Research Seminar in Computational Biology (Spring 2001)

This is a seminar-style course on current research topics in computational biology, intended for students with an active interest in the subject. In consultation with the faculty, each student will read one or more research papers and make a class presentation. Each presentation will be the starting point for a group discussion of research problems. Students will be encouraged to undertake individual or group projects stemming from these discussions. Possible subject areas include the analysis of gene expression and regulatory pathways, comparative genomics, phylogeny, sequencing strategies, protein motif discovery and protein classification.

Course Number: The course can be taken as either Math 290, Section 9 (Course Control No. 55164) or CS 294-2 (Course Control No. 26779).

Instructors:Lior Pachter and Richard Karp

Units: 2

Class Meetings: One meeting per week, for up to 2 hours.

Place and Time: Wednesdays 11-1pm, 939 Evans

Suggested topics and papers

Schedule of Talks:

January 24: Richard Karp, Universal DNA Tag Systems: A combinatorial Design Scheme
January 31: Jane Fridlyand, Comparison of discrimination methods for the classification of tumors using gene expression data
February 7: Lior Pachter, HMMs, Alignment and Gene Finding
February 14: Eric Xing, Feature selection for high-dimensional genomic microarray data in classification and clustering.
February 21: Pete Klosterman, Limitations of using secondary structure to detect functional noncoding RNAs
February 28: Yu Liu, Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines
March 7: Biao Xing, Scoring Genes for Relevance
March 14: David Matters, Modeling of Regulatory Networks
March 21: Dmitriy Ryaboy, Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices
April 4: Ruchira Datta, Using Bayesian Networks to Analyze Gene Expression Data
April 11: Clint Ryan, Prediction of common secondary structures of RNAs: a genetic algorithm approach (The RNAGA program)
April 18: Jaimyoung Kwon, Hunting for transcription factor binding sites: a review and a proposal
April 25: Ashwin Seshia, The human genome (Nature - Feb. 15, 2001, Science - Feb. 16, 2001) - Power point presentation
May 2: Lior Pachter, Sequence assembly and the EULER assembly program