ECS 289A - Modeling Gene Regulation

Winter 2003 (CRN 60478)

Professor

    Vladimir Filkov
    Office: 3023 EU II
    Office Hours: Thursday, 2-4pm
    Email: filkov@cs.ucdavis.edu
    Phone: (530) 752-8393

Time and Place

Lecture:
       MW, 1:10 pm - 2:30 pm
       Bainer Hall, Room 1062

Discussion:
       MW, 2:30 pm - 3:00 pm
       Bainer Hall, Room 1062

Course Information:

    This is an introductory course in Computational Functional Genomics.
    In this course we will study computational methods for (1) analysis of
    microarray and other large-scale genomic data, (2) inferring regulatory
    relationships among genes, and (3) modeling gene networks.

    Final Grades!

    Syllabus

Lectures:

    Lecture Schedule Updated!

    Lecture 1, 1/6/03, Intro to Molecular Biology
    Lecture 2, 1/8/03, Biotechnologies
    Lecture 3, 1/13/03, CS for Biologists
    Lecture 4, 1/15/03, Microarray Data: Normalization and Differential Expression
    Lecture 5, 1/22/03, Classification Methods
    Lecture 6, 1/24/03, Clustering Methods
    Lectures 7 & 8, 1/27/03 & 1/29/03, Modeling and Gene Regulation
    Lecture 9, 2/3/03, Static Graph and Linear Models
    Lecture 10, 2/5/03, Boolean Network Models
    Lectures 11 & 12 , 2/10/03 & 2/12/03, Bayesian Network Models, part I and II
    Lecture 13 & 14, 2/19/03 & 2/24/03, Continuous Models
    Lecture 15, 2/26/03, Methods for Cis-region Analysis
    Lecture 16 & 17, 3/3/03 & 3/5/03, Data Integration
    Lecture 18, 3/10/03, Realistic Models of Gene Regulation

    List of papers on which the lectures are partially based can be found here.

Projects and presentations:

    Project List
    Student Presentations
    List of registered students (for group forming) as of 1/24/03

Text:

    No textbooks are required for this course.

Recommended Texts:

        Recombinant DNA, 2nd Edition, Watson, Gilman, Witkowski, Zoller
        Freeman and Co., 1992

        Microarrays For an Integrative Genomics, Kohane, Kho, Butte
        MIT Press, 2003

        DNA Microarrays and Gene Expression, Baldi and Hatfield
        Cambridge University Press, 2002

Related Courses:

    UC Davis:
        EAD 289D - Statistical Bioinformatics, WQ 2003 (David Rocke)

    Other Places:
        Gifford and Young's Computational Functional Genomics at MIT
        Ron Shamir's Analysis of Gene Expression Data, DNA Chips and Gene Networks, at Tel Aviv University

Computational Biology Resources on the Web:

    Link to recent papers on microarrays