Biophysics 101:  Genomics and Computational Biology

George Church
Tim Chen
Tao Wei
Bob Freeman

Teaching fellows and problem set consultants:
Daniel Janse
Abby McGuire
Jeremy Edwards

Harvard Computational Biology Studies
Program in Biological and Biomedical Sciences (BBS)
Harvard-MIT Division of Health Sciences and Technology (HST)

Meeting Times: 11:30 AM to 1:00 PM Tuesdays and Thursdays.
Tuesdays meet in the Harvard Science Center room 309 ( One Oxford Street just north of Harvard Yard, Cambridge Campus).
Thursdays meet in Warren Alpert Building Seminar room 561 (200 Longwood Ave. HMS campus).
Harvard Cambridge (Quincy Street) to HMS (Longwood Ave.) Shuttle bus schedule

Open to upper level undergraduates, and all graduate students.
Course description:   This course will assess the relationships between sequence, structure and function in complex biological networks as well as progress in realistic modeling of quantitative, comprehensive functional-genomics analyses.  Exercises will include algorithmic, statistical, database, and simulation approaches and practical applications to biotechnology, drug discovery and genetic engineering.  Future opportunities and current limitations will be critically assessed.  Problem sets and a course project will emphasize hands-on analyses using these concepts. 
The prerequisite is enthusiastic interest in molecular biology, statistics, and computing.

Schedule and topics for Fall 1999:

Date    	Topics

Tue Sep 21 Given the building blocks of life & computers, then what? Thu Sep 23 Metrics, models, and molecular databases: How and Why? Tue Sep 28 High-level statistics, database, and programming tools Thu Sep 30 Genome sequencing: new methods and results Tue Oct 5 Comparative genomics: Gene-finding and pathways Thu Oct 7 3D homology modeling, molecular dynamics ... but function? Tue Oct 12 Hidden Markov Models: probabilistic protein interaction motifs Thu Oct 14 Regulatory networks: DNA chip/microarray analyses Tue Oct 19 Hierarchical clustering (e.g. using RNA levels) Thu Oct 21 Regulatory networks: DNA & RNA interaction motifs Tue Oct 26 Dynamic programming, blast Thu Oct 28 multiple sequence alignment algorithms Tue Nov 2 Mass spectrometric quantitation of proteins and metabolites Thu Nov 4 Metabolic network flux models: Differential equation & optimization methods Tue Nov 9 Signal transduction and cell interactions Tue Nov 16 What chemistry &biology can do for computing: self-assembly, genetic algorithms, neural nets Thu Nov 18 Information theory, simulated annealing and Monte Carlo Tue Nov 23 Darwinian organismal population growth Tue Nov 30 Association of polymorphisms with phenotypes Thu Dec 2 Drug Discovery and Design Tue Dec 7 Phylogenetics and evolution of function Thu Dec 9 Projects Tue Dec 14 Projects Thu Dec 16 Projects and course summary

Below are two texts for background reference (limited parts of these will be covered in this course). Recent articles will constitute the main readings.

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
by R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Cambridge University Press, 1998.

Understanding the Control of Metabolism
by David Fell Frontiers in Metabolism Ser. ; No. 2, 1997

Links to resources:
Countway Library of Medicine electronic Journals
HollisPlus Electronic Journals
PubMed Journal searching
Genome and proteome searches
HMS Research Computing Center
Center for Genomics Research
Lipper Center for Computational Genetics

Updated 15-Sep-1999 (original page 7-Apr-1999), email: