang Lab)
Molecular signatures & systems biology networks (Ideker Lab)
Dynamic cellular and molecular changes associated with clinical response (Pfizer and Samsung Medical Center)
Modelling bistable tumour population dynamics to design effective treatment strategies (Yeang lab)
Mathematical and computational models to study the behavior of signaling networks (Stites Lab)

Principal Investigators

Trey Ideker, Ph.D. Professor of Medicine, UCSD. Director, San Diego Center for Systems Biology
Kun Zhang, Ph.D. Professor of Bioengineering, UCSD
Prashant Mali, Ph.D. Assistant Professor ​Bioengineering, UCSD
Chen-Hsiang Yeang, Ph.D. Associate Research Fellow, Institute of Statistical Science, Academia Sinica, Taiwan
Zhengyan (George) Kan, Ph.D. Computational Biology, Pfizer Oncology
Edward Stites, MD Ph.D. Assistant Professor, Integrative Biology Laboratory, Salk Institute
William Kim, Ph.D. Assistant Professor of Medicine, Division of Medical Genetics, UCSD
Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD

CCAL Team

Kwat Medetgul-Ernar

We are one of the collaborating teams of the Cancer Cell Map Initiative UCSD project (NIH 5U54CA209891). The Cancer Cell Map Initiative is a large project that focus on developing an approach to generate low-dimensional network representations that summarize the functional interactions in many genomically characterized cancer cell lines.

Principal Investigators

Trey Ideker, Ph.D. Professor of Medicine, UCSD. Director, San Diego Center for Systems Biology
Nevan Krogan

Key Personnel

Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD
Jill Mesirov, Ph.D. Professor of Medicine, Associate Vice-Chancellor, Computational Health Sciences, UCSD

CCAL Team

Kwat Medetgul-Ernar

Post-transcriptional RNA processing is a fundamental biological process that is important for regulation of most aspects of life. One such RNA modification that has previously been overlooked since it is difficult to detect by conventional sequencing strategies is circular RNA (circRNA). Using the RNA-targeting Cas13 protein and CRISPR technology or RNAi we have developed an approach that enables knockdown of a circRNA without perturbing the linear mRNA. We will develop a genome wide CRISPR and RNAi circRNA targeting library and use this for phenotypic screens in a panel of 10 cell lines from different lineages. This will allow us to map the functions of circRNAs and find those that are essential for general cell processes as well as context specific circRNAs.

Principal Investigators

Joseph Rosenbluh, Ph.D. Associate Professor, Department of Biochemistry and Molecular Biology, Monash University
Director of the Functional Genomics Platform at the Hudson Institute of Medical Research.
William Kim, Ph.D. Assistant Professor of Medicine, Division of Medical Genetics, UCSD
Pablo Tamayo, Ph.D. Professor of Medicine, Division of Medical Genetics, UCSD
Jill Mesirov, Ph.D. Professor of Medicine, Associate Vice-Chancellor, Computational Health Sciences, UCSD

Research Staff

Jiangning Song, Ph.D. Associate Professor and Group Leader, Head of the Bioinformatics and Computational Biology Laboratory, Monash University