The Cancer Biology, Informatics & Omics Training (CBIO) training program in the School of Medicine (SOM) at the University of California, San Diego (UCSD) provides graduate students and post-doctoral scholars with training in discovery cancer research that is directly relevant to the nation’s goal of lessening the burden of cancer.
The proposed training is based on three rationales:
(i) Advancements in cancer diagnosis and treatment are propelled by basic research discoveries on cancer-relevant biological processes
(ii) Cancer Genomics has provided a wealth of data to enable cancer-relevant translation of new knowledge and insights from model organism research
(iii) Modern investigation of cancer biology in the human system requires proficiency in omics technologies and computational tools.
Based on these principles, the CBIO program has designed a training curriculum to (a) achieve research excellence in advanced systems and approaches, (b) provide foundation knowledge on cancer and bioinformatics through coursework, (c) develop translational insights through participation in Tumor Boards at the Moores Cancer Center (MCC), (d) keep pace with advancements through MCC and SOM seminars as well as Systems Biology workshops, and (e) foster a collaborative community through program meetings and retreats. With these activities, the CBIO program aims to accelerate the pace of discovery and to advance the delivery of precision cancer medicine.
The CBIO program leverages the continuing expansion of biomedical research in the UCSD SOM to identify faculty mentors with cancer-relevant research expertise, productive research programs, principled research conduct and outstanding training history from the Departments of Cellular & Molecular Medicine, Medicine, Pathology, Pediatrics,Pharmacology and Surgery. The CBIO program activities expose the trainees as well as the faculty to the diversity of systems, approaches and technologies that must be employed to investigate the complex biology of cancer.
The CBIO program selects pre-doc trainees with outstanding academic achievements and cancer-relevant thesis projects from PhD students in the Biomedical Sciences graduate program. Previous pre-doc trainees of the CBIO program have established productive careers as faculty, research scientists and science writers. In the past five years, the CBIO program has extended training to post-doc scholars interested in cancer research with the goal of enhancing the career opportunities of highly qualified post-docs who are already in the biomedical research workforce pipeline.
The CBIO program Executive Committee, consisting of the CBIO Program Director, Co-Directors, and two other CBIO faculty mentors with global perspectives on cancer research and leadership roles in diversity enhancement, selects and evaluates trainees and faculty. The CBIO External Advisory Committee reviews program statistics and metrics to identify the strengths and weaknesses of training activities, trainees and faculty. With these activities and support from the SOM and the MCC, the CBIO program will continue to function as a nexus for cancer-focused basic research and training in the SOM at UCSD.
Faculty Mentors
Program Director – Jean Wang, PhD: Dr. Wang is a professor of Medicine and of Molecular Biology in the Division of Biological Sciences. She currently researches death mechanisms activated by DNA damage, and metabolic stress in p53-Deficient Cancer Cells. https://biology.ucsd.edu/research/faculty/jywang
Co- Director – Steven Dowdy, PhD: Dr. Dowdy is a professor of Cellular & Molecular Medicine. His current research pertains to cell cycles, chemical biology, and the development of modified RNA for cancer therapy. https://medschool.ucsd.edu/som/cmm/faculty/Pages/Steven-Dowdy.aspx
Co- Director – Pradipta Ghosh, MD: Dr. Ghosh is an Associate Professor of Medicine and Cellular & Molecular Medicine. Her lab researches signaling interphases between G-protein coupled, and tyrosine kinase receptors in cancer. https://medschool.ucsd.edu/som/medicine/divisions/gastro/research/labs/ghosh/Pages/default.aspx
Executive Committee Member – Richard Kolodner, PhD: Dr. Kolodner is a professor of Cellular & Molecular Medicine. He is currently working on cancer genome instability, cause, and targeted therapy. https://medschool.ucsd.edu/som/cmm/faculty/Pages/Richard-Kolodner.aspx
Other Program Faculty:
| Medicine |
Genetics of Myeloid Malignancies |
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| Medicine |
Network Perturbing Cancer Mutations |
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| Surgery |
Brain Tumor Surgery & Targeted Therapy |
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| Don Cleveland, Ph.D. | CMM* |
Aneuploidy & Tumorigenesis |
| Arshad Desai, Ph.D. | CMM* |
Genome Segregation Fidelity in Mitosis |
| Jeff Esko, Ph.D. | CMM* |
Proteoglycans & Tumor Formation |
| Gen-Sheng Feng, Ph.D. | Pathology |
Liver Tumorigenesis & Leukemogenesis |
| Kelly Frazer, Ph.D. | Pediatrics | Functional Cancer Genomics, Genetic Markers for Tumor Sub-typing and Drug Response |
| Xiang-Dong Fu, Ph.D. | CMM* | Regulated RNA Processing in Cancer |
