Introduction

• (01/15) Basic molecular biology: Proteins, DNA, Genes, Transcription, Translation, Transcriptional Regulation, Genome.   Powerpoint Slides
• (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

Sequence Alignment

• (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

Motif Finding

• (02/21) Paper presentation (Instructor) : "A statistical method for finding transcription factor binding sites." - Sinha and Tompa, ISMB 2000. PostScript Powerpoint Slides
• (02/26) Paper presentation (Michael): Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment - Lawrence et al. Science 1993. PDF Slides
• (02/28) Paper presentation (Chandra): Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics - Nimwegen et al. PNAS 2002. Powerpoint slides

Module Finding

• (03/04) Paper presentation (Reza): A probabilistic method to detect regulatory modules. Sinha et al. Bioinformatics 2003. PDF notes from presentation
• (03/06) Paper presentation (Thyago): CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.- Zhou & Wong. PNAS 2004. PDF slides Powerpoint

Evolution

• (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

Population genetics

• (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

Heterogeneous data

• (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

Final lecture