Difference between revisions of "BCH391L 2015"
From Marcotte Lab
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== Lectures & Handouts == | == Lectures & Handouts == | ||
| − | + | '''May 5 - 7, 2015 - Final Projects''' | |
| − | ''' | + | <!--* [https://sites.google.com/site/virtualscreeningofnovelligands/ Virtual Screening of Novel Ligands]--> |
| − | * [https://sites.google.com/site/virtualscreeningofnovelligands/ Virtual Screening of Novel Ligands] | + | |
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| − | '''April | + | '''April 30, 2015 - Synthetic Biology II''' |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_SyntheticBio2_Spring2015.pdf Today's slides] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/GenomeTransplantation.pdf Genome Transplantation] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/JCVI-1.0.pdf JCVI-1.0] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/EllingtonDNAFab.jpg A DNA Fab], courtesy of [http://ellingtonlab.org/ Andy Ellington] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/OneStepAssemblyInYeast.pdf One step genome assembly in yeast] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH391L_2015/NewCellFromChemicalGenome.SOM.pdf SOM] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome] |
| − | * & the latest: [http://www.marcottelab.org/users/ | + | * & the latest: [http://www.marcottelab.org/users/BCH391L_2015/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome] |
Food for thought:<br> | Food for thought:<br> | ||
[http://www.nationalgeographic.com/deextinction De-extinction I] and [http://science.kqed.org/quest/video/reawakening-extinct-species/ II] | [http://www.nationalgeographic.com/deextinction De-extinction I] and [http://science.kqed.org/quest/video/reawakening-extinct-species/ II] | ||
| − | '''April | + | '''April 28, 2015 - Synthetic Biology I''' |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_SyntheticBio1_Spring2015.pdf Today's slides] |
* [http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit Synthetic biology in the news] | * [http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit Synthetic biology in the news] | ||
* [http://en.wikipedia.org/wiki/Gillespie_algorithm The Gillespie algorithm] | * [http://en.wikipedia.org/wiki/Gillespie_algorithm The Gillespie algorithm] | ||
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* [http://www.popsci.com/diy/article/2013-08/grow-photo Take your own coliroids] | * [http://www.popsci.com/diy/article/2013-08/grow-photo Take your own coliroids] | ||
Reading:<br> | Reading:<br> | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/repressilator.pdf The infamous repressilator] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/EdgeDetector.pdf Edge detector] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/nbt.2510.pdf A more recent example of digital logic] |
* An example of metabolic engineering: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12051.html yeast making anti-malarial drugs] | * An example of metabolic engineering: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12051.html yeast making anti-malarial drugs] | ||
| − | '''April | + | '''April 23, 2015 - Networks II & Phenologs''' |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_Phenologs_Spring2015.pdf Today's slides] |
| − | * [http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010.pdf Phenologs] and the [http://www.marcottelab.org/paper-pdfs/PLoSBiology_TBZ_2012.pdf drug discovery story] we | + | * [http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010.pdf Phenologs] and the [http://www.marcottelab.org/paper-pdfs/PLoSBiology_TBZ_2012.pdf drug discovery story] we'll discuss in class |
* Search for phenologs [http://www.phenologs.org/ here]. You can get started by rediscovering the plant model of Waardenburg syndrome. Search among the known diseases for "Waardenburg", or enter the human genes linked to Waardenburg (Entrez gene IDs 4286, 5077, 6591, 7299) to get a feel for how this works. Also, here's [http://www.nytimes.com/2010/04/27/science/27gene.html?_r=0 Carl Zimmer's NYT article] about phenologs and the scientific process. | * Search for phenologs [http://www.phenologs.org/ here]. You can get started by rediscovering the plant model of Waardenburg syndrome. Search among the known diseases for "Waardenburg", or enter the human genes linked to Waardenburg (Entrez gene IDs 4286, 5077, 6591, 7299) to get a feel for how this works. Also, here's [http://www.nytimes.com/2010/04/27/science/27gene.html?_r=0 Carl Zimmer's NYT article] about phenologs and the scientific process. | ||
