CIS 455 - Bioinformatics

Instructor Information

Instructor: Dr. Xiaoqin Shelley Zhang
- Office: 302C Dion
- Office Hours: Tuesday 11 - 1, Thursday 11- 12, Friday 1:30 - 2:30PM or by appointment.
- Phone: (508) 999-8294
- Email: shelley.zhang@umassd.edu
TA: Harmeet K Chawla
- Email: hchawla@umassd.edu
- Office Hours: Wednesday 12 - 1, Thursday 12 - 1, DION 311.

Course Description

Prerequisites: CIS 360 Algorithms and data structures
This course introduces biological and algorithmic ideas together and link issues in computer science to biology. It is organized according to the following algorithmic principles:

Exhaustive Search
Greedy Algorithms
Dynamic Programming Algorithms
Divide-and-Conquer Algorithms
Graph Algorithms
Clustering and Trees

These algorithms are introduced and discussed for solving the following biological problems:

Mapping DNA
Sequencing DNA
Comparing Sequences
Predicting Genes
Finding Signals
Identifying Proteins
Microarray Gene Expressions
Genome Rearrangements
Molecular Evolution

Course Objectives

Study the basic algorithms and methods in bioinformatics.
Learn about the available resource (algorithms, tools and dataset) in bioinformatics.
Apply computing technologies to biology problems.

Course Outcomes

Upon finishing this course, students are expected to have:

Knowledge of computational issues in bioinformatics
Understanding of computational methods used in various bioinformatics applications
Design of algorithms in analyzing molecular sequences

Course Resources and Information

Textbook
- Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, The MIT Press, 2004, ISBN 0-262-10106-8, http://www.bioalgorithms.info/
Important Web Links
- Course Homepage: http://www.cis.umassd.edu/~xqzhang/courses/CIS455/, with links to syllabus, announcement, and other resources.
- Lecture notes, homework and project material are available on learning portal: http://web.cis.umassd.edu/portal/index.html.
- Textbook Homepage: http://www.bioalgorithms.info/
Recommended References
- Molecular Biology for Computer Scientists: http://www.biostat.wisc.edu/~craven/hunter.pdf
- Bioinformatics—An Introduction for Computer Scientists: http://www.cl.cam.ac.uk/~pl219/cohen_bioinformatics.pdf
- Introduction to Matlab: http://www.cs.dartmouth.edu/~farid/tutorials/matlab.intro.html
- Matlab online documentation: http://www.mathworks.com/access/helpdesk/help/helpdesk.html
- Matlab Primer

Course Requirements and Grading

There will be one midterm exam, one final exam, homework assignments, projects, and one class presentation. The material of all exams will come from either a material covered in class, homework, project and/or assignment readings. Class attendance is mandatory. Complete all required work on time. In the event that an exam must be missed, or required work cannot be completed on time, due to illness or other serious and unavoidable circumstance, notify the professor as far in advance as possible by phone or e-mail. Make-up exams will not be given for any reason. The evaluation will be based on:

20% Midterm
45% Homework and project
25% Final Exam
10% Presentation and class participation.

Academic Honesty

You are encouraged to discuss assigned problems with other people but you must individually design and write your own solutions / code for all assignments. Furthermore, you should explicitly acknowledge any sources of ideas used that are not your own; this includes other people, books, web pages, etc. "Sharing" of solutions to homework problems and lab exercises is strictly prohibited. Submitting modified versions of other people's work as your own is considered cheating. Academic dishonesty will be "rewarded" with a grade of "F".