7.89J | Fall 2010 | Graduate

Topics in Computational and Systems Biology


Course Meeting Times

Lectures: 1 session / week, 2 hours / session


First-year CSB Ph.D. student or permission of instructor.

Course Description

Topics in Computational and Systems Biology is a seminar based on research literature. Papers covered are selected to illustrate important problems and approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments. The course is intended for first-year Computational and Systems Biology (CSB) Ph.D. students.


Assigned readings will be from the primary literature. However, the following texts may be useful as references.

Zvelebil, Marketa, and Jeremy O. Baum. Understanding Bioinformatics. New York, NY: Garland Science, 2007. ISBN: 9780815340249.
(Note: this text is highly recommended for 7.91 also)

Alon, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall, 2006. ISBN: 9781584886426. (A newer book that’s worth a look — systems biology from a physicist’s perspective.)

Watson, J. D., T. A. Baker, S. P. Bell, A. Gann, M. Levine, and R. Losick. Molecular Biology of the Gene. 6th ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2007. ISBN: 9780805395921. (An updated version of the classic text.)

Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. Molecular Biology of the Cell. 5th ed. New York, NY: Garland Science, 2008. ISBN: 9780815341055. (Another classic text.)

Berg, J. M., J. L. Tymoczko, and L. Stryer. Biochemistry. 6th ed. New York, NY: W.H. Freeman, 2007. ISBN: 9780716787242. (Yet another classic.)

Branden, C., and J. Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Garland Pub., 1999. ISBN: 9780815323051. (A gentle but authoritative introduction to the topic.)


All class sessions will consist of discussions of research literature in computational and systems biology. Discussions will be led by course staff or jointly led by a designated student discussion leader and the staff. From time to time, there will be guest faculty discussion leaders. The papers have been chosen to represent important concepts, approaches, and ways of thinking in a wide range of subject areas within computational and systems biology, broadly defined, as well as a few papers outside of the field which have influenced the field.

One of the themes of this course is tracing the origins of different approaches to problems in computational and systems biology deriving from fields such as computer science, statistics, evolutionary biology, biochemistry, genetics, physics, and various branches of engineering. Another theme that will be explored is the relationship between technology (including both high-throughput experimental methods and computational/analytical methods) and discovery.

Homework and Grading

The largest component of students’ time will be spent reading, re-reading, thinking about and discussing the papers. Students are responsible for understanding the essential ideas, results, and methods used in each paper in as much depth as possible, which may require reading the supplementary information or background reference material. Students are encouraged to discuss the papers with other students in the course before class at the regularly scheduled time (and/or other times), to deepen their understanding.

Short (1-2 page) written assignments will be due for the course sessions noted in the calendar below. These assignments will usually, but not always, relate to the papers being discussed that week, and are intended to encourage critical thinking about the papers and to provide practice in scientific writing.

Grades will be assigned based on:

  1. Participation in class discussions
  2. Leadership of class discussions of assigned papers
  3. Homework assignments
  4. Attendance, which is required at all class sessions



Course organization/introduction (Burge)

Genomics and protein function (Burge)

2 Function of nucleic acid binding factors (Burge) Written assignment 1 due
3 Gene expression & medicine (Student-led) Written assignment 2 due
4 Evolutionary dynamics (Guest instructor: Jeff Gore, Biophysics, Systems Biology)  
5 Proofreading in biology (Student-led) Written assignment 3 due
6 Sequencing & translation (Guest instructor: Wendy Gilbert, Biology)  
7 Network motifs in biology (Student-led) Written assignment 4 due
8 Pathway modeling (Guest instructor: Bruce Tidor, Biological Engineering and Computer Science)  
9 Variability between cells (Student-led)  
10 Synthetic biology (Student-led)  
11 Metagenomics (Burge)  
12 Signal transduction (Guest instructor: Forest White, Biological Engineering)