* One good tool for discovering orthologs is [http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid]. Note: InParanoid annotation lags a bit, so you'll need to find the [http://www.ensembl.org/index.html Ensembl] protein id, or try a text search for the common name. | * One good tool for discovering orthologs is [http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid]. Note: InParanoid annotation lags a bit, so you'll need to find the [http://www.ensembl.org/index.html Ensembl] protein id, or try a text search for the common name. | ||
| − | '''April | + | '''April 16-21, 2015 - Networks''' |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_Networks_Spring2015.pdf Today's slides] |
| − | * Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] (it's interactive, e.g. here's [http://web.expasy.org/cgi-bin/pathways/show_image?E5&left enolase]), the current state of the [http://www.marcottelab.org/users/ | + | * Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] (it's interactive, e.g. here's [http://web.expasy.org/cgi-bin/pathways/show_image?E5&left enolase]), the current state of the [http://www.marcottelab.org/users/BCH391L_2015/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], and older but still relevant review of [http://www.marcottelab.org/users/BCH391L_2015/ChIP-chipReview.pdf transcriptional networks] (with the current record holder in this regard held by [http://www.genome.gov/10005107 ENCODE]), and an early review of [http://www.marcottelab.org/users/BCH391L_2015/vonmering.pdf protein interaction extent and quality] whose lessons still hold. |
* Useful gene network resources include: | * Useful gene network resources include: | ||
** [http://www.functionalnet.org FunctionalNet], which links to human, worm, Arabidopsis, mouse and yeast gene networks. Not the prettiest web site, but useful, and helped my own group find genes for a wide variety of biological processes. Try searching HumanNet for the myelin regulatory factor MYRF (Entrez gene ID 745) and predicting its function, which is now known but wasn't when the network was made. | ** [http://www.functionalnet.org FunctionalNet], which links to human, worm, Arabidopsis, mouse and yeast gene networks. Not the prettiest web site, but useful, and helped my own group find genes for a wide variety of biological processes. Try searching HumanNet for the myelin regulatory factor MYRF (Entrez gene ID 745) and predicting its function, which is now known but wasn't when the network was made. | ||
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* [http://www.marcottelab.org/paper-pdfs/ng-fraser-review.pdf Functional networks] | * [http://www.marcottelab.org/paper-pdfs/ng-fraser-review.pdf Functional networks] | ||
* [http://www.marcottelab.org/paper-pdfs/JProteomics_GBAReview_2010.pdf Review of predicting gene function and phenotype from protein networks] | * [http://www.marcottelab.org/paper-pdfs/JProteomics_GBAReview_2010.pdf Review of predicting gene function and phenotype from protein networks] | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks] |
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'''Apr 14, 2015 - Genome Engineering''' | '''Apr 14, 2015 - Genome Engineering''' | ||
* Guest speaker: [http://cssb.utexas.edu/fellows/christopher-yellman/ Dr. Chris Yellman] | * Guest speaker: [http://cssb.utexas.edu/fellows/christopher-yellman/ Dr. Chris Yellman] | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/synthetic-biology-genome-engineering-2-2014.ppt Today's slides] |
| − | ''' | + | '''Apr 9, 2015 - Principal Component Analysis (& the curious case of European genotypes)''' |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_PCA_Spring2015.pdf Today's slides] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/EuropeanGenesPCA.pdf European men, their genomes, and their geography] |
