Difference between revisions of "CH391L 2013"
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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] | ||
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* [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 | + | 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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| − | * | + | 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] | + | * '''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] | |
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* [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 12:34, 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
- 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: 1, 2, 3, 4, 5 6 7 8 9 10
- Fly - the genome
- Fly - the genome assembly
- GigAssembler
Feb 26, 2013 - Assembling genomes
- BACs, YACs, and cosmids, oh my!
- The H. influenzae genome paper
- Next-gen sequencing news, surveying the field just 2 years ago
- Sequencing, sequencing, sequencing - new technologies, yet more, and even more
- Prenatal screening by sequencing, now whole fetal genomes
- HW2.1
- published T segment histograms and in our own data
- One published strategy that does what you tried in your homework: TMHMM
- General: You're now ahead of the pack...
Feb 21, 2013 - Gene finding
- The GeneMark.hmm paper and the program
- The GENSCAN paper
- A nice review of gene finding
- Evaluating gene annotations: GASP, EGASP, & nGASP
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
- Breaking news: science of the highest importance!
- HMM primer
- Problem Set 2, due Feb. 26, 2013
- State sequences
- Soluble sequences
- Transmembrane sequences
Feb 12, 2013 - Profiles
- Bayesian statistics primer, Wiki Bayes, and a simple example
- For the masochists in the class: Care to practice your regular expressions? (In python?) Try this crossword puzzle.
- Profile analysis, as originally described
- A commentary on computational challenges arising from DNA sequencing
- The remarkable growth of Genbank, and similarly, UniProt
Feb 7, 2013 - BLAST
- The original BLAST paper
- Teaching BLAST
- The protein homology graph paper. Just for fun, here's a link to a stylized version we exhibited in the engaging Design and the Elastic Mind show at New York's Museum of Modern Art.
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
- An example of dynamic programming using Excel, created by Michael Hoffman (a former CH391L student; you can read more about Michael here)
- Dynamic programming primer
Jan 24, 2013 - Sequence Alignment I
- BLOSUM primer
- The original BLOSUM paper (hot off the presses from 1992!)
- BLOSUM miscalculations improve performance
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)
- Python primer
- Problem Set 1, due Feb. 5, 2013
- E. coli genome
- T. volcanium genome
- 3 mystery genes (for Problem 5): Mgene1, Mgene2, Mgene3
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
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
- If you don't have a unix/linux account to do the homework and/or project, send email to 'john.woods at marcottelab dot org'.
- CH391L_2013/Connecting_Server (If you don't know how to use the account info, this are the instructions.)
- If you are having trouble transferring files from your computer to server, here are some GUI programs that can help you:
- http://winscp.net/eng/index.php (WinSCP, Windows)
- http://cyberduck.ch/ (CyberDuck, Mac)
- http://filezilla-project.org/ (FileZilla, all platforms)
- How to make a web site for the final project
- Other relevant courses on campus:
- Geometric (Bio-) modeling and visualization
- Statistical and Discrete Methods for Scientific Computing
- BIO 337: Developmental Biology, emphasizing how to how to critically read and dissect papers.
