Difference between revisions of "CH391L 2013"

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'''TA:''' John Woods, john.woods at marcottelab dot org<br>
 
'''TA:''' John Woods, john.woods at marcottelab dot org<br>
 
*'''TA Office hours:''' Tuesday/Friday 10:00 – 11:00 AM in MBB 3.128 '''Phone:''' 232-3919<br>
 
*'''TA Office hours:''' Tuesday/Friday 10:00 – 11:00 AM in MBB 3.128 '''Phone:''' 232-3919<br>
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** NOTE #1: John will be out of town 4/18 through 4/22. If you need to meet with him, email him and schedule a gchat meeting for Friday sometime.
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** NOTE #2: TA office hours will start at 10:30am the week of 4/22 instead of 10am (and will end at 11:30am). If you can't make it during those hours, as always, email John to set up an appointment.
  
 
== 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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* [https://webspace.utexas.edu/jl37857/CH391L/Project_FinalWriteup-formatted.pdf Searching for tissue-specific genomic neighborhoods]
 
* [https://webspace.utexas.edu/jl37857/CH391L/Project_FinalWriteup-formatted.pdf Searching for tissue-specific genomic neighborhoods]
  
May 3, 2011 - Synthetic biology
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-->
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May 2, 2013 - Some of the (few!) publicly-viewable final projects.  Many private ones this time!
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* [http://microarray.icmb.utexas.edu/annab_ch391l_project/ An Investigation of the Effects of Sequencing Depth on Binding Region Identification in ChIP-seq Data]
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* [https://www.sites.google.com/site/bioinfonsa237/ Extraction and Analysis of microRNA Precursor Sequences from Human RNA-Seq Datasets]
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* [https://sites.google.com/site/structureandevolutionofaprd4/home Structure and Evolution of AprD4]
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* [https://sites.google.com/site/emilo83/home Identifying differentially expressed genes]
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* [https://sites.google.com/site/finalprojectch391l/home Changes in host gene expression from Bordetella infection or toxicity]
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* [https://sites.google.com/site/bioinformaticsfinalproject/home Diagnosing breast cancer based on PBMC gene expression profile using Bayesian additive regression trees (BART) method]
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* [https://sites.google.com/a/utexas.edu/2013_bioinformatics/home Divergence of FRIGIDA in Arabidopsis thaliana ecotypes]
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April 30, 2013 - Synthetic biology
 
* [http://www.marcottelab.org/users/CH391L/Handouts/GenomeTransplantation.pdf Genome Transplantation]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/GenomeTransplantation.pdf Genome Transplantation]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/JCVI-1.0.pdf JCVI-1.0]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/JCVI-1.0.pdf JCVI-1.0]
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* [http://www.marcottelab.org/users/CH391L/Handouts/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/CH391L/Handouts/NewCellFromChemicalGenome.SOM.pdf SOM]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/CH391L/Handouts/NewCellFromChemicalGenome.SOM.pdf SOM]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/YeastSynthCsome.pdf Synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
  
April 28, 2011 - Synthetic biology
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April 25, 2013 - Synthetic biology
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* Fun science news of the day: [http://www.the-scientist.com/?articles.view/articleNo/35234/title/Families-and-Dogs-Share-Microbiota/ You and your dog share more than you might think]
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* & more [http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit Synthetic biology in the news]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/repressilator.pdf The infamous repressilator]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/repressilator.pdf The infamous repressilator]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/toggleswitch.pdf The infamous toggle switch]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/toggleswitch.pdf The infamous toggle switch]
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* [http://www.marcottelab.org/users/CH391L/Handouts/BacterialPhotography.pdf Bacterial photography]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/BacterialPhotography.pdf Bacterial photography]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/EdgeDetector.pdf Edge detector]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/EdgeDetector.pdf Edge detector]
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* & [http://www.marcottelab.org/users/CH391L_2013/Files/nbt.2510.pdf a more recent example of digital logic]
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* Finally, the example on metabolic engineering mentioned in class: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12051.html yeast making malarial drugs]
  