* For those of you using classifiers for your projects, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka] | * For those of you using classifiers for your projects, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka] | ||
* & since he's come up in class several times: [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis] | * & since he's come up in class several times: [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis] | ||
A smattering of links on PCA:<br> | A smattering of links on PCA:<br> | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/NBT_primer_PCA.pdf NBT Primer on PCA] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post] |
| − | * 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 introduction to PCA] that I've reposted [http://www.marcottelab.org/users/ | + | * 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 introduction to PCA] that I've reposted [http://www.marcottelab.org/users/BCH391L_2015/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH391L_2015/2001967Slides-FINAL.ppt slides]) |
| − | ''' | + | '''Apr 7, 2015 - Classifiers I''' |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_Classifiers_Spring2015.pdf Today's slides] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/AMLALLclassification.pdf Classifying leukemias] |
| − | ''' | + | '''Apr 2, 2015 - Clustering II |
| − | * We're finishing up the slides from Mar. | + | * We're finishing up the slides from Mar. 31.<br> |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/FuzzyK-Means.pdf Fuzzy k-means] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/SOM-geneexpression.pdf SOM gene expression] |
** Links to various applications of SOMs: [http://en.wikipedia.org/wiki/Self-organizing_map 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://wn.com/Self_Organizing_Maps_Application 4]. You can run SOMs on the [http://www.math.le.ac.uk/people/ag153/homepage/PCA_SOM/PCA_SOM.html following web site]. 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). | ** Links to various applications of SOMs: [http://en.wikipedia.org/wiki/Self-organizing_map 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://wn.com/Self_Organizing_Maps_Application 4]. You can run SOMs on the [http://www.math.le.ac.uk/people/ag153/homepage/PCA_SOM/PCA_SOM.html following web site]. 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/ | + | '''Mar 31, 2015 - Functional Genomics & Data Mining - Clustering I''' |
| + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_LargeScaleExperiments_Spring2015.pdf Today's slides] | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/nature_review_2000.pdf Review of phylogenetic profiles] | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/Bcelllymphoma.pdf B cell lymphomas] | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/NBTPrimer-MicroarrayClustering.pdf Primer on clustering] | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/K-means-Example.ppt K-means example (.ppt)] | ||
| + | [http://www.marcottelab.org/users/BCH391L_2015/ProblemSet3_2015.pdf '''Problem Set 3], due before midnight Apr. 9, 2015'''. You will need the following software and datasets:<br> | ||
* The clustering and treeview software is available [http://rana.lbl.gov/EisenSoftware.htm here]. Previous students have said the Mac/Linux versions of the tree viewing program can be a bit buggy; however, the Windows version (TreeView) seems to be fine.<br> | * The clustering and treeview software is available [http://rana.lbl.gov/EisenSoftware.htm here]. Previous students have said the Mac/Linux versions of the tree viewing program can be a bit buggy; however, the Windows version (TreeView) seems to be fine.<br> | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/yeast_aaseqs Yeast protein sequences] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/yeast_microarraydata2.txt Yeast mRNA expression profiles] |
| − | '''Mar | + | '''Mar 26, 2015 - Mapping protein complexes''' |
| + | * Guest speaker: [http://www.blakeb.org/ Blake Borgeson] | ||
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| + | '''Mar 24, 2015 - Mass spectrometry proteomics''' | ||
* Welcome back from Spring Break. A gentle reminder that HW3 is '''due by 11:59PM tonight'''... | * Welcome back from Spring Break. A gentle reminder that HW3 is '''due by 11:59PM tonight'''... | ||
