CS 238 Homepage



HW3 has been posted via the class mailing list, and is due on Friday, May 31.
Please subscribe to the class mailing list via the link given at the bottom of this page ASAP.


Lectures:

TR 11:00-12:20pm, OLMH 1208. The lectures are offered only in-person this quarter, but the recordings of similar past lectures can be made available on Canvas/Yuja upon request.

Instructor :

Tao Jiang (jiangATcs.ucr.edu)
Office hours: TR 9:30-10:30am. Office: WCH 336.

Teaching assistant and office hours:

Jingong Huang (jhuan381ATucr.edu) Office hours: M 1-2pm.
The TA office hours are held in WCH 110.
Here is the syllabus in PDF. Note that, although our main textbook is "An Introduction to Bioinformatics Algorithms" by Neil C. Jones and Pavel Pevzner, the MIT Press, 2004, the books "Bioinformatics Algorithms: An Active Learning Approach" by Phillip Compeau and Pavel Pevzner, "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 can be very useful reference books. The former two also cover more modern topics, while the latter book by Gusfield provides more details for some of the important algorithms. If you have no background in biology or bioinformatics, the introductory book by Krane and Raymer could be a good starter, as well as the book by Widlak (also available on eLearn/Canvas), and 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.

Bioinformatics and early studies of the novel coronavirus

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. The presentations will begin on May 21 and run through the final exam day (Monday, June 10, 8-11am). Here is the Final Presentation Schedule.


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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.