Following is the outline for the classes taught thus far. It is not all the material! See class notes for specific information.

• Jan. 9 & 11, Wednesday & Friday.
  • Class has not met officially, but you are expected to buy the textbooks, and read the first chapter of Introduction to Computational Molecular Biology.
  • Handout:
    1. Handout #1: Bravo! We're Decoded, But a Mystery Still, From the Washington Post, Sunday Feb. 18, 2001.
• Jan. 14, Monday.
  • Overview of DNA - more to follow!
  • Class time changed to 9 am
• Jan. 16, Wednesday.
  • Chapter 1 discussion
  • Handout:
    2. Handout #2: Class notes, DNA, Proteins, Genes, Exons, Introns, by K. Kaplan, 2001.
• Jan. 18, Friday.
  • Visitor - My husband Lt. Col. J. Kaplan, Ph.D.
  • More review.
• Jan. 21, Monday.
  • No class - MLK Day
• Jan. 23, Wednesday, Jan. 25, Friday.
  • Chapter 2 discussion
• Jan. 27, Monday, Jan. 29, Wednesday
  • Handouts:
    3. Handout #3: Approximate String Matching Algorithm with disk
    4. Handout #4: Dynamic Programming Examples
• Feb. 4, Monday.
  • Class cancelled
• Feb. 6, Wednesday.
  • Discussion of NP, NP-complete, P
  • Discussion of approximate string matching being NP-complete
  • Program must be converted to C++ and working by next Friday
• Feb. 8, Friday.
  • Handouts:
    5. Handout #5: Calculation of DNA String Matching Problem Complexity, K. Kaplan, 2002.
    6. Handout #6: Group of articles from IEEE Spectrum, Nov. 2000.
    7. Handout #7: Scientists Create First Genetically Altered Monkey
  • More information about string matching and K. Kaplan's algorithm, including reversals.
• Feb. 11, Monday.
  • Handouts:
    8. Celera to Share Human Genentic Map, Washington Post, Feb. 8, 2001.
    9. Techno Bytes, Intellectual Property Today, Feb. 2001.
  • Discussion: Celera & IP
  • Note: Program due Friday.
• Feb. 13, Wednesday.
  • Discussion of program information
    10. Programming Assignments 1 & 2
• Feb. 15, Friday.
  • Program Due.
• Feb. 18, Monday.
  • No class, President's day
• Feb. 20, Wednesday.
  • Handouts:
    11. Handout #11: Information from Redesigning Creation: Debating the Biotech Revolution
    12. Handout #12: Chapters 1 & 2, Dr. Kaplan's disseration
• Feb. 22, Friday.
  • Program #2 due
  • Handout:
    13. Handout #13: Some Terms and Definitions in Bioinformatics
  • Chapter 3 discussion
• Feb. 25, Monday
  • Handouts:
    14. Handout #14: Programming Assignment #3 and In-Class Assignment #1
  • In-Class Assignment
• Feb. 27, Wednesday.
  • Discussed reverse sequences with LCA
  • Handouts:
    15. Handout #15: Reverse sequence examples 1, 2, 3, and 4
• Mar. 1, Friday.
  • No class.
• Mar. 4, Monday.
  • Handouts:
    16. Handout #16: Programming Assignment #4 with disk
    17. Handout #17: An Algorithm to Find All Sorting Reversals, by Siepel, Adam, UNM, Oct. 18, 2001.
• Mar. 6, Wednesday.
  • Discussion of reversals.
  • Read chapter 7.
• Mar. 8, Friday.
  • No class - Howard University Convocation
• Mar. 11, Monday.
  • Discussion of paper and chapter 7
• Mar. 13, Monday.
  • Discussion of NIH summer course; submit transcripts ASAP
  • Discussion of paper given; visit web-site for further discussion on Friday
  • Program due
• Mar. 15, Friday.
  • Discussion of handout
    18. Handout #18: Genome Rearrangements Biological Background.
• Mar. 18, 20, & 21, Monday, Wednesday, & Friday.
  • S PR I NG   BR EA K
  • Be careful Mr. A.
• Mar. 25, Monday.
  • Class canceled
• Mar. 11, Monday.
  19. Handout #19: Bioinformatics - Trying to Swim in a Sea of Data
  20. Handout #20: 43rd Annual IEEE Symposium on Foundations of Computer Science Information
  • Discussion of bioinformatics, stem cell research, and embryo research
  • There will be no class on Monday, April 1st.
• Mar. 29, Friday.
  • Ate donuts
  • Entertained visitor - Candice!
    21. Handout #21: Programming Assignment #5.
        Note the program handout in class states "#3" but the assignment is actually #5.
    22. Handout #22: "Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals," by Hannenhalli & Pevzer, 1999.
• Apr. 1, Monday.
  • No class.
• Apr. 3, Wednesday.
  • Reversals
  • Handout:
    23. Handout #23: Reversals Assignment
• Apr. 5, Friday.
  • Hurdles, Non-hurdles, Super-hurdles, Simple-hurdles
  • Reversals of Unoriented Blocks
  • Handout:
    24. Handout #24: Abstracts from papers for conference
  • Read Chapter 5, Physical Mapping of DNA
• Apr. 8, Monday.
  • Candice visits! Donuts for all!
  • Chapter 5 material discussed
• Apr. 10, Wednesday.
  • Chapter 5 material finished.
  • Homework due today.
  • Senior final on Friday.
• Apr. 12, Friday.
  • Where is Mr. A?
  • Final for seniors.
• Apr. 15, Monday.
  • Discussion of abstracts from conference.
  • No class on Wednesday - conference starts Wednesday night.
• Apr. 17, 19, 22, Wednesday, Friday, Monday
  • RECOMB Conference
• April 24, Wednesday
  • Last class
  • Discussion of conference
  • Final is scheduled for Friday, May 3, 2002