Graduate Bioinformatics: Comparative Methods -- CBMG 688G/Q
Syllabus Spring 2009 (with Tentative Lecture Schedule)
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Graduate Bioinformatics: Comparative Methods -- CBMG 688G/Q |
| Date | Topic | Notes | ||
| M | Jan | 26 | No Class |
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| W | 28 | No Class | ||
| M | Feb | 2 | Introduction to genomics and comparative bioinformatics | Wu Et al., 2004. PLOS 2:327-341 |
| W | 4 | Contemporary sequencing technologies | ||
| M | 9 | Pairwise sequence alignment -- Needleman Wunsch, Smith Waterman | ||
| W | 11 | Pairwise sequence alignment -- BLAST and its variants | ||
| M | 16 | Contig assembly | ||
| W | 18 | Gee, I've got a genome. What now? | ||
| M | 23 | Hidden Markov Models |
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| W | 25 | Gene Finding/Gene Prediction | ||
| M | Mar. | 2 | Functional inference -- homology ad ab initio methods | |
| W | 4 | Databases and genome browsers | ||
| M | 9 | Metagenomics and its applications | ||
| W | 11 | Exam | ||
| M | 16 | Spring Break | ||
| W | 18 | |||
| M | 23 | Student presentations | CBMG 688G Ends | |
| W | 25 | |||
| M | 30 | Student presentations |
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| W | Apr. | 1 | ||
| M | 6 | Student presentations | ||
| W | 8 | |||
| M | 13 | Student presentations | ||
| W | 15 | |||
| M | 20 | Student presentations | ||
| W | 22 | |||
| M | 27 | Student presentations | ||
| W | 29 | |||
| M | May | 4 | Student presentations |
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| W | 6 | |||
| M | 11 | Recap | ||
| TBD | Final Exam 1234 Bio/Psych | |||
Old (perhaps obsolete) lecture outlines
| Lecture Topic | Mount Reading | |||
| Introduction; Introduction to whole genome analysis | Chapters 1 | |||
| Case Study: The genomes of bacterial pathogens | ||||
| Pairwise sequence alignment | Chapter 3 | |||
| Amino acid substitution matrices | Chapter 4 | |||
| Pairwise sequence alignment (cont.) | ||||
| Sequence Databases | Chapter 2 | |||
| Constructional Morphology in Genomics | ||||
| Blast and Other Heuristic Alignment Tools | Chapter 6 | |||
| Assessing alignment significance Hidden Markov Models | ||||
| Strategies for sequencing complete genomes & sequencing technologies | Chapter 9 | |||
| Determining the number of genes, gene finding | ||||
| Genomes (cont.) | Chapter 11 | |||
| Contemporary research: Deinococcus radiodurans | ||||
| Midterm exam | ||||
| RNA-coding genes; finding & predicting secondary structure | Chapter 8 | |||
| Contemporary Research: The Anopheles Genome | ||||
| EST Analysis | Chapter 6 | |||
| Gene families | Chapter 5 | |||
| Multiple sequence alignment | ||||
| Phylogenetic analysis:Parsimony methods | Chapter 7 | |||
| Models of Nucleotide Sequence Evolution | ||||
| Model based phylogenetic methods 1: Distance | ||||
| Model based phylogenetic methods 2: Likelihood | ||||
| Gene families revisited | ||||
| Midterm exam | ||||
| Holiday - Thanksgiving break | ||||
| Contemporary research: Functional Genomics | Chapter 10 | |||
| Functional genomics (cont.) | ||||
| Human X & Y chromosomes | ||||
| Analysis of the Arabidopsis genome | ||||
| Review of Molecular Biology | ||||
| 8:00 am - 10:00 am Final Exam 1229 HJ Patterson Hall | ||||
| Genome Exploration: the cDNA approach | ||||
| Determining the number of genes | ||||
| Horizontal Gene Transfer and an example from rubisco | ||||