UW Computational Molecular Biology

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Program Requirements

To accommodate the significant diversity of backgrounds and goals of students in the CMB program, its requirements are deliberately flexible. In addition to the graduation requirements imposed by the student's host department and by the University of Washington Graduate School, the CMB program expects all students to complete the requirements described below. Students who fulfill these requirements will receive the CMB certificate.

As described more fully below, all CMB students will be required to complete the core CMB course, participate in the CMB journal club, attend the Combi seminar series, do at least one lab rotation, and complete a capstone project. Students will also be required to satisfy any remaining CMB prerequisites. These requirements are in addition to the Ph.D. requirements of the host department. Each participating department has established a "CMB track" for students in the program, with adjustments to the usual departmental requirements in order to allow the student time to participate in CMB activities.

Each student will choose a CMB advisor from among participating faculty, preferably during the first year. The CMB advisor may or may not be the thesis advisor. Usually the CMB advisor will be in the student's host department, but cross-disciplinary and co-advising arrangements are common and encouraged. The host department will be responsible for administering appropriate examinations and awarding the degree.

CMB Requirements:

  • The core required CMB course is Genome 541. This is a one-quarter overview course that is team taught by five CMB faculty members each year, typically during spring quarter. The course is arranged into two-week modules that cover a variety of topics in computational molecular biology. The specific topics vary annually but typically include molecular evolution, protein structure analysis, regulatory networks, etc.

  • One CMB elective, selected from the list below.

  • At least one 10-week lab rotation is required. For students without prior significant wet lab experience, this rotation should involve exposure to wet lab work, either involving actual experiments in the lab or a "shadowing" component where the student observes lab work and then helps to analyze the resulting data. Rotations may be co-mentored by a wet-lab biologist together with a CMB faculty member. Students who need help identifying possible rotations may contact Bill Noble for assistance.

  • The CMB journal club is CSE 590C, a weekly seminar on Readings and Research in Computational Biology offered every autumn, winter, and spring. Regular participation is required of all CMB students. In this seminar, senior students mentor beginning students by working together on presentations.

  • The CMB seminar series is the weekly COMBI seminar, offered every autumn and winter. This series features research presentations by outside speakers as well as by participating CMB faculty. The latter is a primary mechanism by which students become familiar with the available potential research areas prior to choosing a thesis advisor. Regular participation is required of all CMB students.

  • All students complete a capstone project under the supervision of CMB faculty and present the project to the CMB community. This presentation usually takes place at the annual CMB Symposium. The capstone project may be a component of your thesis research or a separate project if you choose.

Elective Courses:

The following list summarizes a wide variety of courses of potential interest to CMB students.

Note that not all courses are offered every year and that some have enrollment limitations. For more detailed information on individual courses, consult the University time schedule, individual course web pages, and/or the instructor.

Applied Mathematics

AMATH 522:       Computational Modeling of Biological Systems

AMATH 523:       Mathematical Analysis in Biology and Medicine

AMATH 531:       Mathematical Theory of Cellular Dynamics

AMATH 532:       Mathematics of Genome Analysis and Molecular Modeling


BIOC 530: Advanced Biochemistry


BIOEN 423/CSE 486/EE 423 Introduction to Synthetic Biology

BIOEN 424/CSE 487/EE 424 Advanced Systems and Synthetic Biology

BIOEN 488/588 Computational Protein Design

BIOEN 523/CSE 586/EE 523 Introduction to Synthetic Biology

BIOEN 524/CSE 587/EE 524 Advanced Systems and Synthetic Biology

Computer Science and Engineering

CSE 427: Computational Biology

CSE 428: Computational Biology Capstone

CSE 527: Computational Biology

CSE 486/BIOEN 423/EE 423 Introduction to Synthetic Biology

CSE 487/BIOEN 424/EE 424 Advanced Systems and Synthetic Biology

CSE 586/BIOEN 523/EE 523 Introduction to Synthetic Biology

CSE 587/BIOEN 524/EE 524 Advanced Systems and Synthetic Biology

Genome Sciences

GENOME 540 Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis

GENOME 562 Population Genetics

GENOME 570 Phylogenetic Inference

GENOME 590 Population Genetics Seminar


CONJ 548: Modeling proteins and proteomes

CONJ 549: Microbial Population Biology

Statistical Genetics core courses, including the following:

BIOSTAT/STAT 550 Statistical Genetics I: Mendelian Traits

BIOSTAT/STAT 551 Statistical Genetics II: Quantitative Traits

BIOSTAT/STAT 552 Statistical Genetics III: Design and Analysis in Medical Genetics Studies