| − | * [http://www.marcottelab.org/users/ | + | * Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz] |
| − | * [http://www.marcottelab.org/users/ | + | |
| − | * [http://www.marcottelab.org/users/ | + | '''Mar 17-19, 2015 - SPRING BREAK''' |
| − | * [http://www.marcottelab.org/users/ | + | |
| − | * [http://www.marcottelab.org/users/ | + | '''Mar 12, 2015 - Motifs''' |
| + | <!-- * [http://www.eigenvector.com/Docs/LinAlg.pdf A linear algebra refresher] --> | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_Motifs_Spring2015.pdf Today's slides] | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?] | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/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.marcottelab.org/users/BCH391L_2015/GibbsSampling.pdf Gibbs Sampling] | ||
| + | * [http://www.marcottelab.org/users/BCH391L_2015/AlignAce.pdf AlignAce] | ||
| − | '''Mar | + | '''Mar 10, 2015 - Genomes II, Gene Expression'''<br> |
| + | * Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 24'''. | ||
* Science news of the day: [http://www.nytimes.com/2014/03/06/health/study-gives-hope-of-altering-genes-to-repel-hiv.html Genome engineering vs. HIV] | * Science news of the day: [http://www.nytimes.com/2014/03/06/health/study-gives-hope-of-altering-genes-to-repel-hiv.html Genome engineering vs. HIV] | ||
| − | * We're finishing up the slides from Mar. | + | * We're finishing up the slides from Mar. 5. Note: we'll increasingly be discussing primary papers in the lectures<br> |
| − | Note: we'll increasingly be discussing primary papers in the lectures<br> | + | * [http://www.marcottelab.org/users/BCH391L_2015/DNASeqOverview.pdf An overview of the current state of DNA sequencing and applications] |
| − | * [http://www.marcottelab.org/users/ | + | |
& on to RNA expression! | & on to RNA expression! | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/ESTs.pdf Gene expression by ESTs] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/SAGE.pdf Gene expression by SAGE] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/Affy2.pdf Affy microarrays 1] & [http://www.marcottelab.org/users/BIO337_2014/Affy1.pdf Affy microarrays 2] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/DeRisi.pdf cDNA microarrays] |
* [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq] | * [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq] | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/eisen.pdf Clustering by gene expression] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/Spellman.pdf Cell cycle data] |
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering] | * [http://en.wikipedia.org/wiki/Cluster_analysis Clustering] | ||
| − | '''Mar | + | '''Mar 5, 2015 - Genome Assembly''' |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_GenomeAssembly_Spring2015.pdf Today's slides] |
| − | + | * [http://www.marcottelab.org/users/BCH391L_2015/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH391L_2015/DeBruijnSupplement.pdf Supplement] | |
| − | * [http://www.marcottelab.org/users/ | + | |
| − | ''' | + | '''Mar 3, 2015 - Gene finding II''' |
| − | * We're finishing up the slides from Feb. | + | * We're finishing up the slides from Feb. 26. A gentle reminder that HW2 is '''due by 11:59PM tonight'''... |
| + | * '''Due March 12 by email''' - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators. This assignment will account for 5 points out of your 25 total points for your course 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://sites.google.com/site/structureandevolutionofaprd4/home 5] [https://sites.google.com/site/modelingpyrosequencingerror/ 6] [https://sites.google.com/site/bioinformaticsch391lproject/ 7] [https://sites.google.com/site/emilo83/home 8] [https://sites.google.com/site/ch391lchipseq/ 9] [https://sites.google.com/site/arabmybgrant/ 10] [https://sites.google.com/site/biogridviewer/home 11] [https://sites.google.com/a/utexas.edu/immunoglobulin-team/home 12] [https://metabolicnetworkpathways.wordpress.com/ 13] [https://sites.google.com/a/utexas.edu/quantum-tunneling-on-enzymatic-kinetics/home 14]<br> | ||