April 26, 2011 - Network alignment and motifs
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April 18-23, 2013 - Networks
* [http://www.marcottelab.org/users/CH391L/Handouts/Networkmotifs.pdf Network motifs]
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* [http://www.bio.miami.edu/dana/250/250S11_13.html Hox genes]
* [http://www.marcottelab.org/users/CH391L/Handouts/Networkmotifreview.pdf Network motif review]
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* [http://www.marcottelab.org/users/CH391L/Handouts/Networkmotifprofiles.pdf Network motif profiles], [http://www.marcottelab.org/users/CH391L/Handouts/Networkmotifcomment1.pdf Comment1], [http://www.marcottelab.org/users/CH391L/Handouts/Networkmotifcomment2.pdf Comment2]
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April 21, 2011 - Networks
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* [http://www.marcottelab.org/users/CH391L/Handouts/Enterotypes.pdf Enterotypes]
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* [http://www.marcottelab.org/users/CH391L/Handouts/HowManyPPIs.pdf How many PPIs]
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* [http://www.marcottelab.org/users/CH391L/Handouts/networkalignment.pdf PathBlast], [http://www.marcottelab.org/users/CH391L/Handouts/networkalignmentsupp.pdf Supplement]
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April 19, 2011 - Networks
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* [http://www.bio.miami.edu/dana/250/25009_12.html Hox genes]
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* [http://www.marcottelab.org/users/CH391L/Handouts/Koller.pdf Module networks]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/Koller.pdf Module networks]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/smallworld.pdf Small world networks]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/smallworld.pdf Small world networks]
* [http://en.wikipedia.org/wiki/Dijkstra%27s_algorithm Dijkstra's algorithm]
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* [http://en.wikipedia.org/wiki/Dijkstra%27s_algorithm Dijkstra's algorithm] ([http://www.marcottelab.org/users/CH391L_2013/Files/Djikstra-wikiexampleslowed.pptx animated])
 
* [http://www.marcottelab.org/users/CH391L/Handouts/scalefreedom.pdf Scale-free networks]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/scalefreedom.pdf Scale-free networks]
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* [http://www.marcottelab.org/users/CH391L/Handouts/ErrorAttackNetworks.pdf Attack tolerance]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/lethalitycentrality.pdf Lethality-centrality]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/lethalitycentrality.pdf Lethality-centrality]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/YeastComplexes.pdf Yeast complexes]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/YeastComplexes.pdf Yeast complexes]
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* [http://www.marcottelab.org/users/CH391L/Handouts/networkalignment.pdf PathBlast], [http://www.marcottelab.org/users/CH391L/Handouts/networkalignmentsupp.pdf Supplement]
  
April 14, 2011 - Networks
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April 16, 2013 - Networks
* [http://www.marcottelab.org/users/CH391L/Handouts/mirSOM.pdf mirSOM]
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* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] & the current state of the [http://www.marcottelab.org/users/CH391L_2013/Files/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network]
* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart]
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* 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], and [http://www.marcottelab.org/users/CH391L/Handouts/HeritableTFsites.pdf heritability]
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* Protein interactions: [http://www.marcottelab.org/users/CH391L_2013/Files/PPIIntro-4-2013.pptx overview], [http://www.marcottelab.org/users/CH391L/Handouts/uetz.pdf one of 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/Handouts/PPIIntro.ppt overview], [http://www.marcottelab.org/users/CH391L/Handouts/uetz.pdf large-scale screens] & [http://www.marcottelab.org/users/CH391L/Handouts/schwikowski.pdf networks]
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* [http://www.marcottelab.org/users/CH391L/Handouts/vonmering.pdf Protein interaction extent and quality]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/vonmering.pdf Protein interaction extent and quality]
  
April 12, 2011 - Motifs
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April 11, 2013 - Motifs
* Two linear algebra refreshers: [http://www.stanford.edu/~vvoelz/lectures/linalg-refresher.pdf 1], [http://www.eigenvector.com/Docs/LinAlg.pdf 2]
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* [http://www.eigenvector.com/Docs/LinAlg.pdf A linear algebra refresher]
* [http://www.marcottelab.org/users/CH391L/Handouts/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
* [http://www.marcottelab.org/users/CH391L/Handouts/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
 
* [http://www.rcsb.org/pdb/explore/explore.do?structureId=1L1M The biochemical basis of a particular motif]
 
* [http://www.rcsb.org/pdb/explore/explore.do?structureId=1L1M The biochemical basis of a particular motif]
* [http://www.marcottelab.org/users/CH391L/Handouts/GibbsSampling.pdf Gibbs Sampling]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/GibbsSampling.pdf Gibbs Sampling]
* [http://www.marcottelab.org/users/CH391L/Handouts/AlignAce.pdf AlignAce]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/AlignAce.pdf AlignAce]
  
April 7, 2011 - PCA/SVD
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April 9, 2013
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* 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
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extending the homework due date to April 11.
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April 2-4, 2013 - Classification & PCA/SVD
 
