CS 5670 Bioinformatics II, Spring 2008

• Time and place: Mon Wed Fri 2:30pm - 3:20pm, Main 117
• Course website: http://www.cs.usu.edu/~mjiang/cs5670/spring2008/
• Professor: Dr. Minghui Jiang
  • Contact: mjiang at cc.usu.edu, 435-797-0347
  • Office hours: Mon Wed Fri 11:30am - 12:30pm, Main 402G
• Textbook: Neil C. Jones and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms. MIT Press. ISBN: 0-262-10106-8.
• Course goals: The student will
  • Gain knowledge on a variety of effective algorithmic techniques and mathematical methods of bioinformatics.
  • Be able to utilize different techniques and methods in solving various bioinformatics problems and compare their effectiveness.
  • Be able to use common bioinformatics tools and understand its underlying principles.
  • Be prepared for research in bioinformatics.
• Prerequisite: CS5660 or consent of instructor.
• Grading
  • Homework (40%):
  • Project (60%):
• Resources:
  • Journals: JCB TCBB JBCB Bioinformatics BMCB NAR
  • Links: Delta uShuffle
  • Papers:
    • S. F. Altschul and B. W. Erickson. Significance of nucleotide sequence alignment: a method for random sequence permutation that preserves dinucleotide and codon usage. Molecular Biology and Evolution, 2(6):526-538, 1985.
    • D. Kandel, Y. Matias, R. Unger, P. Winker. Shuffling biological sequences. Discrete Applied Mathematics, 71(1-3):171-185, 1996.
• Lectures (schedule subject to change):
  • Jan 7 9 (11): Introduction.
  • Jan 14 16 18: RNA survey.
  • Jan (21) 23 25: Pseudobase.
  • Jan 28 30 Feb 1:
  • Feb 4 6 8:
  • Feb 11 13 15:
  • Feb (18) 20 22:
  • Feb 25 27 29:
  • Mar 3 5 7:
  • Mar (10 12 14): Spring Break.
  • Mar 17 19 21:
  • Mar 24 26 28:
  • Mar 31 Apr 2 4:
  • Apr 7 9 11:
  • Apr 14 16 18:
  • Apr 21 23 25:
• Registration policy:
  • The last day to add this class is January 28.
  • The last day to drop this class without notation on your transcript is January 28.
  • Attending this class beyond January 28 without being officially registered will not be approved by the Dean's Office. Students must be officially registered for this course. No assignments or tests of any kind will be graded for students whose names do not appear on the class list.
• Code of conduct:
  • Every student should read and follow the department code of conduct.
  • Students are encouraged to discuss and exchange ideas on homework and projects, but each student must write up the solutions independently.
  • Students who are caught cheating immediately receive "Fail" grades.
• DRC statement: Students with physical, sensory, emotional or medical impairments may be eligible for reasonable accommodations in accordance with the Americans with Disabilities Act and Section 504 of the Rehabilitation Act of 1973. All accommodations are coordinated through the Disability Resource Center (DRC) in Room 101 of the University Inn, 797-2444 voice, 797-0740 TTY, or toll free at 1-800-259-2966. Please contact the DRC as early in the semester as possible. Alternate format materials (Braille, large print or digital) are available with advance notice.