1. Problem Set #9 has been posted in the Section of Weekly Reading Assignments and Problem Sets below. (11/21/2005)

2. The presentation schedule has also been posted in the same section. (11/21/2005)

3. Correction: The dates of the presentations are Tuesday and Thursday (11/29 and 12/01). Sorry for the confusion! -- Ming, 11/28/2005, 10:58AM.

Synopsis:

A genome is a set of DNA molecules that encode the entire genetic information of an organism or species. Such information is copied and transported by RNA to produce proteins in cells. A major goal of bioinformatics is to determine the information in the human genome and those of other species. This interdisciplinary course focuses on basic computational problems that arise from sequencing and comparing DNA as well as from analyzing RNA and proteins. As new technologies of processing DNA, RNA and proteins become available, different problems will take the center stage. For this reason, this course emphasizes fundamental algorithmic techniques instead of specific problems. These techniques have proven useful for many current problems and are chosen to provide a foundation upon which further techniques can be developed to solve future problems.

Instructor:

Email: kao@northwestern.edu
Class  Webpage: http://www.cs.northwestern.edu/~kao/cs395-bioinformatics
Office Hours: 10:30--11:30 on Tuesday and Wednesday or by appointment (see my calendar for appointment slots)

Teaching Assistant:

Email: manan@cs.northwestern.edu
Office Hours: 4:00-5:00 on Monday and 10:30-11:30 on Thursday or by appointment

Prerequisites:

CS 336 Design and Analysis of Algorithms or permission of the instructor.

Course Work and Grading Policy:

There will be no midterm or final examination. The course grade will be based on weekly problem sets (72%) and presentations (28%).

• Weekly problem sets: A problem set will be given on each Tuesday from Week 2 through Week 10 and will be due at the start of class on the following Tuesday. There will be 9 problem sets. Each problem set is worth 8% of your course grade. No late problem set will be accepted without a Dean's excuse.

• Presentations: Each student will give one or more presentations during the last week of class (from 11/28 through 12/2). A typical presentation can be based on a technical paper or can demonstrate a software. The presentation is worth 28% of your course grade.

Textbooks:

• Required:
  • An Introduction to Bioinformatics Algorithms. Neil C. Jones and Pavel A. Pevzner. MIT Press, 2004.

Supplemental Course Materials:

1. PubMed --- a large database of journals in life sciences.
2. Possible journals and conferences for publication of research projects:
   • Proceedings of the RECOMB conference
   • Journal of Computational Biology
3. Technical papers:

Tentative Lecture and Discussion Schedule:

Discussion details as well as guest lectures will be added to the schedule as they become available.

1. Introduction (1 meeting, 9/20)
2. Algorithms and Complexity (2 meetings, 9/22, 9/27)
3. Molecular Biology Primer (2 meetings, 9/29, 10/4)
4. Exhaustive Search (2 meetings, 10/6, 10/11 )
5. Greedy Algorithms (2 meetings, 10/13, 10/18)
6. Dynamic Programming Algorithms (2 meetings, 10/20, 10/25)
7. Divide-and-Conquer Algorithms (2 meetings, 10/27, 11/1)
8. Graph Algorithms (2 meetings, 11/3, 11/8)
9. Combinatorial Pattern Matching (2 meetings, 11/10, 11/15)
10. Clustering and Trees (2 meetings, 11/17, 11/22)

Weekly Reading Assignments and Problem Sets:

• Week 1 (9/19--9/23).
  • Reading Assignment: Chapter 1 for Tuesday's discussion; Chapter 2 for Thursday's.
  • Problem Set: none for this week.
• Week 2 (9/26--9/30).
  • Reading Assignment: Chapter 2 for Tuesday's discussion; Chapter 3 for Thursday's.
  • Problem Set #1:  posted 7:54AM, 9/27/2005.
• Week 3 (10/03--10/7).

  • Reading Assignment: Chapter 3 for Tuesday's discussion; Chapter 4 for Thursday's.

  • Problem Set #2: posted 6:15AM, 9/30/2005.

• Week 4 (10/10--10/14).

  • Reading Assignment: Chapter 4 for Tuesday's discussion; Chapter 5 for Thursday's.

  • Problem Set #3: posted 14:43, 10/10/2005.

• Week 5 (10/17--10/21).

  • Reading Assignment: Chapter 5 for Tuesday's discussion; Chapter 6 for Thursday's.

  • Problem Set #4: posted 11:54, 10/17/2005.

• Week 6 (10/24--10/28).

  • Reading Assignment: Chapter 6 for Tuesday's discussion; Chapter 7 for Thursday's.

  • Problem Set #5: posted 21:43, 10/24/2005.

• Week 7 (10/31--11/4).

  • Reading Assignment: Chapter 7 for Tuesday's discussion; Chapter 8 for Thursday's.

  • Problem Set #6: posted 22:28, 10/31/2005.

• Week 8 (11/7--11/11).

  • Reading Assignment: a guest lecture on Tuesday; Chapter 9 for Thursday's.

  • Problem Set #7: posted 20:30, 11/07/2005.

• Week 9 (11/14--11/18).

  • Reading Assignment: Chapter 9 for Tuesday's discussion; Chapter 10 for Thursday's.

  • Problem Set #8: posted 20:20, 11/14/2005.

• Week 10 (11/21--11/25). No class on Thanksgiving, Thursday, 11/24.

  • Reading Assignment: Chapter 10 for Tuesday's discussion.

  • Problem Set #9: posted 19:33, 11/21/2005.

• Week 11 (11/28--12/2). Student presentations will take place during this week.

• Week 12 (12/5--12/9). Final Exanimation Week. This class has no final examination.