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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
James Fraser and John Gross in Fall, Robert Stroud and Oren Rosenberg in Winter

BP 204A: This is a team-based class where students work in small groups develop their own analysis of real data that they have collected. The course will function in three modules. In module 1 “data collection” students collect either NMR, negative stain EM, and X-ray crystallographic data. In module  2 “fundamentals of analysis”,  students will are mixed into new groups for lectures and hands-on computational tutorials. These lessons emphasize connections to both the molecular interpretations and the fundamental physical principles that generated the data. In module 3 “integrative structural biology”, the students will finalize their analysis and lectures will emphasize computational frameworks for integrative structural modeling.  Finally, each group will present to their findings to the class and course faculty. 

BP 204B: In this course, we will pursue a qualitative and quantitative understanding of the physical basis of macromolecular function.  We will examine: the nature and quantification of the forces that drive macromolecular interactions, both intramolecular (macromolecular folding), and with other proteins and ligands; diffusion of macromolecules; the structural underpinnings of the kinetics and thermodynamics of macromolecular reactions; and the physical basis of important biophysical methods.  We will examine the distinctions for macromolecules residing in lipid bilayers.  The classwork will be mostly interactive with a weekly lecture that informs in class problem solving and discussion of relevant classic and current literature.

BP 205 A and B: Dynamical Systems

Fall/winter
4 units each
Martin Kampmann in Fall, Steve Altschuler, Lani Wu and Hani Goodarzi in Winter

BP 205 A: Physical Underpinnings of Biological Systems (PUBS)

This course will teach the 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 will learn and use cutting-edge experimental and computational tools to characterize protein structure and function within a model organism.

BP 205 B: Dynamical Systems Modeling (Required only for those with a designated emphasis in Complex Biological Systems, elective for others)

Our re-imagined 2017 systems biology class will tackle the challenge of identifying governing principles of an immensely complex and interconnected cellular signaling hub. The class will self-organize into teams that develop strategies to identify, analyze and model interconnections and consequences of this hub organization. Diverse data sets will include—but not be limited to—high-content image based screens, protein-protein interaction and drug response profiles of perturbations to the hub and its partners. The 10-week class will be organized by: 

1:  Literature review and proposals

2-6: Data acquisition and analysis

7-8: Integration and validation of results

9-10: Draft of manuscript and presentations.

Our systems biology class will have an unprecedented opportunity to make exciting scientific discoveries based on unpublished data.

BMI 206: Statistical Methods for Bioinformatics

Fall
3 units
Katie Pollard

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
Ryan Hernandez

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.

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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