Formal Coursework

The academic program in Cancer Biology will require that each student take at least nine graded courses, six quarters of Introduction to Experimental Cancer Biology, and complete two research rotations for a total of 10.5 course credits.

Accordion: 
Cancer Biology Programmatic Core (all students take the core sequence)

Cancer Biology Fundamentals (CABI 30800).  This course introduces students to key aspects of cancer biology, including fundamental molecular mechanisms (includes tumor suppressor and oncogene function, cell cycle checkpoint control, cytokinesis defects and aneuploidy, DNA damage sensing & repair, cell death mechanisms, cellular senescence) underpinning the initiation and progression of disease. These lectures are taught alongside an introduction to clinical and translational perspectives, on the topics of epidemiology, pathology, diagnosis and staging, and the basis for various therapeutic strategies with an emphasis on four different organ sites to illustrate key points. The course concludes with an examination of how to identify important research questions in cancer biology and the importance of innovation in research. Course Director - Lingen. Autumn.

Translational Approaches in Cancer Biology (CABI 32000). This is a lab/clinic-based course in which students complete training objectives in multiple modules of translational/applied cancer research (clinical, animal models, targeted therapy, intellectual property, bioinformatics, nanotechnology and population science). The emphasis of the course is hands-on experience and a high degree of independence is expected. Trainees select a topic on which to write up a final discussion paper and each student will deliver a presentation on their topic that incorporates elements of the different translational elements discussed during the quarter. Course Director -Macleod. Spring.

Hypothesis Design and Grant Writing Skills (CABI 31600).  This is a course based on developing and testing hypotheses that will provide an overview and real-world experience of the grant-writing process (F31 format), as well as responding to criticisms and presenting one’s grant in a precise but concise manner. As it is a course centered around in-class discussion, it is dependent on the consistent creativity and participation of students in order to provide and receive useful feedback to and from their colleagues. The grant will formulate hypotheses around the student’s own research project and the completed grant should provide a strong basis for future F31 or other fellowship applications. Review and input from each student’s PI is encouraged. Course Directors –Xiaoyang Wu, Lev Becker.  Taken in Autumn quarter of 2nd year (once students have joined a research lab).

Introduction to Experimental Cancer Biology (CABI 39000).  This is a primary literature-based course that tracks our outstanding CCB Seminar Series and also incorporates seminars of interest from other Divisional programs. Typically, students meet to discuss research papers published by the following week’s seminar speaker, attend the seminar, and then meet with the speaker afterward.  The goal of the course is to broaden the student’s exposure to current research and encourage discussion of scientific ideas among peers, as well introduce students to some of the major figures in cancer research with whom they may pursue future post-doctoral opportunities. All students start with an “A” grade but lose grade points if class performance or attendance is inadequate. Students are required to take this course for six quarters during years 1-2. Course Directors - McNerney, Spiotto, Wang.  Autumn, Winter, and Spring.

Cancer Biology Electives

Pharmacogenomics: Discovery and Implementations (CABI 47510; CCTS 40001; BIOS 25310).  This class is aimed at advancing our knowledge of the genetic basis for variable drug response. The study of pharmacogenomics is complicated by the fact that response and toxicity are multigenic traits and are often confounded by nongenetic factors (e.g., age, co-morbidities, drug-drug interactions, environment, diet, etc). Using knowledge of an individual’s DNA sequence as an integral determinant of drug therapy has not yet become standard clinical practice; however, several genetics-guided recommendations for physicians have been developed and will be highlighted.  Stranger, Huang.  Spring.

Heterogeneity in Human Cancer: Etiology and Treatment (BIOS 25308). This course addresses the importance of understanding human tumor heterogeneity (organ site by organ site) in terms of predicting whether tumors will progress to malignancy and how tumors will respond to standard treatments or require tailored molecular therapeutics. Alternating lecture and discussion lectures will explore and tease apart the controversies in the field that limit progress in cancer prevention, diagnosis and treatment. At the end of the course, students should have an in-depth understanding of the complexities, challenges and opportunities facing modern cancer researchers and clinical oncologists and be able to discuss novel scientific approaches to solving these issues. Macleod. Spring

The General Basic Science Core (students will be required to take 1 course from each of the following 4 areas)

Biochemistry

Protein Fundamentals (BCMB/HGEN/MGCB 30400).  The course covers the physical chemical phenomena that define protein structure and function.  Topics include:  the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology.  Keenan.  Autumn.

