Fall 2015
EECS 395/495: Algorithmic Techniques for Bioinformatics

3:30--4:50 Tuesday and Thursday

2122 Sheridan Road, Classroom 250


Department of Electrical Engineering and Computer Science
Northwestern University


class homepage:



(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.)



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.


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



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.