BMS students may choose any departmental or inter-departmental course approved by your advisor to be an elective course. Not all courses are offered every year. Please check with the department or program for specific course dates and schedules, as they may change from year to year. You may also check the PIBS website for quarterly graduate course listings. The quarter in which each of these courses is given may vary from year to year. Some courses are also given only in alternate years. Additional courses and seminars will be recommended by the graduate advisor and the student’s dissertation advisor.

Fall Quarter
Biochem 200A Macromolecules
Course Director: Jonathan Weissman
Website: http://macromolecules.ucsf.edu

Biochemistry 242 Protein Crystallography
Stroud and Staff (Offered alternate years)

BMI 209 Statistical Methods in Bioinformatics: Case Studies
Instructors: MR Segal, RF Yeh, Y Xiao
Website: http://www.biostat.ucsf.edu/cbmb/bmi209
This course is intended to expose students to approaches to formulating and tackling important data analytic problems that arise in the context of contemporary, high-throughput technologies. These include DNA microarrays, ChIP-chip studies, SNP arrays, and whole-genome sequencing. It is expected that students will acquire the ability to frame statistical hypotheses in such settings and be able to identify corresponding data analytic techniques. While such techniques will be introduced here via case studies, they pertain to more broadly encountered research questions and study domains. Examples (and the settings where they arise) include data preprocessing (expression, tiling and SNP arrays), multiple hypothesis testing (evolution, CpG island methylation), sequence analysis (motif finding, nucleosome positioning), clustering (SNP arrays, DLBCL), and classification and methods (CpG island methylation, copy number data).


Biophysics 202 Biophysical Methods
Course Director: Dan Minor

Chem 244 Reaction Mechanisms
Course Director: Kevan Shokat
Description: This course is designed to develop the student's knowledge of organic reaction mechanisms. This interactive course involves some lectures, but enforces student learning through intensive arrow pushing sessions with students at the board. Current topics include: electrocyclic reactions, Woodward-Hoffman rules, sigmatropic reactions, migration reactions, neighboring group effects, carbanions and free radicals, carbenes, carbenoids, nitrenes, six-membered heterocyclic rings, five-membered heterocyclic rings.

Chem 241 Molecular Thermodynamics
Course Director: Ken Dill
Description: This is a course on molecular thermodynamics and statistical mechanics. It covers the concepts of entropy, enthalpy, heat capacity, free energy, ligand binding, solvation, the properties of water, the hydrophobic effect, solution electrostatics, adsorption, and physical and chemical kinetics.

Genetics 200A Genetics and Development
Course Director: Hiten Madhani
Website: http://biochemistry.ucsf.edu/~genetics/index.html

Microbiology 204 Molecular and Cellular Immunology
Course Director: Tony DeFranco
Website: http://www.ucsf.edu/immuno/courses/micro204/index.html
An advanced overview that considers in depth the development and function of the B and T cell lineages, signal transduction by B and T cell antigen receptors, diversity generation in antibody molecules and in T cell receptor repertoire, the cell biology of antigen presentation, costimulatory molecules, cytokine biology, natural killer cells and other cellular and molecular components of the innate immune system.

N201A Basic Concepts in Cellular and Molecular Neuroscience
Course Director: Dorit Ron
Website : http://www.neuroscience.ucsf.edu/neurograd/courses/courses.htm Description: An interdisciplinary introduction to fundamental aspects of nervous system function. The course emphasizes the ionic and molecular basis of excitability, synaptic transmission and signal transduction.

NS 245 Behavioral Neuroscience (this course is not offered every year)
Course Director: Patricia Janak
Website: http://www.neuroscience.ucsf.edu/neurograd/courses/courses.htm
Description: Lectures and discussion of primary research concerning the neural basis of behavior. Topics will include basic concepts of learning and neuroethology with examples from vertebrate and invertebrate systems. A comparative approach will be taken to understanding psychological constructs such as drive, motivation and emotion. Emphasis will be placed on neural circuit analysis of behaviors such as sound localization, drug self-administration, and fear conditioning.

PC 204 Introduction to Computer Programming
Course Director: Tom Ferrin
Description: An introduction to computer programming using the C language and the UNIX operating system. During the course, students learn to write, test, and debug programs of increasing complexity. Emphasis is on the basic principles in writing well-structured and modular code.

PSPG 245A Basic Principles of Pharmaceutical Sciences
Course Director: Kathleen M. Giacomini
Website: http://www.ucsf.edu/dbps/curriculum/materials.html

Winter Quarter
Biochemistry 201 Biological Regulatory Mechanisms
WINTER 3 units
Joachim Li, course director
(Biochem 200A + Genetics 200A are prerequisites)
Advanced discussion of the contemporary molecular understanding of gene regulation, including: DNA and chromatin structure and replication; transcriptional and post-transcriptional regulation in pro- and eukaryotes; RNA splicing; RNA editing; polyadenylation; ribosome structure and function, translational regulation.

BMI 206 Introduction to Bioinformatics
WINTER 3 units Course Director: P. Babbitt
Basic concepts in genomics, proteomics, genome biology and molecular evolution relevant to bioinformatics. Generation and annotation of genetic information. Types, organization, and uses of bioinformatics databases, database searching, sequence analysis, and evaluation of results.

Biochemistry 297 Cancer Biology: Molecular Pathology of Neoplasia
WINTER 3 units Course Director: Tlsty

NS 201BBasic Concepts in Cellular and Molecular Neuroscience WINTER 3 Units Course Director: Ulrike Heberlein
An interdisciplinary introduction to development and neuroscience systems.