News of the day, regarding the application of next gen sequencing to fetal diagnostics:<br> | News of the day, regarding the application of next gen sequencing to fetal diagnostics:<br> | ||
* [http://well.blogs.nytimes.com/2014/02/26/new-dna-test-better-at-predicting-some-disorders-in-babies-study-finds/?hp Timely article in the New York Times] | * [http://well.blogs.nytimes.com/2014/02/26/new-dna-test-better-at-predicting-some-disorders-in-babies-study-finds/?hp Timely article in the New York Times] | ||
* [http://www.acog.org/Resources_And_Publications/Committee_Opinions/Committee_on_Genetics/Noninvasive_Prenatal_Testing_for_Fetal_Aneuploidy Official recommendations for doctors] | * [http://www.acog.org/Resources_And_Publications/Committee_Opinions/Committee_on_Genetics/Noninvasive_Prenatal_Testing_for_Fetal_Aneuploidy Official recommendations for doctors] | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/FetalAneuploidyDiagnostics.pdf Detecting fetal aneuploidy by NGS of maternal blood] |
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/FetalAneuploidyTrial.pdf A recent fetal aneuploidy trial] |
| − | '''Feb | + | '''Feb 26, 2015 - Gene finding''' |
| − | + | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L-GeneFinding-Spring2015.pdf Today's slides] | |
| − | + | ||
| − | * [http://www.marcottelab.org/users/ | + | |
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570 The UCSC genome browser] | * [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570 The UCSC genome browser] | ||
Reading:<br> | Reading:<br> | ||
| − | * [http://www.marcottelab.org/users/ | + | * [http://www.marcottelab.org/users/BCH391L_2015/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH391L_2015/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH391L_2015/BurgeKarlin-main.pdf GENSCAN] |
'''Feb 24, 2015 - HMMs II''' | '''Feb 24, 2015 - HMMs II''' | ||
| Line 188: | Line 160: | ||
* [http://www.marcottelab.org/users/BCH391L_2015/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BIO337_2014/NBTPrimer-Bayes.pdf Bayesian statistics primer], [http://en.wikipedia.org/wiki/Bayes'_theorem Wiki Bayes] | * [http://www.marcottelab.org/users/BCH391L_2015/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BIO337_2014/NBTPrimer-Bayes.pdf Bayesian statistics primer], [http://en.wikipedia.org/wiki/Bayes'_theorem Wiki Bayes] | ||
* Care to practice your [http://en.wikipedia.org/wiki/Regular_expression regular expressions]? (In [http://www.tutorialspoint.com/python/python_reg_expressions.htm python?]) | * Care to practice your [http://en.wikipedia.org/wiki/Regular_expression regular expressions]? (In [http://www.tutorialspoint.com/python/python_reg_expressions.htm python?]) | ||
| − | + | ||
| − | + | ||
'''Feb 17, 2015 - Next-generation Sequencing (NGS)''' | '''Feb 17, 2015 - Next-generation Sequencing (NGS)''' | ||
* Guest speaker: [http://cssb.utexas.edu/members/scott-hunicke-smith/ Dr. Scott Hunicke-Smith], director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility].--> | * Guest speaker: [http://cssb.utexas.edu/members/scott-hunicke-smith/ Dr. Scott Hunicke-Smith], director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility].--> | ||
<!--* [http://www.marcottelab.org/users/BIO337_2014/bio337_feb18_ngs.pdf Today's slides]--> | <!--* [http://www.marcottelab.org/users/BIO337_2014/bio337_feb18_ngs.pdf Today's slides]--> | ||
| − | |||
* [http://www.youtube.com/watch?v=77r5p8IBwJk Illumina/Solexa Sequencing (Youtube Video)] | * [http://www.youtube.com/watch?v=77r5p8IBwJk Illumina/Solexa Sequencing (Youtube Video)] | ||
* [http://www.youtube.com/watch?v=45vNetkGspo Genome Analyzer (Youtube Video)] | * [http://www.youtube.com/watch?v=45vNetkGspo Genome Analyzer (Youtube Video)] | ||
| Line 199: | Line 169: | ||
'''Feb 12, 2015 - 3D Protein Structure Modeling''' | '''Feb 12, 2015 - 3D Protein Structure Modeling''' | ||
* Guest speaker: [http://bonneaulab.bio.nyu.edu/people.html#kevin Dr. Kevin Drew] | * Guest speaker: [http://bonneaulab.bio.nyu.edu/people.html#kevin Dr. Kevin Drew] | ||
| + | * The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH391L_2015/RosettaOverview.pdf what it can do for you] | ||
'''Feb 10, 2015 - Biological databases''' | '''Feb 10, 2015 - Biological databases''' | ||
