Topics in Computational and Systems Biology >> Content Detail



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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) PhD students.

Text Books

There are no required textbooks for this course. Assigned readings will be from the primary literature. However, the following texts may be useful as references.

Computational Biology

Amazon logo Mount, David. Bioinformatics: Sequence and Genome Analysis. 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2004. ISBN: 9780879696870. (This text is also highly recommended for 7.91.)

Systems Biology

Amazon logo Alon, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall, 2007. ISBN: 9781584886426. (A new book that's worth a look — systems biology from a physicist's perspective.)

Amazon logo 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.)

Amazon logo 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.)

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

Amazon logo 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.)

Structure of Class

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. On occasion, we will have guest discussion leaders who are members of the CSB Graduate Committee. The papers have been chosen to represent important concepts, approaches, and ways of thinking in a broad range of subject areas within computational and systems biology broadly defined. One of the themes of this year's course is to trace the origins of different approaches to problems in computational and systems biology deriving from fields such as computer science, statistics, developmental biology, biochemistry, genetics, physics, and various branches of engineering.


The largest component of your time in the course will be spent reading, re-reading, thinking about and discussing the papers. You 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. Discussing the papers with other students in the course before class at the regularly scheduled time (and/or other times) is a particularly good way to deepen your understanding. At the start of most course sessions, a short (1-2 page) written assignment will be due. 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. The written assignments must be completed individually. Duplicate or nearly identical homework from different students will not be accepted. Assignments should be typed, with double- or 1.5-line spacing, 12 pt. font and minimum 1" margins (may be printed double-sided). Pages should be numbered with your name and the date at the top of each page. These assignments will be graded by course staff.


No exams will be given.


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

Genomics and protein function

2Genomics and RNA functionAssignment 1 due
3Signal transductionAssignment 2 due
4Genetics of gene regulationAssignment 3 due
5Statistical approachesAssignment 4 due
6Gene expression and medicineAssignment 5 due
7Kinetics in biologyAssignment 6 due
8Protein structure and functionAssignment 7 due
9Devices and detectionAssignment 8 due
10Synthetic biologyAssignment 9 due
11Randomness in biologyAssignment 10 due
12Gene networksAssignment 11 due
13Computational and systems biologyAssignment 12 due


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