CS 178: Introduction to Computational Molecular Biology

Instructor: Jacques Cohen
e-mail: jc@cs.brandeis
Office Hours: 2:00pm to 3:00pm Mondays and Wednesdays or by appointment

TA: Sam Blasiak
E-mail: blasiak@brandeis
Office Hours: 12:00pm to 1:00pm Tuesdays and Fridays or by appointment (in the Berrypatch)

Meets on Mondays and Wednesdays from 3:40pm to 5:00pm

Tentative Schedule

Class Party Pictures
Midterm Solutions

Highly Recommended
A fun introduction to molecular biology
  • L. Gonick and G. Wheelis, A Cartoon Guide to Genetics, Harper Perennial, Latest Edition.
Systems Biology recommended URLs
Programming in Python
Books on reserve at the Science Library
  • N. C. Jones, and P. A. Pevzner, 2004. An Introduction to Bioinformatics Algorithms, MIT Press, Cambridge, Mass.
  • L. Gonick and G. Wheelis, A Cartoon Guide to Genetics, Harper Perennial, Latest Edition.
  • L. Gonick and G. Wycoff, A Cartoon Guide to Statistics, Harper Perennial, 1994.
  • Andreas Wagner, Robustness and Evolvability in Living Systems, Princeton University Press, 2005.
  • J. Meidanis and J. Setubal, Introduction to Computational Molecular Biology, PWS Publishing, 1997.
  • R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Biological Sequence Analysis, Cambridge University Press, 1998.
  • D. Krane, and M. Raymer, M. 2003. Fundamental Concepts of BioInformatics. Benjamin Cummings, 2003.
  • Eberhard O. Voit. Computational Analysis of Biochemical Systems. Cambridge University Press 2000.
  • D.W. Mount Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Press: Cold Spring Harbor, NY, latest edition
  • D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, 1997
  • A. Baxevanis, and B.F.F Ouellette, (eds.) Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. New York: Wiley, latest edition
  • J. Pevsner, Bioinformatics and Functional Genomics, Wiley-Liss, 2003.
  • R. Thomas, R. d'Ari, Biological Feedback, CRC Press, 1990.
  • Felsenstein, J.. Inferring Phylogenies, Sinauer Associates. 2003
  • R. A. Dwyer, Genomic Perl: From Bioinformatics Basics to Working Code, Cambridge, University Press, 2003
Interesting URL's for educational purposes
Research Papers URL's
Regulatory Network Simulation Programs