![]() |
Graduate Bioinformatics: Comparative Methods -- CBMG 688G/Q CBMG 688G is two credits and meets until Spring Break. CBMG688Q is three credits and meets for the full semester. |
Date | Topic | Notes | ||
M | Jan | 24 | Introduction to genomics and comparative bioinformatics |
|
W | 26 | Contemporary sequencing technologies | ||
M | Jan | 31 | Pairwise sequence alignment -- Needleman Wunsch, Smith Waterman | Discussion |
W | Feb | 2 | Pairwise sequence alignment -- BLAST and its variants | |
M | 7 | Genbank and other databases |
||
W | 9 | Contig assembly | ||
M | 14 | Gene Finding/Gene Prediction | Discussion | |
W | 16 | No Class | ||
M | 21 | Hidden Markov Models |
||
W | 23 | Noncoding genes | ||
M | 28 | Functional inference -- homology ad ab initio methods | Discussion | |
W | Mar | 2 | Bacterial and Archaeal Genomes | |
M | 7 | Metagenomics and its applications | ||
W | 9 | Eukaryotic Genomes I | ||
M | 14 | Eukaryotic Genomes II | Discussion | |
W | 16 | Exam | CBMG 688G Ends | |
M | 21 | Spring Break | ||
W | 23 | |||
M | 28 | Student presentations |
||
W | 30 | |||
M | Apr | 4 | Student presentations | |
W | 6 | |||
M | 11 | Student presentations | ||
W | 13 | |||
M | 18 | Student presentations | ||
W | 20 | |||
M | 25 | Student presentations | ||
W | 27 | |||
M | May | 2 | Student presentations |
|
W | 4 | |||
M | 9 | 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 | ||||