CS 262: Computational Genomics

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	Genscan, Twinscan, EasyGene, SLAM Gusfield Chapter 5	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	Gene Regulation and Motif Finding references below	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	Durbin Chapters 7.1-7.4, 8.1-8.3	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

Genscan: Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance (PDF)
SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model (PDF)
Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
Integrating Genomic Homology into Gene Structure Prediction (PDF)
Christopher Burge's PhD Thesis (PS) (PDF)

Sequence Alignment

LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (PDF)
Glocal Alignment: Finding Rearrangements During Alignment (PDF)
AVID: A Global Alignment Program (PDF)
BLAT: The BLAST-Like Local Alignment Tool (PDF)
Gapped BLAST and PHI-BLAST (PDF)
Pattern Hunter: Faster and more sensitive homology search (PDF)
The estimation of statistical parameters for local alignment score distributions (PDF)
T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment (PDF)

Fragment Assembly

Genome Sizes (HTML)
Transposons (HTML)
Genomic mapping, mathematical analysis (PDF, PDF)
ARACHNE: A Whole-Genome Shotgun Assembler (PDF)
ARACHNE 2: Whole-genome sequence assembly for Mammalian Genomes (PDF)
The Eulerian path approach to DNA fragment assembly (PDF)

Gene Regulation and Motif Finding

Transcriptional Regulation of the Stem Cell Leukemia Gene (PDF)
Exploring the conditional co-regulation of yeast gene expression through fuzzy k-means clustering (PDF)
Systematic determination of genetic network architecture (PDF)
Identifying DNA and Protein Patterns with Statistically Significant Alignments of Multiple Sequences (PDF)
Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment (PDF)