CS 262
Computational Genomics
Winter 2005


Textbooks

Durbin, Eddy, Krogh, Mitchison "Biological Sequence Analysis"

Gusfield "Algorithms on Strings, Trees, and Sequences"

  

Time & Place

Tuesdays & Thursdays 2:45-4:00, Skilling Auditorium

Teaching Staff

Instructor: Serafim Batzoglou

    Office Hours: Mondays, 3:00-5:00, Clark S266

    Extra office hours: Wednesday March 9, 4:00-5:30

TA: Michael Tung

    Office Hours: Tuesdays, 5:30-7:30pm, Gates B24B (in the basement)

Topics Covered

Old course material

Course Information: Description, Prerequisites, Requirements, Collaboration

Course Material and Schedule

  Topic and Powerpoint Presentation Reading Date Scribe Homeworks

1

Introduction: Biology Background

 

January 4

Edward Peng

 

2

Sequence Alignment--Dynamic Programming

Durbin Chapters 1, 2

Gusfield Chapters 11, 12.1, 12.2, 12.7

January 6

Marina Sirota

 

3

Cont'd--Linear-Space Alignment

              Four-Russian Algorithm

January 11

Marcela Miyazawa

 

4

Indexing-based Local Alignment Techniques

January 13

Shrikanth Shankar

Dan Woods

Homework 1 Out

5

Hidden Markov Models--Decoding & Evaluation

 

Durbin Chapters 3, 4

 

January 18

Ankit Garg

Ross Bayer

Yu Bai

 

6

                                          Evaluation & Learning

January 20

 

 

7

                                          Learning: EM / Baum-Welch

January 25

David Domyancic

 

8

Pair HMMs for Sequence Alignment

Durbin Chapter 4

January 27

Homework 1 Due

Homework 2 Out

9

DNA Sequencing

ARACHNE, Euler, Genome sizes, transposons, genomic mapping--mathematical analysis

February 1

 

 

10

DNA Sequencing and Fragment Assembly

February 3

 

 

11

Gene Recognition

Genscan, Twinscan, EasyGene, SLAM

Gusfield Chapter 5

February 8

William Lu
Mukesh Hira

 

12

Comparative Genomics-based Gene Recognition, & Suffix Trees

February 10

William Liu

Homework 2 Due

Homework 3 Out

13

Gene Regulation and Microarrays

Gene Regulation and Motif Finding references below

February 15

Vijay Chauhan

 

14

Regulatory Motif Finding

February 17

Kanishka Shrivastava

 

15

Motif Finding; Rapid Global Alignments

AVID, LAGAN

February 22

Aditya Krishnan

 

16

Chaining Local Alignments; Multiple Sequence Alignment

Chaining: Gusfield 13.3

Multiple Alignment: suggested reading Gusfield 14.1, 14.2, 14.5, 14.5, 14.10.1-14.10.2, and/or Durbin Chapter 6

February 24

Les Fletcher

Homework 3 Due

Homework 4 Out

17

Multiple Sequence Alignment

March 1

Mahesh Kumar Chhaparia
Shyam Maddali

 

18

Evolution and Phylogeny Tree Reconstruction

Durbin Chapters 7.1-7.4, 8.1-8.3

March 3

 

 

19

Evolution, Phylogeny, Some novel sequencing technologies

March 8

David Gleich

 

20

Guest Lectures

 

March 10

Katarzyna Bryc

Homework 4 Due


 

 

Papers and Other Reference Materials

 

The best tutorial on HMMs

A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition (PDF)

GeneFinding

Sequence Alignment

Fragment Assembly

Gene Regulation and Motif Finding