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Courses and course materials

Listed below are all course requirements and suggestions to optional helpful coursework for the Bioinformatics pathway in the Biological and Medical Informatics Graduate Program, including course name and number, quarters offered, units, and instructors.

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Required core courses

BMI 206: Statistical Methods of Bioinformatics

Fall
4 units
Katie Pollard

Syllabus

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.

BP 205A and B: Dynamical Systems

Fall/Winter
4 units each
Martin Kampmann in Fall, Steve Altschuler and Lani Wu 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Our systems biology class will have an unprecedented opportunity to make exciting scientific discoveries based on unpublished data.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 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.

BMI 219: Special Topics in Bioinformatics (mini courses)

Spring
3 units
Faculty

Each course offering focuses on the literature of a current important area of bioinformatics. 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.

BMI 221: Informatics rotations (3 rotations over 2 quarters)

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

Other requirements

BMI 220: Informatics Seminar (BBC Seminar Series)

Fall/winter/spring
1 unit
Thomas Ferrin

Selected topics by guest lecturers

BMI 223: Critical Topics in Biomedical Informatics

Fall/winter/spring
1 unit
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.

Biophysics 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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