Difference between revisions of "CH391L 2013"

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(Lectures & Handouts)
(Lectures & Handouts)
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* [https://sites.google.com/site/bioinformaticsch391lproject/ Determination of antigen-specific antibody design criteria using cluster analysis]
 
* [https://sites.google.com/site/bioinformaticsch391lproject/ Determination of antigen-specific antibody design criteria using cluster analysis]
 
* [https://sites.google.com/site/ch391lanubenthk/ Prediction of improved aglycosylated Fc variants for FcγRs via structure based computation]
 
* [https://sites.google.com/site/ch391lanubenthk/ Prediction of improved aglycosylated Fc variants for FcγRs via structure based computation]
* [http://wcaar.dyndns.org/ch391l/ Determination of Evolutionary Environment via Phylogenetic Analysis]
 
 
* [https://sites.google.com/site/ch391lbrozellproject/ Variance in Human Cys-Loop Family of Transmembrane Proteins as Quantified by the Boltzman Distribution]
 
* [https://sites.google.com/site/ch391lbrozellproject/ Variance in Human Cys-Loop Family of Transmembrane Proteins as Quantified by the Boltzman Distribution]
 
* [http://web.biosci.utexas.edu/whiteley_lab/Jorth_Bioinformatics.html Genome sequencing links natural competence to CRISPR defense systems in the opportunistic pathogen ''Aggregatibacter actinomycetemcomitans'']
 
* [http://web.biosci.utexas.edu/whiteley_lab/Jorth_Bioinformatics.html Genome sequencing links natural competence to CRISPR defense systems in the opportunistic pathogen ''Aggregatibacter actinomycetemcomitans'']
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* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
  
Mar 8, 2011 - Assembling genomes + next-gen sequencing
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Mar 5, 2013 - Assembling genomes + next-gen sequencing
 
* [http://www.marcottelab.org/users/CH391L/FromTA/Mardis2008.pdf NextGen sequencing general review]
 
* [http://www.marcottelab.org/users/CH391L/FromTA/Mardis2008.pdf NextGen sequencing general review]
 
* [http://www.marcottelab.org/users/CH391L/FromTA/FlicekBirney2009.pdf NextGen sequencing analysis review]
 
* [http://www.marcottelab.org/users/CH391L/FromTA/FlicekBirney2009.pdf NextGen sequencing analysis review]
 
* [http://www.marcottelab.org/users/CH391L/FromTA/NGS_mapping_primer.pdf Mapping primer]
 
* [http://www.marcottelab.org/users/CH391L/FromTA/NGS_mapping_primer.pdf Mapping primer]
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* 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.)
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Feb 28, 2013 - Assembling genomes
* Here are a few examples of final projects from previous years: [http://sites.google.com/site/ch391fall08finaloconnellwang/?pageDeleted=%2Fa-monte-carlo-simulation-of-protein-polymerization-in-budding-yeast 1], [http://sites.google.com/site/polyomamirnatargeting/ 2], [http://sites.google.com/site/pathtarandmore/ 3], [http://sites.google.com/site/zlutexas/Home/project-for-ch391l 4], [https://webspace.utexas.edu/aca349/UTMCF/MAQC/UT_MAQC%20Paper.pdf 5]
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* '''Due March 8 by email''' - One (full) paragraph describing your plans for a final project.
 
+
* Here are a few examples of final projects from previous years: [http://sites.google.com/site/ch391fall08finaloconnellwang/?pageDeleted=%2Fa-monte-carlo-simulation-of-protein-polymerization-in-budding-yeast 1], [http://sites.google.com/site/polyomamirnatargeting/ 2], [http://sites.google.com/site/pathtarandmore/ 3], [http://sites.google.com/site/zlutexas/Home/project-for-ch391l 4], [https://webspace.utexas.edu/aca349/UTMCF/MAQC/UT_MAQC%20Paper.pdf 5] [https://sites.google.com/site/modelingpyrosequencingerror/ 6]  [https://sites.google.com/site/bioinformaticsch391lproject/ 7] [http://web.biosci.utexas.edu/whiteley_lab/Jorth_Bioinformatics.html 8] [https://sites.google.com/site/ch391lchipseq/ 9] [https://sites.google.com/site/arabmybgrant/ 10]
Mar 3, 2011 - Assembling genomes
+
* '''Due March 8 by email''' - One paragraph describing your plans for a final project
+
 
* [http://www.marcottelab.org/users/CH391L/Handouts/fly-genome.pdf Fly - the genome]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/fly-genome.pdf Fly - the genome]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/fly-assembly.pdf Fly - the genome assembly]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/fly-assembly.pdf Fly - the genome assembly]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/GigAssembler.pdf GigAssembler]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/GigAssembler.pdf GigAssembler]
  
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Feb 26, 2013 - Assembling genomes
 
Feb 26, 2013 - Assembling genomes
 
* [http://www.marcottelab.org/users/CH391L/Handouts/BACsYACsCosmidsOhMy.pdf BACs, YACs, and cosmids, oh my!]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/BACsYACsCosmidsOhMy.pdf BACs, YACs, and cosmids, oh my!]
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* [http://www.marcottelab.org/users/CH391L/ProblemSets/HW2.txt HW2.1]
 
* [http://www.marcottelab.org/users/CH391L/ProblemSets/HW2.txt HW2.1]
 
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143985/pdf/9568909.pdf published T segment histograms] and [http://www.marcottelab.org/users/CH391L/ProblemSets/state_sequences-Tsegmenthistogram.pdf in our own data]
 
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143985/pdf/9568909.pdf published T segment histograms] and [http://www.marcottelab.org/users/CH391L/ProblemSets/state_sequences-Tsegmenthistogram.pdf in our own data]
 +
* One published strategy that does what you tried in your homework: [http://www.marcottelab.org/users/CH391L_2013/Files/TMHMM.pdf TMHMM]
 
* General: [http://www.code.org/ You're now ahead of the pack...]
 
* General: [http://www.code.org/ You're now ahead of the pack...]
  

Revision as of 11:34, 28 February 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

Feb 28, 2013 - Assembling genomes

Feb 26, 2013 - Assembling genomes

Feb 21, 2013 - Gene finding

Feb 19, 2013 - HMMs and gene finding

  • Given that we're running a lecture behind, HW#2 will be due on Feb. 26, rather than the 21st.
  • Fly cell Markov chains

Feb 14, 2013 - HMMs

Feb 12, 2013 - Profiles

Feb 7, 2013 - BLAST

Feb 5, 2013 - Sequence Alignment III

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

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