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Courses and course materials

This information is currently being revised to reflect 2017 curriculum so please refer to the Graduate Program Administrators for current course information until further notice. 

Listed below are course requirements and suggestions to optional helpful coursework for the Biophysics Graduate Program, including course name and number, quarters offered, units, and instructors. 

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Required core courses

BP 204 A and B: Macromolecular Structure and Interactions

Fall/winter
4 units each
Robert Stroud

This course seeks to achieve a rigorous understanding of the physical principles of macromolecular structure and interactions, and the methods used to define the molecular basis for macromolecular interactions and their function in biology.

BP 205 A and B: Dynamical Systems

Fall/winter
4 units each
Joseph DeRisi and Hana El Samad

BP 205 A: This course teaches fundamentals of dissecting and understanding complex biological systems using didactic instruction in addition to practical lab experience in the context of a team-based project. For each project, students learn and use modern genomic and proteomic tools to characterize transcriptional circuits within a model organism.

BP 205 B: This course teaches the fundamentals of dissecting and understanding complex biological systems using didactic instruction in addition to practical laboratory experience in the context of a team-based project. For each project, students learn and use modern genomic and proteomic tools to characterize transcriptional circuits within a model organism. This course is a continuation of material introduced in 204 A.

BMI 206: Introduction to Bioinformatics

Fall
3 units
Patricia Babbitt

Broad survey of bioinformatics with accompanying assignments. Topics covered include genomics, database searching, family/super-family analysis, structural genomics, complex systems, genetic circuits, and protein-protein interactions.

BMI 203: Biocomputing Algorithms

Winter
3 units
Ajay Jain

Introduction to computational issues and methods used in the fields of bioinformatics and computational biology. This course emphasizes the implementation, analysis, and validation of methods. It is about attacking computational problems in biology and not the expert use of existing tools. Areas addressed include analytical thinking, problem decomposition, and algorithm design and implementation. Assignments will focus on the design and implementation of key bioinformatics algorithms.

BMI 207: Statistics

Winter
2 units
Jun Song

This course will introduce basic probability theory and fundamental ideas in statistics. It will cover probability distributions, random variables, Monte Carlo techniques, Markov processes, parametric and non-parametric statistical tests, and linear models. Examples will be drawn from genomics. Familiarity with linear algebra and calculus is assumed.

CHEM 241: Molecular Thermodynamics

Fall
5 units
Bo Huang

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.

BP 219: Special Topics in Biophysics (mini courses)

Spring
3 units each
Faculty

Each course offering focuses on the literature of a current important area of biophysics. Students read assigned papers critically before class and to present and discuss papers in class. Students write and present a brief research proposal based upon their readings. Topics in molecular, cellular, developmental, systems, and computation biology are covered in separate course offerings.

Other requirements

BP 215: Laboratory Rotations (3 rotations over 2 quarters)

Winter/spring (first year only)
2 units each rotation

BP 220: BBC Seminar Series

Fall/winter/spring
1 unit each
Selected topics by guest lecturers

BMI 223: Critical Topics in Biomedical Informatics (QBC Journal Club)

Fall/winter/spring
1 unit each
Thomas Ferrin

QBC Journal Club, critical review of published scientific papers from scholarly journals, including comprehension, analysis, and evaluation of published scientific data.

BMI 224: Graduate Research Opportunities Seminar (BBC Pizza Talks)

Fall/winter
1 unit
Thomas Ferrin

This course offers first-year students a series of weekly presentations on research interests of basic science faculty. The purpose is to acquaint new graduate students with research projects and opportunities in faculty laboratories.

BP 297: Special Study (NSF Workshop)

Fall
1 unit
Zev Gartner

First-year students meet weekly to hone their grant-writing skills with the objective of submitting a fellowship proposal to the National Science Foundation.

BIOCHEM 212:  Best Teaching Assistant Training Course (second-year students)

Fall
1 unit
Tracy Fulton

This course is intended to enrich and structure the teaching experience of graduate students teaching this year, and to provide a foundation for their development as teachers throughout their careers. It will introduce and demonstrate techniques, theories, and practices that underlie effective science teaching at the graduate and undergraduate levels. Participants practice and receive feedback on their use of new teaching techniques.

NEURO 214: Ethics and the Responsible Conduct of Research

Spring second year, eight sessions
1 unit
Faculty

Sessions cover data management, animals in research, human subjects in research, rules and etiquette of publications, procedures and rules of grants, corporate-academic interactions.

Optional online coursework

The following are suggestions from our students to other resources that can be helpful in this program:

  • For statistics: OpenIntro - free online course, free textbook
  • Class Central - a list of free online courses
  • Udacity - very engaging, about 3 to 5 hours per course

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