CIS 602: Special Topics in Computer Science: Advanced Bioinformatics

Instructor

Li Shen
Office: Dion 307A
Phone: (508) 910-6691
Email: lshen@umassd.edu
Office Hours: Tue 11am-12:30pm, Thu 11am-12:30pm, Fri 12-1pm (or by appointment)

TA

Na Ni
Office: Dion 305
Email: nni@umassd.edu
Office Hours: Mon 2:30-3:30pm, Thu 11am-noon

Lectures

Tue and Thu, 3:30-4:45 pm, Dion 105

Prerequisites

CIS 360 Algorithms and data structures, or permission of the instructor

Course Description

Advanced coverage of computational approaches used in bioinformatics. The course focuses on algorithmic challenges in analyzing molecular sequences, structures, and functions. It covers the following topics: Sequence comparison, assembly and annotation. Phylogenetic analysis. RNA secondary structure. Protein structure comparison, prediction, and docking. Microarrays, clustering, and classification. Genome, Hapmap, SNPs, and phenotypes. Proteomics and protein identification. Determining protein function and metabolic pathways.

Course Objectives

• To study algorithmic challenges in analyzing molecular sequences: what genes encode an organism, and how are genes related across organisms?
• To study algorithmic challenges in analyzing molecular structures: what do the proteins constructed for these genes look like, and what does that tell us about their mechanisms?
• To study algorithmic challenges in analyzing molecular functions: what do these things do, and how do they interact with each other in doing it?

Course Outcomes

• Knowledge of computational issues in bioinformatics
• Knowledge of publicly available databases and tools in bioinformatics
• Understanding of computational methods used in various bioinformatics applications
• Design of algorithms in analyzing molecular sequences, structures and functions

Course Materials

• Textbook
  • David W. Mount, Bioinformatics : sequence and genome analysis. 2nd edition , Cold Spring Harbor Laboratory Press, July, 2004, ISBN 0-87969-712-1, http://www.bioinformaticsonline.org/
• Important Web Links
  • Course Homepage: http://www.cis.umassd.edu/~lshen/courses/200607_fall_cis602/index.htm
  • Textbook Homepage: http://www.bioinformaticsonline.org/
• Recommended References
  • 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/
  • 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: http://ise.stanford.edu/Matlab/matlab-primer.pdf

Homework

• Homework assignments will be posted online. Homework is due at the beginning of class on the announced due date. Any exceptions must be approved by the instructor in advance. Late homework will not be accepted.
• Some of the exercises will be routine, but others will be more challenging. I hope that you will benefit from working on the more difficult ones.
• I encourage discussion of homework assignments between students. However, your submitted homework must be entirely your own. You may not copy anything directly from another student's work. You should note with whom you discussed the problem at the beginning of your solution write-up. Note that discussion between two students will be most useful when both students have already made serious attempts to solve the problem on their own.

Requirements and Grading

There will be homework assignments, a class presentation, a term project, a midterm exam, and a final exam. Class attendance is mandatory. You are responsible for all announcements and for all material presented in the lecture sessions. Come prepared for class and read the assigned material in advance of lectures. After the lecture, re-read the material. The evaluation will be based on:

• Homework: 25%
• Presentation: 10%
• Term project: 15%
• Midterm exam: 20%
• Final exam: 25%
• Class participation: 5%

The letter grades will be assigned using the following approximate scale: (A+,A,A-)[100-90], (B+, B, B-)[90-80], (C+,C,C-)[80-70], (D+,D,D-)[70-60], and F[60-0].

Important Dates

• 10/26/06 (in class): Midterm exam
• 11/21/06: Project and presentation topic proposal due
• 12/14/06: Project due
• 12/19/06 (3:00pm-6:00pm Tuesday): Final exam

Academic Honesty

• The UMass Dartmouth Academic Ethical Standards and Student Judicial Code apply to your conduct in this course. Please refer to the following materials for details.
  • Student Handbook (http://www.umassd.edu/studenthandbook/)
  • Academic Ethical Standards (http://www.umassd.edu/studenthandbook/academicregs/ethicalstandards.cfm)
  • Student Judicial Code (http://www.umassd.edu/studenthandbook/studentjud/)
• All work submitted for credit must be your own. You may, however, discuss your homework assignments and term project with your classmates and Professor Shen.
  • For written homeworks, you should writeup your own solutions and neither read nor copy another person's solution or portions of their solution - this includes solutions from any web page (other than our class web page) that you find on the web.
  • For programs, you should create and type in your own code, and any copying (electronic or otherwise) of another person's code or code fragments is a violation of the Academic Ethical Standards.
  • You cannot collaborate or copy in any way on exams.
• If you have any questions as to whether some action would be acceptable under the Academic Ethical Standards, please speak to me, and I will be glad to help clarify things. It is always easier to ask beforehand than to have trouble later!

Disability Statement

If you have a disability and feel you will need accommodation in order to complete course requirements, please contact Office of Disabled Student Services, Group I, Lower Level.