Difference between revisions of "CH391L 2013"

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* Repeats in the human genome, tallied [http://www.biochem.arizona.edu/classes/bioc471/pages/Lecture7/a6GenomeRepeats.jpg here]
 
* Repeats in the human genome, tallied [http://www.biochem.arizona.edu/classes/bioc471/pages/Lecture7/a6GenomeRepeats.jpg here]
  
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Jan 31, 2013 - Sequence Alignment II
 
Jan 31, 2013 - Sequence Alignment II
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/GALPAS.xls An example of dynamic programming using Excel], created by [http://noble.gs.washington.edu/~mmh1/ Michael Hoffman] (a former CH391L student; you can read more about Michael [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/MichaelHoffman.pdf here])
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* [http://www.marcottelab.org/users/CH391L_2013/Files/GALPAS.xls An example of dynamic programming using Excel], created by [http://noble.gs.washington.edu/~mmh1/ Michael Hoffman] (a former CH391L student; you can read more about Michael [http://www.marcottelab.org/users/CH391L_2013/Files/MichaelHoffman.pdf here])
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Lecture5-NBT-primer-dynamicprogramming.pdf Dynamic programming primer]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/Lecture5-NBT-primer-dynamicprogramming.pdf Dynamic programming primer]
  
 
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Jan 24, 2013 - Sequence Alignment I
 
Jan 24, 2013 - Sequence Alignment I
 
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* [http://www.marcottelab.org/users/CH391L/CH391L_SeqAlign1.pdf Taejoon's presentation file]
 
* [http://www.marcottelab.org/users/CH391L/CH391L_SeqAlign1.pdf Taejoon's presentation file]
 
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* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Lecture4-NBT-primer-BLOSUM.pdf BLOSUM primer]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/Lecture4-NBT-primer-BLOSUM.pdf BLOSUM primer]
* [http://www.marcottelab.org/users/CH391L/Handouts/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
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* [http://www.marcottelab.org/users/CH391L_2013/Files/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
  
 
Jan 22, 2013 - Intro to Python
 
Jan 22, 2013 - Intro to Python
 
* Just FYI, we seem to be having a few issues with the server, but it should be up and running now (as of 9:50PM)
 
* Just FYI, we seem to be having a few issues with the server, but it should be up and running now (as of 9:50PM)
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Lecture3-Python_primer-Spring2013.pdf Python primer]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/Lecture3-Python_primer-Spring2013.pdf Python primer]
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/ProblemSet1_Spring2013.pdf Problem Set 1], due Feb. 5, 2013
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* [http://www.marcottelab.org/users/CH391L_2013/Files/ProblemSet1_Spring2013.pdf Problem Set 1], due Feb. 5, 2013
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Ecoli_genome.txt E. coli genome]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/Ecoli_genome.txt E. coli genome]
* [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Tvolcanium_genome.txt T. volcanium genome]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/Tvolcanium_genome.txt T. volcanium genome]
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Mgene1 Mgene1], [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Mgene2 Mgene2], [http://www.marcottelab.org/users/CH391L_2013/ProblemSets/Mgene3 Mgene3]
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* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/CH391L_2013/Files/Mgene1 Mgene1], [http://www.marcottelab.org/users/CH391L_2013/Files/Mgene2 Mgene2], [http://www.marcottelab.org/users/CH391L_2013/Files/Mgene3 Mgene3]
  
 
Jan 17, 2013 - Newsworthy computational biology story of the week!
 
Jan 17, 2013 - Newsworthy computational biology story of the week!
* [http://www.marcottelab.org/users/CH391L_2013/Papers/321.full.pdf ''Gymrek et al.''] ([http://www.marcottelab.org/users/CH391L_2013/Papers/1229566.Gymrek.SM.pdf Supplement]) show that genomic datasets are not as anonymous as we thought!]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/321.full.pdf ''Gymrek et al.''] ([http://www.marcottelab.org/users/CH391L_2013/Files/1229566.Gymrek.SM.pdf Supplement]) show that genomic datasets are not as anonymous as we thought!]
* There are some associated commentaries, if you're curious: [http://www.marcottelab.org/users/CH391L_2013/Papers/275.full.pdf #1] [http://www.marcottelab.org/users/CH391L_2013/Papers/262.full.pdf# 2] [http://io9.com/5976845/your-biggest-genetic-secrets-can-now-be-hacked-stolen-and-used-for-target-marketing #3]
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* There are some associated commentaries, if you're curious: [http://www.marcottelab.org/users/CH391L_2013/Files/275.full.pdf #1] [http://www.marcottelab.org/users/CH391L_2013/Files/262.full.pdf# 2] [http://io9.com/5976845/your-biggest-genetic-secrets-can-now-be-hacked-stolen-and-used-for-target-marketing #3]
  
 
== Syllabus & course outline ==
 
== Syllabus & course outline ==

Revision as of 12:29, 31 January 2013

Contents

CH364C/CH391L Bioinformatics

Course unique #: 52716/52990
Lectures: Tuesday/Thursday 2:00 – 3:30 PM in WEL 3.260
Instructor: Edward Marcotte, marcotte@icmb.utexas.edu

  • Office hours: Wednesdays 2:00 – 3:00 PM in MBB 3.148BA Phone: 471-5435

TA: John Woods, john.woods at marcottelab dot org

  • TA Office hours: Tuesday/Friday 10:00 – 11:00 AM in MBB 3.128 Phone: 232-3919

Lectures & Handouts

Jan 31, 2013 - Sequence Alignment II

Jan 24, 2013 - Sequence Alignment I

Jan 22, 2013 - Intro to Python

Jan 17, 2013 - Newsworthy computational biology story of the week!

  • Gymrek et al. (Supplement) show that genomic datasets are not as anonymous as we thought!]
  • There are some associated commentaries, if you're curious: #1 2 #3

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, synthetic biology, analysis of gene expression 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
Assorted bioinformatics resources on the web: #1, #2
Python coding for beginners
Beginning Python for Bioinformatics
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 April 30, 2013.

Helpful links