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Welcome to CS238: Algorithmic Techniques in Computational Biology



Instructor :

Tao Jiang (jiang@cs.ucr.edu)
Office hours: TuTh 2-3pm. Office: WCH 336.

Teaching assistant and office hours:

TBA (tbaATcs.ucr.edu) Office hours: TBA.
TA office hours are held in WCH 110.
Here is the syllabus in PDF. Note that, although the main textbook is "An Introduction to Bioinformatics Algorithms" by Neil C. Jones and Pavel Pevzner, the MIT Press, 2004, the books "Genome-Scale Algorithm Design" by Veli Makinen, Djamal Belazzougui, Fabio Cunial and Alexandru I. Tomescu and "Algorithms for Strings, Trees, and Sequences: Computer Science and Computational Biology" by Dan Gusfield could be very useful reference books. If you have no background in biology or bioinformatics, the introductory book by Krane and Raymer could be a good starter, as well as chapter 3 of the textbook. A Primer on Molecular Genetics provides a sequencing-centric introduction. On the other hand, chapter 2 of the textbook provides a good review of fundamental concepts in algorithms.

The following are the lecture notes to be used in the class. Note that most of these slides are provided along with the textbook by Jones and Pevzner, and can be found at this website. However, they have been updated extensively below.

A shortened introductory lecture

Updated slides on DNA mapping

Updated slides on motif finding

Updated slides on probabilistic algorithms for motif finding

Updated slides on genome rearrangement

Slides on sequence alignment and dynamic programming

Updated slides on multiple sequence alignment

Updated slides on gene prediction

Updated slides on similarity based gene prediction

Updated slides on graph algorithms for DNA sequencing

Updated slides on the reconstruction of evolutionary trees

Approximation of shortest common superstrings

In addition, material from my old slides will be added from time to time to provide coverage on more sophisticated algorithms in computational biology.

You should check the Topics of Presentation and let me know your preferences (topics and presentation time slots) as early as possible.


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The following mapping shows how your overall scores will be translated into letter grades at the end of the quarter: 90+ -> A+, 85+ -> A, 80+ -> A-, 77+ -> B+, 73+ -> B, 70+ -> B-, 67+ -> C+, 63+ -> C, 60+ -> C-, 57+ -> D+, 53+ -> D, 50+ -> D-, 49- -> F.