CS 238 Homepage
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.
Please subscribe to the CS 238 class mailing list ASAP.
Make sure you turn off the "batch mode".
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.