CS 262: Computational Genomics

CS 262
Computational Genomics
Winter 2006

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

Section (optional but useful): Fridays 3:15-4:05, Skilling 193 (starts Jan. 20)

Teaching Staff

Instructor: Serafim Batzoglou

Office Hours: Tuesdays 4:15-5:30 or by appt., Clark Center S266.

TAs:

George Asimenos

Office Hours: Wednesdays 4:00-6:00, Clark Center S260 (4:00-4:30 prioritized for SCPD).

Andreas Sundquist

Office Hours: Thursdays 12:30-2:30, Clark Center S260 (12:30-1:00 prioritized for SCPD).

Communication:

The class newsgroup is su.class.cs262. This can be used to form study groups amongst yourselves or for online discussions. This newsgroup is not monitored.

Email us at cs262-win0506-staff@lists.stanford.edu. We will respond within 24 hours.

During office hours the TAs can also be reached at (650) 725-6094 and through instant messaging on AIM/Yahoo/MSN with screen name cs262win06.

People auditing the class (NOT enrolled through AXESS): make sure you sign up on our guest list by sending "subscribe cs262-win0506-guests" to majordomo@lists.stanford.edu (students enrolled through AXESS are already set up for that).

Announcements:

1/10: If you are having problems finding people for teams, we recommend the following:

1) go to the class newsgroup (su.class.cs262) and post a message asking people to create a team, and maybe mention your qualifications.

2) if you're an SCDP student, at the CS262 SCPD online-classroom webpage, there are links on the right such as "Share Email Address With Other Students" and "Discussion Group" that you can use to post messages and interact with other SCPD students.

3) speak up at the beginning of the next class and you can recruit team members there.

Topics Covered

Old course material

Course Information: Description, Prerequisites, Requirements, Collaboration

Course Material and tentative Schedule

	Topic and Powerpoint Presentation	Reading	Date	Scribe	Homeworks
1	Introduction	"Antedisciplinary" Science	1/10	Olga Russakovsky
2	Sequence Alignment & Dynamic Programming Global alignment, local alignment, affine gaps	Durbin Chapters 1, 2 Gusfield Chapters 11, 12.1, 12.2	1/12	Shirley Wu
3	Sequence Alignment (cont'd) Linear-space alignment, BLAST	Durbin Chapters 1, 2 Gusfield Chapters 11, 12.1, 12.2	1/17	Ryo Shimizu	HW 1 out
4	Sequence Alignment wrapup, Hidden Markov Models--Definitions	Durbin Chapter 3, Gusfield Chapter 12.7	1/19	Wen Liu
Recitation 1, Introduction to Biology, by George Asimenos
5	HMMs (cont'd) Decoding, Evaluation & Learning	Durbin Chapter 3	1/24	Kyle Bruck
6	HMMs (cont'd) Baum-Welch	Durbin Chapter 3	1/26	Vignesh Ganapathy
7	Conditional Random Fields	CRF Paper, CRF Introduction	1/31	Andrew Schwartz	HW 1 due, HW 2 out
8	Pair HMMs and Protein Alignment	Durbin Chapter 4	2/2	Ben Handy
9	DNA Sequencing		2/7	Susan Tang
10	Fragment Assembly	(optional) references below	2/9	Julie Tung
11	Context Free Grammars and RNA structure	Durbin 9.3-9.6, 10.1-10.2	2/14	Anjalee Sujanani	HW 2 due, HW 3 out
12	Phylogeny trees and Multiple Sequence Alignment	Durbin 7.1-7.4, 8.1-8.3	2/16	Subie Patel
13	Phylogeny trees and Multiple Sequence Alignment	Durbin Chapter 6	2/21	Ari Greenberg
14	Genomic Alignment		2/23	Yangfan Wang
15	Chaining of Local alignments, Protein Profile HMMs and Classification Gene Recognition		2/28	Ilya Shlyakhter	HW 3 due, HW 4 out
16			3/2	Sean Kandel
17	Gene Regulation, Microarrays Motif Finding		3/7	Eric Willgohs
18	Gene Regulation, Microarrays Motif Finding		3/9	~~Luke Surazski~~
19	Protein Interaction Networks		3/14	Mike Polcari	HW 4 due
20	Protein Structure Prediction		3/16	Arjun Talwar

Papers and Other Reference Materials

General

"Antedisciplinary" Science: a commentary on the birth of computational biology

The best tutorial on HMMs

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

Conditional Random Fields

Semi-Markov Conditional Random Fields for Information Extraction (PDF)
Conditional Random Fields: An Introduction (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)