* [http://www.marcottelab.org/users/CH391L/Handouts/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post]
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* Science Signaling (more specifically, Neil R. Clark and Avi Ma’ayan!) had a [http://stke.sciencemag.org/cgi/content/full/sigtrans;4/190/tr3/DC1 nice, very gentle introduction to PCA] that I've reposted [http://www.marcottelab.org/users/CH391L_2013/Files/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/CH391L_2013/Files/2001967Slides-FINAL.ppt slides])
 
* [http://www.marcottelab.org/users/CH391L/Handouts/Nbt_primer-PCA.pdf NBT Primer on PCA]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/Nbt_primer-PCA.pdf NBT Primer on PCA]
 
April 5, 2011 - Classification
 
 
* The best open software for do-it-yourself data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka]
 
* The best open software for do-it-yourself data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka]
* [http://www.isibang.ac.in/pcm.htm Mahalanobis]
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* [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis] & his [http://www.aiaccess.net/English/Glossaries/GlosMod/e_gm_mahalanobis.htm Mahalanobis distance]
* [http://www.marcottelab.org/users/CH391L/Handouts/Fedoroff.pdf SVD of gene expression 1], [http://www.marcottelab.org/users/CH391L/Handouts/Alter.pdf 2]
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* [http://www.marcottelab.org/users/CH391L/Handouts/Fedoroff.pdf SVD of gene expression]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
  
Mar 31, 2011 - Clustering & Classification
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Mar 28, 2013 - Clustering & Classification
 
* [http://www.marcottelab.org/users/CH391L/Handouts/AMLALLclassification.pdf AML vs ALL]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/AMLALLclassification.pdf AML vs ALL]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/DLBCL-redux.pdf Diffuse large B cell lymphoma redux]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/DLBCL-redux.pdf Diffuse large B cell lymphoma redux]
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* Network visualization [http://www.marcottelab.org/users/CH391L_2013/Files/NBTPrimer-NetworkVisualization.pdf primer], [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf LGL], [http://www.cytoscape.org/ Cytoscape]
  
