Fall 2010
EECS 395/495: Algorithmic Techniques for Bioinformatics
2:00--3:20 Tuesday and Thursday
Technology Institute, Room M152
Ming-Yang
Kao
Department of Electrical Engineering and Computer Science
Northwestern University
www.cs.northwestern.edu/~kao/eecs395-bioinformatics
(last updated,
9/20/2010)
Please check here often for
important announcements:
1.
Please go ahead to purchase the two
required textbooks. (8/20/2010)
2.
If you are not certain whether you should
take the course, you are welcome to audit it. (9/20/2010)
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:
Ming-Yang Kao
Office: Technology Institute, Room M324
Phone: 847-230-9867
Email: kao@northwestern.edu
Office Hours: 10:30--11:30 on Tuesday and Wednesday or by appointment.
Teaching Assistant:
None.
Prerequisites:
Strong
intellectual curiosity about computer science and biology is essential.
Technical knowledge about biology, programming, data structures, and algorithms
are useful, but not required.
Course Work and
Grading Policy:
Active participation in class-room discussions, and a survey
paper are required. Also, one or more presentations may be required. Original
research is optional but encouraged. There will be no midterm or final
examination.
Textbooks:
o
Required:
o Neil C. Jones and Pavel A. Pevzner, "An Introduction to
Bioinformatics Algorithms", MIT Press, 2004.
o Wing-Kin Sung, "Algorithms in Bioinformatics: A
Practical Introduction", CRC Press, 2009.
Supplemental Course
Materials:
1.
PubMed -- a large
database of journals in life sciences.
2.
Possible places to publish results
from your course projects:
a. Proceedings
of the RECOMB conference
b. Journal
of Computational Biology
3.
Technical papers: More information
will be added when available.
Discussion and
Event Schedule:
The
following list is subject to update. Also, more information will be added to
the schedule when available.
1.
Week 1 (9/21 & 9/23)
Introduction (2 meetings)
o
PPT
of Tuesday, 9/21 (in pdf).
2.
Week 2 (9/28 & 9/30) Algorithms
and Complexity (2 meetings)
3.
Week 3 (10/5 & 10/7) Molecular
Biology Primer (2 meetings)
4.
Week 4 (10/12 & 10/14)
Exhaustive Search (2 meetings)
5.
Week 5 (10/19 & 10/16) Greedy
Algorithms (2 meetings)
6.
Week 6 (10/26 & 10/28) Dynamic
Programming Algorithms (2 meetings)
7.
Week 7 (11/2 & 11/4)
Divide-and-Conquer Algorithms (2 meetings)
8.
Week 8 (11/9 & 11/11) Graph
Algorithms (2 meetings)
9.
Week 9 (11/16 & 11/18)
Combinatorial Pattern Matching (2 meetings)
10. Week 10 (11/23 & 11/25) Clustering and Trees (1 meeting)
o
There is no meeting on Thanksgiving, Thursday,
11/25.
11. Week 11 (11/30 & 12/2) Clustering and Trees (2 meetings,
continuation from the previous week)
o
The survey paper is due via email by midnight on
Friday, 12/3/2010.