Course Catalog

Cancer Biology

Courses

Director:
Laura Attardi, PhD

Julien Sage, PhD

Program Administrator:
Grace Batoon

Department web site:
http://med.stanford.edu/cancerbiology/HOME.html

Faculty of Cancer Biology:
http://med.stanford.edu/cancerbiology/ParticipatingFaculty.html

Cancer Biology:

The Cancer Biology Program at Stanford University is an interdisciplinary program leading to the Ph.D. degree. During the past three decades, understanding of cancer has increased with the discovery of oncogenes, tumor suppressor genes, pathways of DNA damage and repair, cell cycle regulation, angiogenesis and responses to hypoxia, and the molecular basis of metastasis among others. In addition, methods of parallel analysis including gene expression arrays, protein arrays, and tissue arrays have begun to refine and redefine the taxonomy of cancer diagnosis. This explosion of basic and clinical science has resulted in the first successful cancer chemotherapies and immunotherapies based on the knowledge of specific molecular targets. Stanford presents a unique environment to pursue interdisciplinary cancer research because the Schools of Medicine, the School of Humanities and Sciences, and the School of Engineering are located on a single campus, all within walking distance of one another.

The goal of the Cancer Biology Ph.D. program is to provide students with education and training that enables them to make significant contributions to this field. Course work during the first year is designed to provide a broad understanding of the molecular, genetic, cell biological, and pathobiological aspects of cancer. Students also learn about the current state of the epidemiology, clinical diagnosis, treatment, and prevention of human cancers. Equally important during the first year is a series of three rotations in research laboratories chosen by each student. By the beginning of the second year, each student chooses a research adviser and begins work on the dissertation project. A qualifying examination must be completed by the end of the second year. An annual Cancer Biology conference at Asilomar in Pacific Grove, California provides students with an opportunity to present their research to one another and to faculty. The expected time to degree is four to five years.

Our students are not limited to a single department in choosing their research adviser. The Cancer Biology Ph.D. program currently has approximately 65 graduate students located in basic science and clinical departments throughout the School of Medicine and the School of Humanities and Sciences.

DOCTOR OF PHILOSOPHY IN CANCER BIOLOGY

University requirements for the Ph.D. are described under the "Graduate Degrees" section of this bulletin.

A small number of applicants are admitted to the program each year. Applicants should have completed an undergraduate major in the biological sciences; applicants with undergraduate majors in physics, chemistry, or mathematics may be admitted if they complete background training in biology during the first two years of study. During the first year, each student is required to complete a minimum of three, one quarter laboratory rotations. Students must choose a dissertation adviser prior to the end of Summer Quarter, first year, but not before the end of Spring Quarter, first year.

The requirements for the Ph.D. degree are as follows:

1. Training in biology equivalent to that of an undergraduate biology major at Stanford.

2. Completion of the following courses:

BIOS 200 Foundations in Experimental Biology

CBIO 240 Molecular Genetic Basis of Cancer

CBIO 242 Cellular and Clinical Aspects of Cancer

CBIO 245 Lecture Seminar Series in Cancer Biology Program (1st & 2nd year)

CBIO 280 Cancer Biology Journal Club (1st & 2nd year)

MED 255 Responsible Conduct in Research

CCRTP Comprehensive Cancer Research Training Program

CBIO 241 Molecular, Cellular, and Genetic Basis of Cancer 5 units

CBIO 243 Principles of Cancer Systems Biology 3 units

BIO 214 Advanced Cell Biology 4 units

3. Core Knowledge Courses:

BIOS 201 Next Generation Sequencing and Applications

BIOS 205 Introduction to R

CBIO 243 Principles of Cancer Systems Biology

CS106A Design and Analysis of Algorithms

GENE 211 Genomics

GENE 218 Computational Analysis of Biological Information: Introductions to Python for Biologists (ME 218, PATH 218)

NENS 230 Analysis Techniques for Biosciences Using MATLAB

4. Additional Courses:

BIOE 217 Translational Bioinformatics

BIOMEDIN 214 Representations and Algorithms for Computational Molecular Biology (BIOE 214, CS 274, GENE 214)

BIOS 214 Advanced Cell Biology

CBIO 275 Tumor Immunology

CS 106B Programming Abstractions (ENGR 70B)

CSB 210 Cell Signaling

DBIO 201 Development and Disease Mechanisms

GENE 245 Statistics and Machine Learning Methods for Genomics (BIO 268, BIOMEDIN 245, CS 373, STATS 345)

IMMUNOL 201 Advanced Immunology I

IMMUNOL 207 Essential Methods in Computational and Systems Immunology

MI 215 Principles of Biological Techonologies

SBIO 241 Biological Macromolecules

STATS 60 Introduction to Statistical Methods: Precalculus (PSYCH 10, STATS 16)

STATS 116 Theory of Probability

STATS 202 Human Genetics

STATS 216 Introduction to Statistical Learning

5. Presentation of research at the annual Cancer Biology Conference on at least three occasions, at least one being an oral presentation. An oral presentation of research at the Tuesday Science Pizza Talks.

6. Completion of a qualifying examination in Cancer Biology is required for admission to Ph.D. candidacy. The exam consists of an NRSA-style written grant proposal not to exceed 7 pages (excluding references) and an oral examination. The examining committee includes three faculty members from the Cancer Biology Program but does not include the student's thesis advisor. The composition of this committee is chosen by the student and thesis advisor and must be submitted to and approved by the Program Directors prior to the end of autumn quarter, second year. One non-Cancer Biology faculty members may be substituted, if necessary, to provide specific scientific expertise relevant to the student’s proposal. The written and oral proposal should represent the student’s own efforts to identify a question of interest and to develop appropriate experimental approaches. Preliminary data generated by the student are NOT required. Students are strongly encouraged to develop a written Specific Aims sections by the end of winter quarter, second year. The qualifying exam must be taken by April 1st, second year. If necessary, one retake will be permitted prior to the end of summer quarter, second year. In year three each student is required to hold an annual dissertation committee meeting in order to assess progress towards the degree and for the committee to provide advice. In the fourth year and beyond, students are required to meet with their committees twice a year. The Annual Dissertation Committee Meeting Form should be completed and signed by all the committee members in attendance at each meeting and forms should be returned to Cancer Biology Program Office.

The major accomplishment of each successful Ph.D. student is the presentation of a written dissertation resulting from independent investigation that contributes to knowledge in the area of cancer biology. A University Oral Examination is also required for the Ph.D. degree. In the Cancer Biology Program, a public seminar (one hour) is presented by the Ph.D. candidate, followed by a closed-door oral examination. The oral examination committee consists of at least four examiners and a chair from a different academic department than the student’s advisor. Note that the chair may be a faculty member in the Cancer Biology Program provided that he/she is not in the same academic department as the student’s advisor. All members of the Committee are normally members of the Academic Council, and the oral examination chair must be. With the prior approval of the Program Directors or School Dean, one of the examiners may be a person who is not a member of the Academic Council if that individual contributes expertise not readily available from the Stanford Faculty. Official responsibility for selecting the oral examination chair rests with the Department. Cancer Biology delegates this to the student and dissertation advisor.

 

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