Mar 29, 2011 - Clustering 2
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Mar 27, 2013
* [http://www.marcottelab.org/users/CH391L/Handouts/FuzzyK-Means.pdf Fuzzy k-means]
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* 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).
* [http://www.marcottelab.org/users/CH391L/Handouts/SOM-geneexpression.pdf SOM gene expression]
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** & links to various applications of SOMs: [http://wn.com/Self_Organizing_Maps_Application 1], [http://www.bentley.edu/csbigs/documents/hua.pdf 2], [http://vizier.u-strasbg.fr/kohonen.htx 3], [http://en.wikipedia.org/wiki/Self-organizing_map 4], and a picture of [http://www.cis.hut.fi/research/som-research/teuvo.html Teuvo] himself
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** (From TA) You can run SOM clustering with Open Source Clustering package (alternative to Eisen's Cluster) with '-s' option, or GUI option. See http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM for detail. (FYI, it also supports PCA). If you are not happy with Cluster SOM function, statistical package R also provides a package for SOM (http://cran.r-project.org/web/packages/som/index.html).  
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An assortment of datasets for [http://www.marcottelab.org/users/CH391L/ProblemSets/ProblemSet4_2011.pdf '''Problem Set 4], due Apr. 12, 2011'''
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Mar 26, 2013 - Clustering 2
* [http://www.marcottelab.org/users/CH391L/ProblemSets/yeast_aaseqs Yeast protein sequences]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/FuzzyK-Means.pdf Fuzzy k-means]
* [http://www.marcottelab.org/users/CH391L/ProblemSets/yeast_phyloprofiles Yeast protein phylogenetic profiles]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/SOM-geneexpression.pdf SOM gene expression]
* [http://www.marcottelab.org/users/CH391L/ProblemSets/yeast_microarraydata Yeast mRNA expression profiles]
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** & links to various applications of SOMs: [http://wn.com/Self_Organizing_Maps_Application 1], [http://www.bentley.edu/centers/sites/www.bentley.edu.centers/files/csbigs/hua.pdf 2], [http://vizier.u-strasbg.fr/kohonen.htx 3], [http://en.wikipedia.org/wiki/Self-organizing_map 4], and a picture of [http://www.cis.hut.fi/research/som-research/teuvo.html Teuvo] himself (and his [http://websom.hut.fi/websom/stt/doc/fin/ analyses of Finnish news feeds and USENET articles])
* For simplicity, here are the summary files (edited slightly, showing total read counts, counts of reads where F3 and F5 map to the same organism, counts of F3 and counts of F5 reads) of all of the searches on the 5 environmental samples:
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** You can also run SOM clustering with the Open Source Clustering package (an alternative to Eisen's Cluster) with '-s' option, or GUI option. See http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM for detail. (FYI, it also supports PCA). If you are not happy with Cluster's SOM function, the statistical package R also provides a package for calculating SOMs (http://cran.r-project.org/web/packages/som/index.html).  
** [http://www.marcottelab.org/users/CH391L/ProblemSets/V3BC21_read_freq V3BC21]
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** [http://www.marcottelab.org/users/CH391L/ProblemSets/V3BC22_read_freq V3BC22]
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** [http://www.marcottelab.org/users/CH391L/ProblemSets/V3BC23_read_freq V3BC23]
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** [http://www.marcottelab.org/users/CH391L/ProblemSets/V3BC24_read_freq V3BC24]
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** [http://www.marcottelab.org/users/CH391L/ProblemSets/V3BC25_read_freq V3BC25]
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** & A link to the [http://www.marcottelab.org/index.php/CH391L/UTpond raw data]
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** <b>(From TA) I found a bug in my script to generate read_freq files, so if you downloaded these files before Apr. 5th (Tues), discard previous files and use these new ones.</b>
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Mar 24, 2011 - Clustering
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An assortment of datasets for [http://www.marcottelab.org/users/CH391L_2013/Files/ProblemSet4_2013.pdf '''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.
* [http://www.nature.com/nature/journal/v471/n7339/full/nature09837.html#/mutations-in-non-coding-regions News of the day: multiple myeloma cancer genomes]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/yeast_aaseqs Yeast protein sequences]
* [http://www.marcottelab.org/users/CH391L/Handouts/PNAS_phylogenetic_profiles.pdf Phylogenetic profiles]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
* [http://www.marcottelab.org/users/CH391L/Handouts/nature_review_2000.pdf Review of phylogenetic profiles]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/yeast_microarraydata2.txt Yeast mRNA expression profiles]
* [http://www.marcottelab.org/users/CH391L/Handouts/neuro_pass1.jpg Example phylo profiles from Neurospora]
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Mar 21, 2013 - Clustering
* [http://www.marcottelab.org/users/CH391L/Handouts/Bcelllymphoma.pdf B cell lymphomas]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/PNAS_phylogenetic_profiles.pdf Phylogenetic profiles 1] and [http://www.marcottelab.org/paper-pdfs/shailesh-natbt.pdf 2]
* [http://www.marcottelab.org/users/CH391L/Handouts/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/nature_review_2000.pdf Review of phylogenetic profiles]
* [http://www.marcottelab.org/users/CH391L/Handouts/K-means-Example.ppt K-means example (.ppt)]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/neuro_pass1.jpg Example phylo profiles from Neurospora]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/Bcelllymphoma.pdf B cell lymphomas]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/K-means-Example.ppt K-means example (.ppt)]
  
Mar 22, 2011 - Gene expression
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Mar 19, 2013 - Gene expression
* [http://www.marcottelab.org/users/CH391L/Handouts/ESTs.pdf Gene expression by ESTs]
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Wrapping up sequencing:
* [http://www.marcottelab.org/users/CH391L/Handouts/SAGE.pdf Gene expression by SAGE]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/DNASeqOverview.pdf An overview of the current state of DNA sequencing and applications]
* [http://www.marcottelab.org/users/CH391L/Handouts/Affy2.pdf Affy microarrays 1]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/kmerMutations.pdf Forward genetics by kmer comparisons]
* [http://www.marcottelab.org/users/CH391L/Handouts/Affy1.pdf Affy microarrays 2]
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& on to RNA expression!
* [http://www.marcottelab.org/users/CH391L/Handouts/DeRisi.pdf cDNA microarrays]
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* [http://www.marcottelab.org/users/CH391L_2013/Files/ESTs.pdf Gene expression by ESTs]
* [http://www.marcottelab.org/users/CH391L/Handouts/eisen.pdf Clustering by gene expression]
+
* [http://www.marcottelab.org/users/CH391L_2013/Files/SAGE.pdf Gene expression by SAGE]
* [http://www.marcottelab.org/users/CH391L/Handouts/Spellman.pdf Cell cycle data]
+
* [http://www.marcottelab.org/users/CH391L_2013/Files/Affy2.pdf Affy microarrays 1]
 +
* [http://www.marcottelab.org/users/CH391L_2013/Files/Affy1.pdf Affy microarrays 2]
 +
* [http://www.marcottelab.org/users/CH391L_2013/Files/DeRisi.pdf cDNA microarrays]
 +
* [http://www.marcottelab.org/users/CH391L_2013/Files/eisen.pdf Clustering by gene expression]
 +
* [http://www.marcottelab.org/users/CH391L_2013/Files/Spellman.pdf Cell cycle data]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
  