Spring Quarter
Biochem 160 Food Facts, Fads & Pharmacology
Course Director: Clyde Wilson
Description: This 1-unit elective for medical, pharmacy and other UCSF students consists of a review of the epidemiological and clinical research related to eating patterns and misconceptions of the public, the mechanisms of pharmacological effects of food, and related topics common to patient nutritional concerns.

Biochem 210 Course Title: Principles and Practice of Light Microscopy
Course Director: Orion Weiner
Days: Mondays
Time: 10:00 - 12:00 noon
Location: BH 212

Biochem 246 Developmental Biology
Course Director: Kevah Ashrafi
Days: Mondays & Wednesdays (April 2nd - May 2nd follow by minicourse)
Time: 2:00 - 3:00 PM
Location: RH Auditorium
First day: Monday, April 2, 2007
Website: http://anatomy.ucsf.edu/Pages/devbio/course.htm

BMS/ NS 214 Ethics and the Responsible Conduct of Research
Course Director: for BMS 214 – Kevin Shannon ; NS 214 – Scott Baraban

BMS 220 Basic & Clinical Aspects of Stem Cell Biology
Course Director: Susan Fisher
Website: http://www.ucsf.edu/bms/courses/bms220/index.html
Description: This course provides an overview of stem cell biology that integrates a description of basic concepts and technologies. Emphasis is on using stem cells to treat common human diseases such as diabetes, neurodegenerative disorders, and cancer and practical limitations that must be overcome to achieve the goal of widespread therapeutic use.

BP205 Introduction to Dynamical Systems
Course Director: Chris Voigt

CB 245 Cell Biology
Course Director: Robert Edwards
Website: http://cellbio.ucsf.edu
Description: The course will NOT survey all of cell biology but will rather focus on a few selected exciting topics in cell biology. Particular emphasis will be placed on emerging concepts concerning cell organization, structure and function and on how complex problems can be approached experimentally. There will be required reading each week (separate from the discussion papers). The lecturers will assume that students are familiar with basic biochemistry, genetics, and molecular biology through previous course work. If lacking background in these areas, students will be expected to do extra background reading to keep up with the pace of the lectures and/or attend review sessions by the TAs.

Chem 243 Chemical Biology
Course Director: Charles Craik
Days: Mondays, Weddnesdays, & Fridays
Description: Basics of chemical biology with a particular emphasis on understanding and manipulating molecular mechanisms of complex biochemical phenomena. Lectures address macromolecular structure, function, mechanisms, synthesis and metabolism applications.

Micro 202 Cell Biology / Molecular Mechanisms of Microbial Pathogenesis
Course Director: Joanne Engel
Website: http://www.ucsf.edu/micro/pathogenesis/course/materials.htm
Description: Micro 202/Cell Biology 202 is a graduate level course that comprehensively covers the molecular mechanisms of microbial pathogenesis, including bacteria, fungi, and protozoan parasites. It does not cover viruses. The course includes lectures covering bacterial physiology, host defense mechanisms, general principles of microbial pathogenesis, adhesion and invasion strategies, intracellular survival strategies, antibiotic resistance, bacterial toxins, fungal pathogenesis, parasite pathogenesis, biofilms, and quorum sensing.

NS 235 Neurobiology of Disease (this course is not offered every year)
Course Director: Bob Messing & Steve Finkbeiner
Website: http://www.neuroscience.ucsf.edu/neurograd/courses/courses.htm
Description: Lectures and student-led discussions on physiological and molecular bases of diseases such as Alzheimer's, Parkinson's, multiple sclerosis, epilepsy, autism, addiction, triple repeat and prion diseases.

NS 201C Genetics, Development, and Cell Biology of the Nervous System
Course Director: Herwig Baier
Website: http://www.neuroscience.ucsf.edu/neurograd/courses/courses.htm
Description: N201C introduces the students to genetic and cell biological approaches to the assembly and function of the nervous system. The first set of lectures will cover overarching principles of cellular neurobiology in the context of the developing nervous system, including signaling, cell adhesion, and cytoskeletal dynamics. Topics will include neurogenesis, axon guidance, dendrite formation, and synaptogenesis. The second set of lectures will cover forward and reverse genetic analyses of complex neurobiological processes, including brain patterning, neuroendocrine signaling, circadian rhythms, sensory processing, and behavior. Tutorials and review sessions will deepen the students' perspective of material presented in the lectures. Emphasis will be placed on an understanding of basic concepts, as well as an appreciation of the major questions that drive current research in these areas.

PC231 Principles of Macromolecular NMR Spectroscopy
Course Director: John Gross
Description: This course will introduce the underlying theory of modern NMR experiments that are commonly used to determine macromolecular structure and dynamics in solution. The objective is to prepare students for advanced studies that rely heavily on NMR methods. The course requires some familiarity with linear algebra and complex numbers. Familiarity with undergraduate level quantum mechanics will be helpful but is not required. All of the requisite mathematics and physics will be introduced during the first two weeks of instruction. The remainder of the course will cover: product operator formalism and applications to multidimensional NMR experiments; relaxation theory including applications for measuring backbone mobility in proteins, the Nuclear Overhauser Effect(NOE), chemical exchange, and transverse relaxation optimized spectroscopy (TROSY). The theory and practice of reintroducing residual anisotropic interactions in solution for measuring orientational restraints will also be discussed.