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Fall
2015 3:30--4:50
Tuesday and Thursday 2122
Sheridan Road, Classroom 250 Department of Electrical Engineering and
Computer Science class homepage: http://www.cs.northwestern.edu/~kao/eecs395-bioinformatics (last
updated 9/22/2015) 1.
Please read this syllabus thoroughly yourself before
attending the first class on Tuesday 9/22/2015. (Posted on 9/16/2015.) 2.
An e-book version of the textbook is available at
Amazon.com. (Posted on 9/16/2015.) 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:
Tech M324 Phone:
847-230-9867 Email: kao@northwestern.edu URL: www.cs.northwestern.edu/~kao Office
Hours: 11:00--1:00 Wednesday, or by appointment Pre-requisites: 1.
Technical knowledge about biology is useful, but
not required. 2.
EECS 336 Design and Analysis of Algorithms is
strongly preferred, but not required. Course Work and Grading Policy: This
class will be taught as a combination of lectures and seminars. The following
grading policy is based on this class format. 1.
0% for weekly reading assignments: Reading assignments
will be posted on the class homepage. You are responsible for the materials
that are assigned but are not covered in detail or at all in class. Some of
such materials are covered in the prerequisites or even earlier courses. 2.
20% for participation in classroom discussions. 3.
40% for one or two presentations. 4.
40% for a term paper, which can be a survey, original
research, or a combination of the two. Required Textbook: 1.
Wing-Kin Sung, "Algorithms in Bioinformatics: A
Practical Introduction", CRC Press, 2009. Tentative Schedule: This
schedule is subject to modification. More details will be added as they
become available. There will be a total of 21 meetings. Some of the meetings
will be presentations by students. 1. (2 meetings): Sequence Similarity
(Chapter 2) 2. (2 meetings): Multiple Sequence
Alignment (Chapter 6) 3. (2 meetings): Introduction to
Molecular Biology (Chapter 1) 4. (4 meetings): DNA Sequencing and
Peptide Sequencing (Chapter 12) 5. (2 meetings): Suffix Tree (Chapter
3) 6. (2 meetings): Database Search
(Chapter 5) 7. (2 meetings): Phylogeny
Reconstruction (Chapter 7) 8. (2 meetings): Phylogeny Comparison
(Chapter 8) 9.
(3 meetings): RNA Secondary Structure Prediction
(Chapter 11) Student
Presentation Schedule: To be posted. Weekly
Reading Assignments: Week 1.
(9/22 and 9/24) (a)
Reading Assignment: Chapter 2. Week 2.
(9/29 and 10/1) (a)
Reading Assignment: Chapter 6. Week 3.
(10/6 and 10/8) (a)
Reading Assignment: Chapter 1. Week 4. (10/13 and 10/15) (a)
Reading Assignment: Chapter 12. Week 5.
(10/20 and 10/22) (a)
Reading Assignment: Chapter 12. Week 6. (10/27 and 10/29) (a)
Reading Assignment: Chapter 3. Week 7.
(11/3 and 11/5) (a)
Reading Assignment: Chapter 5. Week 8.
(11/10 and 11/12) (a) Reading Assignment: Chapter 7. Week 9.
(11/17 and 11/19) (a)
Reading Assignment: Chapter 8. Week 10.
(11/24) (a)
Reading Assignment: Chapter 11. Week 11.
(12/1 and 12/3) (a)
Reading Assignment: Chapter 11. (b) The term paper is due by email to the instructor at
noon Saturday 12/5/2015. |