CS68 Bioinformatics

Announcements

The Final Exam will be in Science Center 181 on December 9 from 12:45pm-3:15pm. There will be a review session on Sunday, December 7 from 3-5pm in the Robot Lab.
Final project reports and file submissions are due Friday, December 19 at noon. Presentations will be during the Final Exam time (December 16 from 2pm-5pm).

This syllabus is a living document; please be aware that many elements on this page will change throughout the semester, including the course schedule. It is the student's responsibility to review this page periodically for updates.

I value any and all student feedback. If you would like to provide anonymous course feedback, use this submission form here. Please be constructive in any comments so that I can adjust the course as best possible.

Schedule

For the reading assignments the section numbers are inclusive, so "1.1-1.1.2" means you should read all the sections from 1.1 up to and including section 1.1.2. This is a tentative schedule, it will change as we go.

WEEK	DATE	ANNOUNCEMENTS	TOPIC & READING	LAB
1	Sep 02		Introduction to Bioinformatics; Molecular Biology Required: Life and Its Molecules: A Brief Introduction by Lawrence Hunter Additional Resources: Primer on Molecular Genetics from the US DOE Molecular Biology for Computer Scientists by Lawrence Hunter	Lab 0 - Central Dogma and Databases
	Sep 04
2	Sep 09		Pairwise Sequence Alignment - Detecting homology Durbin et al., 2.1-2.3 Gapped BLAST and PSI-BLAST by Altschul et al., 1997 Recommended: Durbin et al., The rest of Chapter 2	Lab 1 - Dynamic Programming and Pairwise Sequence Alignment
	Sep 11	Drop/Add ends (Sep 12)
3	Sep 16		Multiple Sequence Alignment Durbin et al., 6-6.4
	Sep 18
4	Sep 23		Phylogentic Trees - Inferring evolutionary relationships Durbin et al., Chapter 7	Lab 2 - Multiple Sequence Alignment
	Sep 25
5	Sep 30
	Oct 02
6	Oct 07		Functional Genomics and Clustering Algorithms - Gene Expression Data Interactive animation of microarray experiments from the University of Utah Exploring the new world of the genome with DNA microarrays by Patrick Brown and David Botstein RNA-Seq: a revolutionary tool for transcriptomes by Zhang Wong, Mark Gerstein, and Michael Snyder Cluster Analysis for Gene Expression Data: A Survey by Daxin Jiang, Chun Tang, and Aidong Zhang	Lab 3 - Inferring the Tree of Life
	Oct 09
	Oct 14	Fall break
	Oct 16
7	Oct 20	Midterm exam - in lab 10/20
	Oct 21		More Clustering Chapter 16: Flat Clustering from Introduction to Information Retrieval by C. Manning, P. Raghavan, and H. Schutze Chapter 17: Hierarchical Clustering from Introduction to Information Retrieval by C. Manning, P. Raghavan, and H. Schutze	Project Proposals
	Oct 23
8	Oct 28		Supervised Machine Learning Using Machine Learning to Design and Interpret Gene-Expression Microarrays by M. Molla, M. Waddell, D. Page and J. Shavlik, in AI Magazine, 2004 A Few Useful Things to Know About Machine Learning by Pedro Domingos in Communications of the ACM, 2012 Decision Trees	Lab 4 - Clustering Gene Expressions
	Oct 30
9	Nov 04			Lab 5 - Classifying Leukemia Patients
	Nov 06	Last day to declare CR/NC or withdraw (Nov 07)
10	Nov 11		Probabilistic Sequence Models - Markov Models Durbin et al., Chapter 1 Durbin et al., Chapter 11 (at a high level) Durbin et al., Chapter 3.1-3.2	(Optional)Practice problems for HMMs
	Nov 13
11	Nov 18
	Nov 20		Hidden Markov Models and applications Durbin et al., Chapter 3.3-3.5 Durbin et al., Chapter 5 Profile hidden Markov models by Sean R. Eddy	Final Project
12	Nov 25
	Nov 27	Thanksgiving
13	Dec 02		Hidden Markov Models and applications Durbin et al., Chapter 3.3-3.5 Durbin et al., Chapter 5 Profile hidden Markov models by Sean R. Eddy (continued)
	Dec 04		Protein Structure Prediction Gamers Unravel the Secret Life of Protein, Wired Magazine Protein Structure Prediction Using Rosetta by Carol A. Rohl, Charlie E.M. Strauss, Kira M.S. Misura, and David Baker in Methods in Enzymology, 2004. Global Optimum Protein Threading with Gapped Alignment and Empirical Pair Score Functions by Richard H. Lathrop and Temple F. Smith in Journal of Molecular Biology, 1996. Protein structure prediction: when is it useful? by Yang Zhang in Current Opinion in Structural Biology, 2009.
	Dec 09	Final exam - 12:45pm - 3:15pm in SC 181
	Dec 16	Project Presentations 2-5pm in SC 183

CS68 - BioinformaticsFall 2014

Announcements

Schedule

CS68 - Bioinformatics
Fall 2014