Class is held every Monday & Wednesday at 12:10 pm.

The course has covered the following topics:
WeekMonday Wednesday
1  1/8/03 & 1/10/03
Introduction of Dr. Kaplan, very small class!
Given Syllabus.
Discussed changing class time.
2 1/13/03
Overview discussion of DNA & Human Genome.
Read Chapter 1 in ICMB. 		1/15/03
Read Chapter 1 in ICMB.
Read up to mapping in CGG.
Read 30 pages in DNAB.
Discussion of Human Genome continued.
Homework: Exercises 1, 2, & 3, chapter 1.
3 1/20/03
No class - Dr. Martin Luther King, Jr. Day		 1/22/03
Homework #1 due today
Read Chapters 2 & 3
Continue with overview
Discussion of material in chapter 2
4 1/27/03
Homework #2 assigned - Chapter 3, #7
Discussion of material in chapter 3 		1/29/03
No one completed the homework!
See email sent and Assignment #2 Hints for more information.
5 2/3/03
Program #1 Assigned.
Discussion of alleles with blood type example.
Genetic versus Physical Map.
Discussion of course project.
Discussion of "opportunity." 		2/5/03
Class cancelled
Made-Up by Midterm on 2/21
6 2/10/03
IP Discussion.
Viewed mouse & human chromosome similarities.
Homework due.		 2/12/03
Chapter 3 wrap-up
Read Chapter 4
72/17/03
No class, President's Day!		 2/19/03
Class Cancelled
82/24/03
Discussion of Midterm
The midterm will be Friday at 12 noon.
Quiz on Chapter 4 on Wed., 3/5/03.
Discussion of Stirling's Formula with relation to string matching complexity.
Assignment #1 Returned.
Assignment #2 Returned.
Assignment #3 due Wednesday.
Handouts:
  • Understanding the Human Genome, Page 33 & bottom of Pages 34 & 35.
  • Calculation of DNA String Complexity.
2/26/03
Assignment #3 is due today.
Midterm is Friday.
9 3/3/03
Something different!
Discussion of Chapter 1 from Redesigning Creation: Debating the Biotech Revolution
 3/5/03
More outside the book reading!
Discussion of Chapter 3 from Redesigning Creation: Debating the Biotech Revolution Quiz on Chapter 4 on Monday.
Assignment #4 given.
10 3/10/03
Quiz on Chapter 4.
Assignment #4 due.
Lecture: Regular Expression (RE) of DNA to genes.
No one submitted Assignment #4 on time!
Assignment #5: Research Dr. Kaplan's RE example.
Read Chapter 5. 		3/11/03
Handout: Project
Lecture: Chapter #5 (started).
Spring Break!
10 3/24/03
Project:
  • Return journal with selection chosen.

Assignment #5: Research on Dr. Kaplan's Regular Expresssion Example due
Quiz on Chapter 5 on Wednesday.
Handout: BLAST and FASTA & FASTP algorithms.
Read Chapter 6.
Returned:
  • Midterm
  • Quiz #1
  • Assignment #3
  • Assignment #4
3/26/03
Lecture: Phylogenetic Trees (Chapter 6)
Handouts:
  • Lecture Figures
  • An example of cladogram construction for vertebrates
  • Papers -
    • Empirical determination of effective gap penalties for sequence comparison
    • Comparing expression profiles of genes with similar promoter regions
    • Data mining of sequences and 3D structures of allergenic proteins
Project:
  • Papers selected given to class.

Quiz on Chapter 5.
11 3/31/03
Lecture: Phylogenetic Trees (Chapter 6) - Continued.
Quiz #2 returned.
 4/02/03
Lecture: Graduate Schools (unscheduled!)
12 4/07/03
Lecture: Genome Rearrangements
Handout: Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals
Read Chapter 7 		4/09/03
Class cancelled - FOSE Exposition.
13 4/14/03
Class cancelled - Dr. Kaplan is at a conference.
Tomorrow, April 15th, is "Bringing the Genome to You" 		4/16/03
Lecture: Genome Rearrangements
Handout: Genome Rearrangements
Project:
  • Presentation hand-out due.
15 4/21/03
Assignment #6 due
Project:
  • Presentations.
4/23/03
Overview of course material
Project:
  • Report Due.
Last Class!