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Graduate Bioinformatics: Comparative Methods -- CBMG 688G/Q
Syllabus Spring 2011 (with Tentative Lecture Schedule)
; PLS 1184

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