Structure and Function of Membrane Proteins (BCMB/MGCB  32300).  This course will be an in depth assessment of the structure and function of biological membranes. In addition to lectures, directed discussions of papers from the literature will be used. The main topics of the courses are: (1) Energetic and thermodynamic principles associated with membrane formation, stability and solute transport (2) membrane protein structure, (3) lipid-protein interactions, (4) bioenergetics and transmembrane transportmechanisms, and (5) specific examples of membrane protein systems and their function (channels, transporters, pumps, receptors). Emphasis will be placed on biophysical approaches in these areas. The primary literature will be the main source of reading. Perozo.  Autumn.

Cell Biology

Cell Biology 1 (MGCB/BCMB/HGEN 31600).  Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocation and sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis, and mechanisms and regulation of membrane fusion. Turkewitz, Glick.  Autumn.

Cell Biology 2 (MGCB/BCMB 31700).  This course covers the mechanisms with which cells execute fundamental behaviors. Topics include signal transduction, cell cycle progression, mitosis, checkpoints, cytoskeletal polymers and motors, cell motility, cytoskeletal diseases, and cell polarity. Each lecture will conclude with a dissection of primary literature with input from the students. Students will write and present a short research proposal, providing excellent preparation for preliminary exams. Cell Bio I 31600 is not a prerequisite.  Glotzer, Kovar.  Winter

Quantitative Analysis of Cellular Dynamics (DVBI 32000). This course covers quantitative approaches to understanding biological organization and dynamics at molecular, sub-cellular and cellular levels. A key emphasis is on the use of simple mathematical models to gain insights into complex biological dynamics. We also will cover modern approaches to quantitative imaging and image analysis, and methods for comparing models to experimental data. A series of weekly computer labs will introduce students to scientific programming using Matlab and exercise basic concepts covered in the lectures. Rust, Munro. Spring

Stem Cells and Regeneration (DVBI 36200). The course will focus on the basic biology of stem cells and regeneration, highlighting biomedically relevant findings that have the potential to translate to the clinic. We will cover embryonic and induced pluripotent stem cells, as well as adult stem cells from a variety of systems, both invertebrate and vertebrates. Ferguson, Prince, Cunningham, De Jong, Wu. Autumn

Genetics and Systems Approaches

Human Genetics 1: Human Genetics (HGEN 47000).  This course covers classical and modern approaches to studying cytogenic, Mendelian, and complex diseases. Topics include chromosome biology, single gene and complex disease, non-Mendelian inheritance, cancer genetics, human population genetics, and genomics. The format includes lectures and student presentations. Ober, Waggoner, Nobrega.  Autumn.

Genetic Analysis of Model Organisms (BCMB/HGEN/MGCB 31400). Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes.  The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature. Bishop, Moskowitz, Ferguson, Malamy. Autumn.

Genomics and Systems Biology (IMMU/HGEN 47300). This lecture course explores the technologies that enable high-throughput collection of genomic-scale data, including sequencing, genotyping, gene expression profiling, assays of copy number variation, protein expression and protein-protein interaction. We also cover study design and statistical analysis of large data sets, as well as how data from different sources can be used to understand regulatory networks (i.e., systems). Statistical tools introduced include linear models, likelihood-based inference, supervised and unsupervised learning techniques, methods for assessing quality of data, hidden Markov models, and controlling for false discovery rates in large data sets. Readings are drawn from the primary literature. Gilad. Spring

Statistical Inference and Stochastic Models for Computational Biologists (HGEN 48600). Covers key principles in probability and statistics that are used to model and understand biological data.   There will be a strong emphasis on stochastic processes and inference in complex hierarchical statistical models.   Topics will vary but the typical content would include:  Likelihood-based and Bayesian inference, Poisson processes, Markov models, Hidden Markov models,  Gaussian Processes, Brownian motion, Birth-death processes,  the Coalescent, Graphical models, Markov processes on trees and graphs, Markov Chain Monte Carlo. Prereq:  STAT 244 or equivalent and comfort with programming, or consent of instructor. Novembre, Stephens. Spring.

Molecular Biology

Molecular Biology 1 (MGCB/BCMB 31200).  Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription, replication and genome stability and dynamics.  Rothman-Denes, Bishop.  Winter.

Molecular Biology 2 (MGCB/BCMB/DVBI 31300).  The content of this course will cover the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions highlight the most significant recent developments, their implications and future directions. Enrollment requires the equivalent of an undergraduate molecular biology course or consent from the instructors. Staley, Ruthenburg.  Spring.

Electives

The student will take two elective courses in an area, or areas, of specific interest to the student, in consultation with the Curriculum Committee, which will keep the individual interests and the goals of the student in mind.  Students may take additional electives according to their specific interests. All course requirements should be completed by the end of the student's second year.