The next presentation

Tuesday, December 3rd

Rommel Regis
Operations Research

(1) Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study abstract, paper (2) Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications abstract, paper

Time and Place

Tuesdays 2:55 pm to 4:10 pm
Rhodes Hall 484

This course is cross-listed as CS 726 (Computer Science),  PB 726 (Plant Breeding) and BSCB 726 (Biometrics)
1 credit, S/U only.
Prerequisites:  Permission of instructor.
The seminar is required from students of the Computational Molecular Biology Program.


Golan Yona (CS), Marty Wells (BSCB), Susan McCouch (PB)



This is a weekly seminar series discussing timely topics in computational molecular biology. The course addresses methodological approaches to sequence and structure analysis, function prediction, study of evolutionary relationships, and analysis of large biological system. Statistical and deterministic computational approaches will be covered and specific and detailed biological examples will be discussed.

After a successful year, we decided to continue in a similar format. In each topic we will select one or two representative papers that made significant advances in this field. The lectures will be given by faculty and students. The seminar is open to all from the life sciences, computational sciences, and the physical sciences. We will try to bridge these disciplines by pairing students/faculty from complementary backgrounds. The topics that will be covered in the fall 2002 semester:

Suggested Papers

Gene networks

session 1+2 - Modeling gene networks using Bayesian Networks

session 3+4 - Modeling gene networks using a system of differential equations

Pathways and cell simulation

session 6 - Pathways

session 7 - Cell simulation/networks

Phylogenetics, Comparative genomics

session 10 - Phylogenetics

session 12 - Phylogenetics/comparative genomics


  1. Waterman, M. S. (1995). Introduction to computational biology. Chapman & Hall, London.
  2. Setubal, J. C. & Meidanis, J. (1996). Introduction to computational molecular biology. PWS Publishing Co., Boston.
  3. Methods in Enzymology, vol 266 (1996). Edited by R. F. Doolittle.
  4. Durbin, Eddy, Krogh, Mitchison (1998). Biological sequence analysis.
  5. Baldi, P. & Brunak, S. (1998). Bioinformatics: the machine learning approach.
  6. Bioinformatics: Sequence, structure, and databanks. Edited by D. Higgins and W. Taylor. Oxford University Press.


Nature Structural Biology
Proceedings of the National Academy of Sciences
Protein Science
Proteins: Structure, Function, and Genetics
Protein Engineering
Nucleic Acids Research
Journal of Computational Biology
Pacific Symposium on Biocomputing
Trends in Biochemical Sciences
Molecular Microbiology

Web journals

Science's Next Wave
BioMedNet 'webzine'

Paper Search and Misc.

Biochemistry and Molecular Biology Journals
IDEAL homepage
PubMed (Medline)
NEC archive
e-Print archive
citation reports (impact factor of scientific journals)

Background reading

For a survey of the classic algorithms for sequence comparison and the statistics of sequence alignment (topics covered in the fall semester 2001) you can download one of the following documents Recommended books and book chapters on