Bioinformatics Applications Course (ZOO 5903/4903)

Jonathan D. Wren
Fall 2006
MW 10:30-11:45
Sutton Hall, Room 312
Course Syllabus (MS Word format)
Class report project (MS Word)
Note: Lectures & homeworks are generally not posted here until after class
.
Exam 1 material (Genomes & DNA) 
 
Lecture 1 - Introduction
      Powerpoint
Lecture 2 - Genome features & sequencing
      Powerpoint
      Homework #1
Lecture 3 - Sequence Alignment
      Powerpoint
Lecture 4 - Multiple Sequence Alignment
      Powerpoint
      Homework #2
Lecture 5 - Phylogenetics
      Powerpoint
Lecture 6 - Genome analysis and diversity
      Powerpoint

Exam 2 material (Transcription & RNA)

Lecture 7 - Gene finding in prokaryotes 
      Powerpoint
Lecture 8 - Gene finding in eukaryotes
      Powerpoint
      Homework #3 + Loots paper,  Test_SeqGenomic_Region_1
Lecture 9 - Alternative splicing and microRNAs
      Powerpoint
Lecture 10 - Gene expression & microarray technology
      Powerpoint
      Homework #4 
Lecture 11 - Microarrays - processing & normalization
      Powerpoint
Lecture 12 - Microarrays - clustering & analysis
      Powerpoint
      Homework #5  Microarray dataset
Lecture 13 - RNA secondary structure 
      Powerpoint

Exam 3 material (Proteins)

Lecture 14 - Introduction to proteomics
      Powerpoint
Lecture 15 - Proteomics II - protein domains & post-translational modifications
      Powerpoint
      Homework #6   Protein1
Lecture 16 - Predicting protein 3D structure
      Powerpoint
Lecture 17 - Susan Schroeder guest lecture
      Powerpoint
      Homework #7
Lecture 18 - Protein-protein interaction networks + order, chaos & complexity
      Powerpoint
Lecture 19 - Immunoinformatics
      Powerpoint
      Homework #8
Lecture 20 - Cheminformatics
      Powerpoint

Exam 4 material (Systems Biology)

Lecture 21 - Network motifs & biological pathways 
      Powerpoint
      Supplementary reading material S6
Lecture 22 - Artificial Life 
      Powerpoint
      Supplementary reading material S7
Lecture 23 - Text mining
      Powerpoint
      Supplementary reading material S8
      Homework #9
Lecture 24 - Cell simulation and modeling 
      Powerpoint
      Supplementary reading material S11
Lecture 25 - Systems Biology
      Powerpoint
      Supplementary reading material S9
Lecture 26 - Synthetic Biology
      Powerpoint
      Supplementary reading material S10
Lecture 27 - Review for Final Exam
      Powerpoint
 
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