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH391L_2015/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Myers] to refresh/explain basic concepts. | * Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH391L_2015/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Myers] to refresh/explain basic concepts. | ||
* [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L-BiologicalDatabases-Spring2015.pdf Today's slides]<br> | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L-BiologicalDatabases-Spring2015.pdf Today's slides]<br> | ||
| − | |||
<!--* The [http://www.marcottelab.org/users/BCH391L_2015/PNAS-2014-Lee-1313039111.pdf EteRNA paper] and the [http://www.marcottelab.org/users/BCH391L_2015/Science-2014-Bohannon-475.pdf news article about it]--> | <!--* The [http://www.marcottelab.org/users/BCH391L_2015/PNAS-2014-Lee-1313039111.pdf EteRNA paper] and the [http://www.marcottelab.org/users/BCH391L_2015/Science-2014-Bohannon-475.pdf news article about it]--> | ||
| − | + | ||
'''Feb 5, 2015 - Guest lecture: Intro to Appsoma''' | '''Feb 5, 2015 - Guest lecture: Intro to Appsoma''' | ||
* We'll have a guest lecture by [http://www.mine-control.com/zack/ Zack Simpson], a Fellow of the [http://web.cssb.utexas.edu/ UT Center for Systems and Synthetic Biology]. For the curious, ''Science'' magazine wrote a nice feature on Zack several years ago ([http://www.marcottelab.org/users/BCH391L_2015/Science_Zack.pdf posted here]). Zack co-founded the bioinformatics startup company [http://www.traitwise.com/ Traitwise] (full disclosure: I'm on their scientific advisory board) and is the lead developer of [https://appsoma.com/home Appsoma], a web-based scientific cloud computing platform that has a number of enhancements (and dedicated computer clusters) specifically for UT students. | * We'll have a guest lecture by [http://www.mine-control.com/zack/ Zack Simpson], a Fellow of the [http://web.cssb.utexas.edu/ UT Center for Systems and Synthetic Biology]. For the curious, ''Science'' magazine wrote a nice feature on Zack several years ago ([http://www.marcottelab.org/users/BCH391L_2015/Science_Zack.pdf posted here]). Zack co-founded the bioinformatics startup company [http://www.traitwise.com/ Traitwise] (full disclosure: I'm on their scientific advisory board) and is the lead developer of [https://appsoma.com/home Appsoma], a web-based scientific cloud computing platform that has a number of enhancements (and dedicated computer clusters) specifically for UT students. | ||
| Line 238: | Line 208: | ||
* [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_Lecture2-Python_primer-Spring2015.pdf Python primer] | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L_Lecture2-Python_primer-Spring2015.pdf Python primer] | ||
* [http://www.marcottelab.org/users/BCH391L_2015/Ecoli_genome.txt E. coli genome] | * [http://www.marcottelab.org/users/BCH391L_2015/Ecoli_genome.txt E. coli genome] | ||
| − | + | ||
'''Jan 20, 2015 - Introduction''' | '''Jan 20, 2015 - Introduction''' | ||
* [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L-IntroAndRosalind-Spring2015.pptx Today's slides]<br> | * [http://www.marcottelab.org/users/BCH391L_2015/BCH364C-391L-IntroAndRosalind-Spring2015.pptx Today's slides]<br> | ||
Revision as of 12:45, 19 January 2015
BCH364C/391L Systems Biology/Bioinformatics
Course unique #: 54995/55095
Lectures: Tues/Thurs 11 – 12:30 PM in BUR 212
Instructor: Edward Marcotte, marcotte@icmb.utexas.edu
- Office hours: Wed 11 AM – 12 noon in MBB 3.148BA
TA: Joe Taft, taft@utexas.edu
- TA Office hours: Mon/Fri 11 AM - 12 noon in MBB 3.310 Phone: listed on the syllabus
Lectures & Handouts
May 5 - 7, 2015 - Final Projects
April 30, 2015 - Synthetic Biology II
- Today's slides
- Genome Transplantation
- JCVI-1.0
- A DNA Fab, courtesy of Andy Ellington
- One step genome assembly in yeast
- New cells from yeast genomic clones
- A new cell from a chemically synthesized genome, SOM
- 1/2 a synthetic yeast chromosome and Build-A-Genome
- & the latest: Entire synthetic yeast chromosome
Food for thought:
De-extinction I and II
April 28, 2015 - Synthetic Biology I
- Today's slides
- Synthetic biology in the news
- The Gillespie algorithm
- Download the synthetic biology comic here!
