Difference between revisions of "CH391L 2013"

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(Lectures & Handouts)
(Lectures & Handouts)
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April 16, 2013 - Networks
 
April 16, 2013 - Networks
* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart]
+
* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] & the current state of the [HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network]
 
* Transcriptional networks: [http://www.marcottelab.org/users/CH391L/Handouts/ChIP-chipReview.pdf ChIP-Chip & ChIP-SEQ], [http://www.marcottelab.org/users/CH391L/Handouts/Lee.pdf large-scale screens-1], [http://www.marcottelab.org/users/CH391L/Handouts/Harbison.pdf large-scale screens-2], [http://www.marcottelab.org/users/CH391L/Handouts/HeritableTFsites.pdf heritability], and [http://www.genome.gov/10005107 ENCODE]
 
* Transcriptional networks: [http://www.marcottelab.org/users/CH391L/Handouts/ChIP-chipReview.pdf ChIP-Chip & ChIP-SEQ], [http://www.marcottelab.org/users/CH391L/Handouts/Lee.pdf large-scale screens-1], [http://www.marcottelab.org/users/CH391L/Handouts/Harbison.pdf large-scale screens-2], [http://www.marcottelab.org/users/CH391L/Handouts/HeritableTFsites.pdf heritability], and [http://www.genome.gov/10005107 ENCODE]
 
* Protein interactions: [http://www.marcottelab.org/users/CH391L_2013/Files/PPIIntro-4-2013.pptx overview], [http://www.marcottelab.org/users/CH391L/Handouts/uetz.pdf The first large-scale screens] & [http://www.marcottelab.org/users/CH391L/Handouts/schwikowski.pdf networks], and [http://www.marcottelab.org/paper-pdfs/Cell_HumanProteinComplexes_2012.pdf a recent map by co-fractionation]
 
* Protein interactions: [http://www.marcottelab.org/users/CH391L_2013/Files/PPIIntro-4-2013.pptx overview], [http://www.marcottelab.org/users/CH391L/Handouts/uetz.pdf The first large-scale screens] & [http://www.marcottelab.org/users/CH391L/Handouts/schwikowski.pdf networks], and [http://www.marcottelab.org/paper-pdfs/Cell_HumanProteinComplexes_2012.pdf a recent map by co-fractionation]

Revision as of 11:38, 16 April 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

April 16, 2013 - Networks

April 11, 2013 - Motifs

April 9, 2013

  • IMPORTANT REMINDER! Today is one of our scheduled NO CLASS DAYS! Given that, and the trouble that several students have had getting clustering software working on Macs, I'm

extending the homework due date to April 11.

April 2-4, 2013 - Classification & PCA/SVD

Mar 28, 2013 - Clustering & Classification

Mar 27, 2013

  • The seminar by Bob Sauer (2:30-3:30, Welch convocation center) conflicts with office hours today, so office hours will be held after seminar instead (3:30-4:30).

Mar 26, 2013 - Clustering 2

An assortment of datasets for Problem Set 4, due Apr. 9, 2013. Someone in the class noted that the phylogenetic profile file was space, not tab, delimited, and that there were a few lines with errors in the mRNA expression data. I've updated the links to be the correct versions. Also, several people have noted that the Mac/Linux versions of the tree viewing program seem to be a bit buggy; however, the Windows version (TreeView) seems to be fine.

Mar 21, 2013 - Clustering

Mar 19, 2013 - Gene expression Wrapping up sequencing:

& on to RNA expression!

Mar 7, 2013 - Assembly and mapping

Mar 5, 2013 - Assembling genomes + next-gen sequencing

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