Mar 8, 2011 - Assembling genomes + next-gen sequencing
+
Mar 7, 2013 - Assembly and mapping
 +
* [http://en.wikipedia.org/wiki/Bellman-Ford_algorithm Bellman-Ford-Moore]
 +
* [http://en.wikipedia.org/wiki/Burrows-Wheeler_transform Burrows-Wheeler]
 +
* [http://en.wikipedia.org/wiki/Suffix_array Suffix Array]
 +
 
 +
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_2013/Files/Euler.pdf de Bruijn graph-based assembly using EULER] and a [http://www.marcottelab.org/users/CH391L_2013/Files/DeBruijnPrimer.pdf de Bruijn primer] (with [http://www.marcottelab.org/users/CH391L_2013/Files/DeBruijnSupplement.pdf Supplement])
 +
* [http://www.marcottelab.org/users/CH391L_2013/Files/velvet-presentation.pdf An intro to the Velvet assembler], assembled (no pun intended) by former UT undergraduate Matthew Tien
 
* [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]
 +
* [http://www.marcottelab.org/users/CH391L_2013/Files/CH391L_AssemblyNGS.ppt Assembly/NGS slides]
  
* 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.)
+
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]
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]
  
-->
 
 
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!]
Line 145: Line 158:
 
* Sequencing, sequencing, sequencing - [http://agbt.org/agenda.html new technologies], [http://www2.technologyreview.com/article/427677/nanopore-sequencing/ yet more], and [http://www.technologyreview.com/news/511311/solid-state-sequencer-debuts-at-genome-conference/ even more]
 
* Sequencing, sequencing, sequencing - [http://agbt.org/agenda.html new technologies], [http://www2.technologyreview.com/article/427677/nanopore-sequencing/ yet more], and [http://www.technologyreview.com/news/511311/solid-state-sequencer-debuts-at-genome-conference/ even more]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/DownSequencing.pdf Prenatal screening by sequencing], now [http://www.marcottelab.org/users/CH391L_2013/Files/FetalGenome.pdf whole fetal genomes]
 
* [http://www.marcottelab.org/users/CH391L/Handouts/DownSequencing.pdf Prenatal screening by sequencing], now [http://www.marcottelab.org/users/CH391L_2013/Files/FetalGenome.pdf whole fetal genomes]
<!--
 
 
* [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...]
  
 
Feb 21, 2013 - Gene finding
 
Feb 21, 2013 - Gene finding
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** [http://www.cs.utexas.edu/~bajaj/cs384R2012/ Geometric (Bio-) modeling and visualization]
 
** [http://www.cs.utexas.edu/~bajaj/cs384R2012/ Geometric (Bio-) modeling and visualization]
 
** [http://slate.ices.utexas.edu/coursewiki/index.php/Main_Page Statistical and Discrete Methods for Scientific Computing]
 
** [http://slate.ices.utexas.edu/coursewiki/index.php/Main_Page Statistical and Discrete Methods for Scientific Computing]
** [http://www.bio.utexas.edu/faculty/wallingford/class2013/ BIO 337: Developmental Biology], emphasizing how to how to critically read and dissect papers.
+
** [http://www.bio.utexas.edu/faculty/wallingford/class2013/ BIO 337: Developmental Biology], emphasizing how to critically read and dissect papers.

Latest revision as of 11:20, 19 December 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
    • NOTE #1: John will be out of town 4/18 through 4/22. If you need to meet with him, email him and schedule a gchat meeting for Friday sometime.
    • NOTE #2: TA office hours will start at 10:30am the week of 4/22 instead of 10am (and will end at 11:30am). If you can't make it during those hours, as always, email John to set up an appointment.

Lectures & Handouts

May 2, 2013 - Some of the (few!) publicly-viewable final projects. Many private ones this time!

April 30, 2013 - Synthetic biology

April 25, 2013 - Synthetic biology

April 18-23, 2013 - Networks

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