Formal Coursework

The program in Cancer Biology requires that each student take at least five graded courses, which include two research rotations:

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 of Year 1.

Readings in Cancer Biology (CABI 40100). Pairs of students sign up for two to four five-week sessions.  Students meet with a CCB faculty member twice a week to dissect and critique a series of recent papers on a single topic.  Students present each paper to the faculty, who provides feedback and commentary and asks questions to probe understanding and depth of preparation.  The course focuses on honing skills in reading, scholarship, critical analysis, presentation and discussion that are tested by the Preliminary Examination and are important for success as an independent researcher.  The course is graded based on faculty evaluation.  Course director: S. Kron.  Fall, Winter and/or Spring of Year 1.

Research Rotations (BSDG 4100). The goal of research rotations is to help students make informed choices for thesis advisors.  During the Fall quarter, students are encouraged to meet as many faculty as possible, speaking one-on-one to learn about shared interests and to find exciting projects and opportunities.  Students then contact faculty and request the opportunity to join their labs for two nine-week rotations or three six-week rotations during Winter and Spring quarters.  During the rotation, the student, the faculty and their group have the opportunity to evaluate the fit and potential for a successful thesis.  With approval of the Curriculum Committee, students who wish to consider more options can pursue another one or two six-week rotations during Summer quarter.  Credit (pass/fail) is awarded upon formally choosing the thesis lab. Course director: S. Kron. Winter, Spring and Summer of Year 1.

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 -Basu, Izumchenko, Bader. Autumn of Year 2.

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 of Year 2.



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.