BCB 568
Tues, Thur 9:30a-10:50a, 1424 MBB
| DAY | DATE | CHAPTER | TOPIC | LECTURER |
| Tues | Jan 12 | 1.1 | Orientation Statistical sequence models | Volker Brendel |
| Thur | Jan 14 | 1.2 | Calculation of pattern probabilities | Volker Brendel |
| Tues | Jan 19 | 2.1 | Markov Models for biomolecular sequence analysis Homework 1 (due Jan 26) Solution | Volker Brendel |
| Thur | Jan 21 | 2.2 | Applications of Markov Models in biomolecular sequence analysis Papers: Borodovsky1993; Kleffe1996 Further studies: Statistics of Exceptional Words | Volker Brendel |
| Tues | Jan 26 | 2.3 | Comments on sequence models and model fitting Homework 2 (due Feb 2) Solution | Volker Brendel |
| Thur | Jan 28 | 3.1 | Introduction to Hidden Markov Models | Volker Brendel |
| Tues | Feb 2 | 3.2 | Algorithms for Hidden Markov Models Homework 3 (due Feb 4) Solution Further reading: Rabiner's 1989 Tutorial | Volker Brendel |
| Thur | Feb 4 | Midterm I Super Solver's Solutions | Instructors | |
| Tues | Feb 9 | 3.3 | Applications of Genome Informatics: PlantGDB | Jon Duvick |
| Thur | Feb 11 | 3.4 | Applications of Hidden Markov Models: protein motifs; eukaryotic gene structure models Further reading: Profile Hidden Markov Models; Prediction of complete gene structures in human genomic DNA Exercise 1 (and solution) | Volker Brendel |
| Tues | Feb 16 | 4.1 | Parameter estimation for Markov Models in sequence ananlysis: Expectation Maximization see Lecture notes on Expectation Maximization Further reading: The Expectation Maximization Algorithm: A short tutorial; by Sean Borman Not covered in class: Interpolated Markov Models (Lecture Notes in Bioinformatics 4463:394) Homework 4 (due Feb 23) Solution | Volker Brendel |
| Thur | Feb 18 | 4.2 | Sequence analysis with scores: motivation and theory Papers: PNAS 87:2264; Science 257:39 | Volker Brendel |
| Tues | Feb 23 | 4.3 | Sequence analysis with scores: applications Amino acid substitution scoring matrices (BLOSUM matrices) Homework 5 (due March 2) Solution | Volker Brendel |
| Thur | Feb 25 | 5.1 | Case study of genome informatics modeling: Splice site prediction in plants Papers: Plant Mol. Biol. 36:573; Nucl. Acids Res. 24:4709 | Volker Brendel |
| Tues | Mar 2 | 5.2 | Case study continued: From splice site prediction to gene structure prediction by spliced alignment Papers: Nucl. Acids Res. 26:4748; Bioinformatics 16:203; J. Mol. Biol. 297:1075 | Volker Brendel |
| Thur | Mar 4 | 6.1 | Introduction to molecular phylogeny and molecular evolution | Xun Gu |
| Tues | Mar 9 | 6.1 | Evolutionary distance between sequences Derivation of Jukes-Cantor Approximation | Xun Gu |
| Thur | Mar 11 | Midterm II Super Solver's Solutions Midterm Scores and Grade Estimates | Instructors | |
| Tues | Mar 16 | SPRING BREAK | n/a | |
| Thur | Mar 18 | SPRING BREAK | n/a | |
| Tues | Mar 23 | 7.1 | Molecular phylogeny: Distance methods | Xun Gu |
| Thur | Mar 25 | 7.2 | Molecular phylogeny: Parsimony methods | Xun Gu |
| Tues | Mar 30 | 7.3 | Molecular phylogeny: Likelihood and Bayesian methods Homework 6 (due April 6) Homework 6 Solution | Xun Gu |
| Thur | Apr 1 | 7.4 | Ancestral genome inference: DNA and protein sequences | Xun Gu |
| Tues | Apr 6 | 8.1 | Introduction to genome phylogeny | Xun Gu |
| Thur | Apr 8 | 8.2 | Statistical analysis of microarray data | Xun Gu |
| Tues | Apr 13 | 9.1 | Advanced topics: Next-generation sequencing technology Homework 7 (due April 20) Homework 7 Solution | Xun Gu |
| Thur | Apr 15 | 9.2 | Advanced topics: Copy number variations (CNV) | Xun Gu |
| Tues | Apr 20 | 9.3 | Advanced topics (1): Genetic robustness and yeast genome-wide deletions Paper: Science 327:425 Presenters: Divya, ViJay, Hyejin, Abhijeet, Krishna Student Course Evaluation | Xun Gu |
| Thur | Apr 22 | 9.4 | Advanced topics (2): Models of duplication gene preservation Paper: Nature reviews. Genetics 11:97 Presenters: Deepak, Marie, Rasna, Will | Xun Gu |
| Tues | Apr 27 | 10.1 | Advanced topics (3): Mutational bias and origin of gene network Paper: Science 325:1686 Presenters: Susan, Chaoliang, Erin Doyle, Xianyan | Xun Gu |
| Thur | Apr 29 | 10.2 | Summary and review | Xun Gu |
| Tues | May 4 | FINAL EXAM WEEK | n/a | |
| Wed | May 5 | 9:45am - 11:45am, 1424 MBB Final examination Super Solver's Solution | Instructors |