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Cancer Biology, Informatics & Omics Training Program (CBIO)

ONE postdoctoral spot available starting July 1st!

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, MedicinePathologyPediatrics,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:

Rafael Bejar, MD, Ph.D.

Medicine

Genetics of Myeloid Malignancies

Hannah Carter, Ph.D.

Medicine

Network Perturbing Cancer Mutations

Clark C. Chen, MD, Ph.D.

Surgery

Brain Tumor Surgery & Targeted Therapy

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

 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)

Required Seminars:

• CMM/LICR (Fall-Winter-Spring, weekly);

• MCC (Oct – June, monthly)

Required Seminars:

• CMM/LICR (Fall-Winter-Spring, weekly);

• MCC (Oct – June) monthly

Required Program Meetings:

• Research meetings (September – June, monthly);

• Retreat (August, annually)

 Required Program Meetings:

• Research meetings (September – June, monthly);

• Retreat (August, annually)

 Other Requirements: Ethics Training; Presenting in National Meeting; Writing a Research Proposal;

Career in Biomedical Sciences Workshops

Postdoctoral Requirements

​ CBIO Postdoc Training Activities – Year 1 ​CBIO Postdoc Training Activities – Year 2

Required Didactic Training:
• CBIO Cancer Biology Tutorials

• 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)

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

Required Seminars:

• CMM/LICR (Fall-Winter-Spring, weekly);

• MCC (Oct – June, monthly)

Required Seminars:

• CMM/LICR (Fall-Winter-Spring, weekly);

• MCC (Oct – June) monthly

Required Program Meetings:

• Research meetings (September – June, monthly);

• Retreat (August, annually)

Required Program Meetings:

• Research meetings (September – June, monthly);

• Retreat (August, annually)

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)

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 
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