Systems Biology
Faculty of the Committee on Higher Degrees in Systems Biology
Pamela A. Silver, Professor of Systems Biology (Medical School) (Chair, Director of Graduate Studies)
Michael P. Brenner, Glover Professor of Applied Mathematics and Applied Physics
Marc W. Kirschner, Carl W. Walter Professor of Systems Biology (Medical School)
Timothy J. Mitchison, Hasib Sabbagh Professor of Systems Biology (Medical School)
Erin K. OShea, Professor of Molecular and Cellular Biology and of Chemistry and Chemical Biology (on leave 2009-10)
Systems Biology students should consult course listings from the departments of Biological Sciences, Biophysics, Chemistry, the School of Engineering and Applied Sciences (Applied Mathematics, Applied Physics, Computer Sciences, Engineering Sciences), and the School of Medical Sciences.
Cross-Listed Courses for Undergraduates and Graduates
Applied Mathematics 115. Mathematical Modeling
[Applied Mathematics 147. Nonlinear Dynamical Systems]
Biophysics 170. Quantitative Genomics
Biophysics 242r. Special Topics in Biophysics
Chemistry 60. Foundations of Physical Chemistry
Chemistry 161. Statistical Thermodynamics
Chemistry 163. Frontiers in Biophysics
Computer Science 181. Intelligent Machines: Perception, Learning, and Uncertainty
Engineering Sciences 145. Physiological Systems Analysis
Engineering Sciences 156. Signals and Systems
Mathematics 153. Mathematical Biology-Evolutionary Dynamics
MCB 111. Mathematics in Biology
[*MCB 173. Optical Imaging in the Biological Sciences]
[MCB 195. Foundations of Systems Biology and Biological Engineering]
[OEB 181. Systematics]
OEB 192. Microbial Evolution
Physics 181. Statistical Mechanics and Thermodynamics
Primarily for Graduates
Systems Biology 200. A Systems Approach to Biology
Catalog Number: 8701
Walter Fontana (Medical School), Jeremy M. Gunawardena (Medical School), and Johan M. Paulsson (Medical School)
Half course (fall term). Tu., Th., 10-11:30, and a weekly section to be arranged. EXAM GROUP: 12, 13
How do the interactions of molecules and cells allow for the complex behavior of organisms? Quantitative techniques and modeling can shed light on this question. Introduces theory and computation in the context of biological problems.
Note: The course will include an introduction to the use of MATLAB for model-building.
Prerequisite: Mathematics 1b required, and MCB 54 or MCB 56 recommended.
Systems Biology 201. Biology of Animals: genetics, genomics, development and evolution
Catalog Number: 5148
Angela DePace (Medical School), Marc W. Kirschner (Medical School), and Sean G. Megason (Medical School)
Half course (spring term). Tu., Th., 2–3:30. EXAM GROUP: 16, 17
A paper-based discussion course focusing on genetics, genomics and systems biology approaches to the development, physiology and evolution of animals. Students will gain practice in critically evaluating data from genetics and genomics experiments, presenting the conclusions of a paper, and leading discussions on the impact of the work. We will also discuss areas where quantitative techniques have not yet been successful, and ask why not. At the end of the course, students will develop and present proposals for how to bring quantitative approaches to bear on specific biological questions.
[Systems Biology 202. Synthetic Biology] - (New Course)
Catalog Number: 30087
Pamela A. Silver (Medical School) and Jack Szostak (Medical School)
Half course (spring term). Hours to be arranged.
This course will cover the design and synthesis of new genetic circuits, construction of novel genomes and the chemical basis for building self-replicating systems.
Note: Expected to be given in 2010–11. Weekly lectures with discussion sections and outside speakers
Systems Biology 203. Fundamentals of Quantitative and Systems Biology - (New Course)
Catalog Number: 83523
Peter K. Sorger (Medical School) and Timothy J. Mitchison (Medical School)
Half course (fall term). M., W., F., 10:30–12. EXAM GROUP: 3, 4
Cell tissue biology from molecular, dynamical systems and information theoretic perspectives. Approaches to modeling biological pathways, collecting quantitative data and deriving mechanistic insight will be presented through weekly lectures, workshops and literature analysis.
Cross-Listed Courses Primarily for Graduates
BCMP 200. Molecular Biology
BCMP 201. Proteins: Structure, Function and Catalysis
BCMP 207. Molecular Approaches to Drug Action, Discovery, and Design
[Biophysics 204. Structural Biology From Molecules to Cells]
Biophysics 205. Computational and Functional Genomics
Biophysics 242r. Special Topics in Biophysics
Cell Biology 201. Molecular Biology of the Cell
Chemical Biology 2100. Introduction to Chemical Biology I
*Engineering Sciences 222. Advanced Cellular Engineering
Genetics 201. Principles of Genetics
Mathematics 243 (formerly Mathematics 234). Evolutionary Dynamics
[MCB 212. Topics in Biophysics]
[Microbiology 200. Molecular Microbiology and Pathogenesis]
Graduate Courses of Reading and Research
*Systems Biology 300hf. Introduction to Systems Biology Research
Catalog Number: 4103
Pamela A. Silver (Medical School) 1595
Half course (throughout the year). M., 6–7:30 p.m.
Introductory lectures introduce the research areas of current program faculty in systems biology.
[*Systems Biology 301. Special Topics in Systems Biology]
Catalog Number: 8834
Instructor to be determined
Half course (fall term). Hours to be arranged.
An exploration of new directions for the field of systems biology. We will identify major unsolved questions in biology and discuss possible new approaches to these questions offered by systems biology.
Note: Expected to be given in 2010–11.
*Systems Biology 350. Systems Biology Research
Catalog Number: 8370
Pamela A. Silver (Medical School) 1595 and members of the Committee
Upper level Systems Biology students register for this course when they permanently join a lab. Students should register under the supervising PI.
*Systems Biology 399. Introduction to Systems Biology: Rotations
Catalog Number: 5863
Pamela A. Silver (Medical School) 1595
Half course (fall term; repeated spring term). Hours to be arranged.
The course will introduce the research areas of faculty performing research in systems biology. Intended for Systems Biology lab rotations.
Cross-Listed Graduate Courses of Reading and Research
*Computer Science 307,308. Biologically-Inspired Multi-Agent Systems, Distributed Systems, and Computational Biology