Problems and Perspectives in Computational Molecular Biology

Cornell University
Spring 2002

The next presentation

Wednesday May 1
Edward Choi (Electrical Engineering)

(1) Correlated mutations contain information about protein-protein interaction. abstract, paper (2) Coevolving Protein Residues: Maximum Likelihood Identification and Relationship to Structure. abstract, paper (3) Co-evolution of Proteins with their Interaction Partners. abstract, paper

Future presentations (schedule your presentation)

Previous presentations and presentation files (Fall 2001)

Time and Place

Wednesdays 1:25 pm to 2:40 pm
Upson Hall 205

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), Doug Knipple (Entomology)
This course is cross-listed as CS 726 (Computer Science),  PB 726 (Plant Breeding) and BSCB 726 (Biometrics)



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 fall semester, 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 spring 2002 semester:

Suggested Papers

Structure analysis

Fold recognition, Threading, Structure prediction

Structure comparison (Dali, CE, Structal, Geometric hashing)

Automatic detection of domains

Structural/evolutionary profiles

Co-evolution, Protein-protein interaction

Gene networks, Whole-cell simulations


  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
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