CS598 SS Probabilistic Methods for Biological Sequence Analysis (Spring 2008)
Instructor: Saurabh Sinha
| Basic Information
| Resources |
- (01/15) Basic molecular biology: Proteins, DNA, Genes, Transcription, Translation, Transcriptional Regulation, Genome.
- (01/17, 01/22) Basic probability and statistics: Bayes rule, Random variables, Expectation and moments, Discrete distributions, Continuous distributions, Likelihood maximization, Hypothesis testing, Markov Chains, Sampling, Entropy. PDF Slides
- (01/22, 01/24) Bayesian Inference , priors, practical priors, likelihood. (BB 2.3, DEKM 11.1) Example: Single die model with counts (BB 3.1). Powerpoint slides by Jin Tae Kwak.
- (01/29) Parameter estimation: Gradient Descent (BB 4.3), Expectation Maximization (DEKM 11.6). Scribe: Charles. PDF slides
- (01/31) Sampling: MCMC & detail balance, Metropolis-Hastings, Gibbs sampling. (DEKM 11.4). Scribe: Thyago. Powerpoint slides
- (02/05, 02/07) Scoring functions (DEKM 2.2). N-W and S-W and affine gap penalties. Significance of scores: Bayesian and Extreme value distribution (DEKM 2.7, DEKM 11.1, EG 6.3, EG 2.11) Scribes: Reza, Chandra. Part 1 Powerpoint Part 2 PDF
- (02/12) Paper presentation (Ryan). "Evolutionary HMMs: a Bayesian approach to multiple alignment" - Holmes and Bruno. Bioinformatics 2001. PPT
- (02/14) No class
- (02/19) Paper presentation (Majid): 1. "MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution." - Keightley and Johnson. Genome Res. 2004. Powerpoint Slides 2. "ProbCons: Probabilistic consistency-based multiple sequence alignment." Do et al. Genome Res. 2005. Powerpoint Slides
- (03/11, 03/13) Evolution models (DEKM 8.1 - 8.3), calculating likelihood of alignment, reversibility, Metropolis algorithm for phylogenetic tree construction (DEKM 8.4), evolutionary models with gaps (DEKM 8.5). Scribe: Majid. PDF slides Powerpoint
- (03/25) Paper presentation (Charles): Combining phylogenetic and hidden Markov models in biosequence analysis. Siepel & Haussler. Proc. 7th Annual Int'l Conf. on Research in Computational Biology (RECOMB '03). PDF slides
- (03/27) Paper presentation (Jin Tae): Improved techniques for the identification of pseudogenes. Coin & Durbin. Bioinformatics, 20 Suppl 1:I94-I100, 2004. Powerpoint
- (04/01, 04/03, 04/08) Wright Fisher model, random drift, with selection only, with mutations only, coalescence theory. Neutral sequence. Scribes: Michael, Ryan. Lectures12-PDF Lecture3-PPT
- (04/10) PhyloGibbs: Siddharthan et al. Motif finding + Evolution (presented by instructor) Powerpoint
- (04/15) Indelign, Transducers for alignment: Alignment + Evolution (Presented by guest lecturer)
- (04/17) Honeybee paper: Sinha et al. : Motifs and Gene expression (Presented by guest lecturer)Powerpoint
- (04/22) Discussion of course projects, led by instructor.
- (04/24) MORPH and EMMA: Alignment + Motifs. (Presented by guest lecturer) Powerpoint
Parameter estimation. Good estimators. Why we like the MLE.