BME 230: Computational Genomics

Spring Quarter, 2004

Time:	TuTh 2-3:45pm
Location:	Baskin Engineering, Rm 372
Course Link:	http://www.soe.ucsc.edu/classes/bme230/Spring04/

Instructors	Todd Lowe	Josh Stuart
Email	lowe@ soe.ucsc.edu	jstuart@ soe.ucsc.edu
Office	227 Sinsheimer Labs	129 Baskin Eng
Office Hours	Wed, Thur 4-5pm & by appt.	Mon 11-12 Wed 2-3

Textbooks

Biological Sequence Analysis by Durbin, Eddy, Krogh, & Mitchison

Bioinformatics: Sequence and Genome Analysis by David Mount

Grading

90%	Homework / Problem sets

10%	Final exam (take-home)

Syllabus

Date	Lecturer	Lecture	Topics	Reading	Assignments
March 30	Stuart Lowe	Course Overview Introduction: Genomes	Historical Perspective Genome Sequencing	Mount, Ch 1, 2 (pp 20-29)
April 1	Stuart	Pairwise Sequence Alignment	Dot Plots Dynamic Programming Global v. Local Scoring Matrices	Durbin, 2.1-2.4 Mount, Ch 3 (pp 51-96)	HW1: Getting to Know Your Genome
April 6	Kent	The 'Kent' Code Base	The browser staff CVS access to the code Object oriented programming in C Code conventions Strings, hashes etc Databases & Code Generators Biological Analysis Stuff
April 8	Lowe	BLAST	FASTA BLAST Family of Programs BLAST Statistics Significance of alignments EVD's Tweaking Searches	Durbin, 2.5-2.9 Mount, Ch 3 (pp. 96-137), Ch 7 (pp. 291-314)	HW2: Pairwise alignment, Adding your first Browser tracks
April 13	Stuart	Multiple Sequence Alignment	Aligning more than 2 sequences Finding regulatory motifs in unaligned sequences Gibbs sampling
April 15	Haussler	HMMs (Special thanks to Bernard Suh for scribing)	Principles of HMMs HMMs for gene finding	Durbin 3.
April 20	Haussler	HMMs (Special thanks to Bernard Suh for scribing)	Viterbi algorithm for most likely hidden state path Forward & backward algorithm for probability of a sequence Higher-order markov chains
April 22	Kent	Advanced Pairwise Alignment and Assembly (Special thanks to Bernard Suh for scribing)	Heuristics for finding homologous regions Chaining local alignments Genome mapping Genome assembly
April 27	Stuart	HMM learning	HMMs for pairwise & multiple sequence alignment Learning HMM parameters from observations Expectation-Maximization with Baum-Welch	Durbin 4-6
April 29	Lowe	RNA Genomics	RNA structure and function Specialized RNA Genefinders QRNA, MFOLD	Eddy, Nature Reviews RFAM paper	HW3: HMMs
May 4	Stuart	Heuristic Phylogenetic reconstruction	Trees Distance Methods: UPGMA, Neighbor-joining Parsimony Bootstrapping	Durbin, Ch 7 Mount, Ch 6
May 6	Stuart	Probabilistic Phylogenetic reconstruction	Likelihood Stationary markov processes Rate matrices Maximum Likelihood Felsenstein’s Post-order traversal Bootstrap revisited Maximum a posteriori Sampling posteriors	Durbin Ch. 8	HW4: Fun with ncRNAs
May 11	Lowe	RNA Genomics (cont) & Grammars		Durbin Ch. 9-10 Mount, Ch 5
May 13	Lowe Stuart	RNA Folding Probabilistic Phylogenetic reconstruction (cont)	Minimum free energy structures Mathews structure prediction using DynAlign	Durbin Ch 8
May 18	Siepel	Evolutionary reconstruction Part I (Cold Spring Harbor Talk) Part II	PhyloHMMs	Siepel & Haussler 2004
May 20	Lowe	Genome Analysis: "Other" Genome Components Comparative Genomics	Repeats (Repeat masker, RECON) Transposons, Structural features of genomes, Pseudogenes Distinguising orthologs from paralogs (gene trees) COGs	Mount, pp. 487-495 Mount, pp. 500-524	Hmwk #5: Phylogenetic reconstruction
May 25	Haussler	Whole-genome comparative genomics
May 28	Stuart	Joint-learning I	Probabilistic Graphical Models Bayesian Networks Conditional Independence Dynamic Bayesian Networks generalize HMMs	N Friedman 2004.
June 1	Stuart	Joint-learning II	Inference in Bayesian Networks Probabilistic relational models Identifying cis-regulatory elements	E Segal et al 2003.
June 3	Stuart	Human Sequence Variation	SNPs Haplotype inference Pharmacogenomics