| Frank Furnari, Ph.D. | Pathology | Gene Expression Networks in Glioma |
| J. Silvio Gutkind, Ph.D. | Pharmacology | Pathway-based Precision Cancer Therapy |
| Sven Heinz, Ph.D. | Medicine | Medical Epigenomics in CLL |
| Wendy Huang, Ph.D. | CMM* | Non-coding RNA in Immune Regulation |
| Trey Ideker, Ph.D. | Medicine | Network Directed Cancer Systems Biology, Computational Models of DNA Damage Response Network |
| Catriona Jamieson, MD, Ph.D. | Medicine | Cancer Stem Cells & Drug Resistance |
| Thomas Kipps, MD, Ph.D. | Medicine | Chronic Lymphocytic Leukemia, Pathogenesis, Novel Therapies |
| Jill Mesirov, Ph.D. | Medicine | Computational Cancer Genomics |
| Paul Mischel, MD | Pathology | Cancer Signaling & Metabolism |
| Karen Oegema, Ph.D. | CMM* | Regulation of Cytoskeleton Dynamics in Mitosis |
| Bing Ren, Ph.D. | CMM* | Chromatin Domains and Long Range Regulation of Gene Expression |
| Debashis Sahoo, Ph.D. | Pediatrics | Boolean Mathematical Models for Cancer |
| Maike Sander, Ph.D. | Pediatrics | Pancreatic Development, Cell Type Specification, Neoplastic Transformation |
| David Traver, Ph.D. | CMM* | Hematopoiesis & Leukemia |
| Eugene Yeo, Ph.D. | CMM* | Gene Regulation by RNA-Binding Proteins |
| Dong-Er Zhang, Ph.D. | Pathology | Gene Expression Defects in AML |
| Jin Zhang, Ph.D. | Pharmacology | Spatiotemporal Regulation of Signaling |
| Huilin Zhou, Ph.D. | CMM* |
Regulatory Genome Maintenance Pathways |
Predoctoral Requirements
| CBIO Predoc Training Activities – Year 1 | CBIO Predoc Training Activities – Year 2 |
|---|---|
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Required Course: • Molecular Pathology of Cancer (Winter); • Genomics, Proteomics & Network Biology (Spring) • CBIO Journal Club (Winter-Spring) |
Recommended Clinical Learning: • Med-Into-Grad (Fall-Winter); Required Courses: • Quantitative Methods in Genetics & Genomics (Winter) • CBIO Journal Club (Winter-Spring) |
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Required Seminars: • CMM/LICR (Fall-Winter-Spring, weekly); • MCC (Oct – June, monthly) |
Required Seminars: • CMM/LICR (Fall-Winter-Spring, weekly); • MCC (Oct – June) monthly |
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Required Program Meetings: • Research meetings (September – June, monthly); • Retreat (August, annually) |
Required Program Meetings: • Research meetings (September – June, monthly); • Retreat (August, annually) |
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Other Requirements: Ethics Training; Presenting in National Meeting; Writing a Research Proposal; Career in Biomedical Sciences Workshops |
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Postdoctoral Requirements
| CBIO Postdoc Training Activities – Year 1 | CBIO Postdoc Training Activities – Year 2 |
|---|---|
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Required Didactic Training: • CBIO Informatics Boot Camp • CBIO Journal Club (Winter-Spring) |
Required Clinical Learning: • Molecular Tumor Board (Fall, Winter and Spring, weekly) Required Didactic Training: • CBIO Journal Club (Winter-Spring) |
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Recommended Courses: • Courses: BIOM256 (Winter) for Postdocs with PhD in Computer Sciences and/or Engineering • BIOM262 (Winter) or CSE283 (Spring) or for Postdocs with PhD in Biological Sciences |
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Required Seminars: • CMM/LICR (Fall-Winter-Spring, weekly); • MCC (Oct – June, monthly) |
Required Seminars: • CMM/LICR (Fall-Winter-Spring, weekly); • MCC (Oct – June) monthly |
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Required Program Meetings: • Research meetings (September – June, monthly); • Retreat (August, annually) |
Required Program Meetings: • Research meetings (September – June, monthly); • Retreat (August, annually) |
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Other Requirements: Ethics Training; Presenting in National Meeting; Writing a Research Proposal; Participating in Career Development Workshops for Postdocs and using the Online IDP Tool (myidp.sciencecareers.org) |
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CBIO Monthly Meetings
| Date | Speaker | Lab | Title of Talk |
|---|---|---|---|
| 2017 / 2018 | |||
| 6/1/18 | Tariq Rana, Ph.D. | Professor of Pediatrics | TBD |
| 5/4/18 | Olivier Harismendy, Ph.D. | Asst. Professor of Medicine | TBD |
| 4/6/18 | S. Park, MD | Bejar Lab | Genomic Correlates of IL-2 Response in Advanced Melanoma and Renal Cell Carcinoma |
| 3/2/18 | Ayush Kishore, Ph.D. | Gutkind Lab | GNAQ-FAK Signaling in Ocular Melanoma |
| 2/2/18 | Nathan Jameson | Furnari Lab | Epigenetic regulation of EGFR in Glioblastoma |
| 1/5/18 | Peter Ly, Ph.D. | NIH Pathway to Independence Awardee | Rebuilding After Catastrophe: How Cell Division Errors Shape the Cancer Genome |
| 12/1/17 | Elaine Guo, BS | Kolodner Lab | Synthetic Lethal Targeting of BRCA-Deficient Cancer |
| 11/3/17 | Jason Ear, Ph.D. | Ghosh Lab | Dissecting the Role of DAPLE in Colorectal Cancer |
| 10/6/17 | Carlos Medina, BS | Dowdy Lab | Genomics of Recurrent Acute Myeloid Leukemia |
| 9/1/17 | Myan Do, BA | Willert Lab | Wnt Receptor FZD7 in Cancers and ES Cells |
