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CH391L Bioinformatics

Course unique #: 52990
Lectures: Tuesday/Thursday 12:30 – 2:00 PM in WEL 3.402
Instructor: Edward Marcotte,

  • Office hours: Wednesdays 2:00 – 3:00 PM in MBB 3.210AA Phone: 471-5435

TA: Taejoon Kwon, taejoon.kwon at mail dot utexas dot edu

  • TA Office hours: Tuesday/Thursday 10:00 – 11:00 AM in MBB 3.210A Phone: 232-3919

Lectures & Handouts

May 5, 2011 - Some of the publicly-viewable final projects

May 3, 2011 - Synthetic biology

April 28, 2011 - Synthetic biology

April 26, 2011 - Network alignment and motifs

April 21, 2011 - Networks

April 19, 2011 - Networks

April 14, 2011 - Networks

April 12, 2011 - Motifs

April 7, 2011 - PCA/SVD

April 5, 2011 - Classification

Mar 31, 2011 - Clustering & Classification

Mar 29, 2011 - Clustering 2

An assortment of datasets for Problem Set 4, due Apr. 12, 2011

Mar 24, 2011 - Clustering

Mar 22, 2011 - Gene expression

Mar 8, 2011 - Assembling genomes + next-gen sequencing

  • We're running a bit behind on our next-gen sequencing datasets, which were intended for Problem Set 3. I'll plan to add these data to Problem Set 4. Instead, for Problem Set 3, I'll give credit for turning in one (full) paragraph laying out your planned work for your final course project. The deadline will be extended to March 10. (Turn them in by email. Remember, no class on the 10th.)
  • Here are a few examples of final projects from previous years: 1, 2, 3, 4, 5

Mar 3, 2011 - Assembling genomes

Mar 1, 2011 - Assembling genomes

Feb 24, 2011 - Gene finding

Feb 22, 2011 - HMMs and gene finding

Feb 17, 2011 - HMMs

Feb 15, 2011 - Profiles

Feb 10, 2011 - BLAST

Feb 8, 2011 - Sequence Alignment III

  • A few examples of proteins with internally repetitive sequences: 1, 2, 3
  • Repeats in the human genome, tallied here

Feb 3, 2011 - Sequence Alignment II

Jan 27, 2011 - Sequence Alignment I

Jan 25, 2011 - Perl primer

Syllabus & course outline

Course syllabus

An introduction to computational biology and bioinformatics. The course covers typical data, data analysis, and algorithms encountered in computational biology. Topics will include introductory probability and statistics, basics of programming, protein and nucleic acid sequence analysis, genome sequencing and assembly, protein structure prediction, analysis of DNA microarray data, data clustering, biological pattern recognition, and biological networks.

Open to graduate students and upper division undergraduates in natural sciences and engineering.
Prerequisites: Basic familiarity with molecular biology, statistics & computing, but realistically, it is expected that students will have extremely varied backgrounds.

Note that this is not a course on practical sequence analysis or using web-based tools. Although we will use a number of these to help illustrate points, the focus of the course will be on learning the underlying algorithms and exploratory data analyses and their applications.

Most of the lectures will be from research articles and handouts, with some material from the...
Recommended text (for sequence analysis): Biological sequence analysis, by R. Durbin, S. Eddy, A. Krogh, G. Mitchison (Cambridge University Press),

For non-molecular biologists, I highly recommend (really!) The Cartoon Guide to Genetics (Gonick/Wheelis)
For biologists rusty on their stats, The Cartoon Guide to Statistics (Gonick/Smith) is also very good.

Some online references:
An online bioinformatics course Various bioinformatics algorithms Assorted bioinformatics resources on the web
Online probability texts: #1, #2, #3

No exams will be given. Grades will be based on 4 problem sets (given every 2 weeks and counting 15% each towards the final grade) and a course project (40% of final grade), which can be individual or collaborative. If collaborative, cross-discipline collaborations are encouraged. The course project will consist of a research paper or project on a bioinformatics topic chosen by the student (with approval by the instructor) containing an element of independent computational biology research (e.g. calculation, programming, database analysis, etc.). This will be turned in as a link to a web page.

The final project is due on May 3, 2011.

From the TA