- iGEM, and an example part (the light sensor)
- Take your own coliroids
Reading:
- The infamous repressilator
- Bacterial photography, and UT's 2012 iGEM entry
- Edge detector
- A more recent example of digital logic
- An example of metabolic engineering: yeast making anti-malarial drugs
April 23, 2015 - Networks II & Phenologs
- Today's slides
- Phenologs and the drug discovery story we'll discuss in class
- Search for phenologs here. You can get started by rediscovering the plant model of Waardenburg syndrome. Search among the known diseases for "Waardenburg", or enter the human genes linked to Waardenburg (Entrez gene IDs 4286, 5077, 6591, 7299) to get a feel for how this works. Also, here's Carl Zimmer's NYT article about phenologs and the scientific process.
- One good tool for discovering orthologs is InParanoid. Note: InParanoid annotation lags a bit, so you'll need to find the Ensembl protein id, or try a text search for the common name.
April 16-21, 2015 - Networks
- Today's slides
- Metabolic networks: The wall chart (it's interactive, e.g. here's enolase), the current state of the human metabolic reaction network, and older but still relevant review of transcriptional networks (with the current record holder in this regard held by ENCODE), and an early review of protein interaction extent and quality whose lessons still hold.
- Useful gene network resources include:
- FunctionalNet, which links to human, worm, Arabidopsis, mouse and yeast gene networks. Not the prettiest web site, but useful, and helped my own group find genes for a wide variety of biological processes. Try searching HumanNet for the myelin regulatory factor MYRF (Entrez gene ID 745) and predicting its function, which is now known but wasn't when the network was made.
- STRING is available for many organisms, including large numbers of prokaryotes. Try searching on the E. coli enolase (Eno) as an example.
- GeneMania, which aggregates many individual gene networks.
- MouseFunc, a collection of network and classifier-based predictions of gene function from an open contest to predict gene function in the mouse.
- The best interactive tool for network visualization is Cytoscape. You can download and install it locally on your computer, then visualize and annotated any gene network, such as are output by the network tools linked above. There is also a web-based network viewer that can be incorporated into your own pages (e.g., as used in YeastNet).
Reading:
- Functional networks
- Review of predicting gene function and phenotype from protein networks
- Primer on visualizing networks
Apr 14, 2015 - Genome Engineering
- Guest speaker: Dr. Chris Yellman
- Today's slides
Apr 9, 2015 - Principal Component Analysis (& the curious case of European genotypes)
- Today's slides
- European men, their genomes, and their geography
- For those of you using classifiers for your projects, here's the best open software for do-it-yourself classifiers and data mining: Weka
- & since he's come up in class several times: Mahalanobis
A smattering of links on PCA:
- NBT Primer on PCA
- A PCA overview (.docx format) & the original post
- Science Signaling (more specifically, Neil R. Clark and Avi Ma’ayan!) had a nice introduction to PCA that I've reposted here (with slides)
Apr 7, 2015 - Classifiers I
Apr 2, 2015 - Clustering II
- We're finishing up the slides from Mar. 31.
- Fuzzy k-means
- SOM gene expression
- Links to various applications of SOMs: 1, 2, 3, 4. You can run SOMs on the following web site. 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).
Mar 31, 2015 - Functional Genomics & Data Mining - Clustering I
- Today's slides
- Review of phylogenetic profiles
- B cell lymphomas
- Primer on clustering
- K-means example (.ppt)
Problem Set 3, due before midnight Apr. 9, 2015. You will need the following software and datasets:
- The clustering and treeview software is available here. Previous students have said the Mac/Linux versions of the tree viewing program can be a bit buggy; however, the Windows version (TreeView) seems to be fine.
- Yeast protein sequences
- Yeast protein phylogenetic profiles
- Yeast mRNA expression profiles
Mar 26, 2015 - Mapping protein complexes
- Guest speaker: Blake Borgeson
Mar 24, 2015 - Mass spectrometry proteomics
- Welcome back from Spring Break. A gentle reminder that HW3 is due by 11:59PM tonight...
- Guest speaker: Dr. Daniel Boutz
Mar 17-19, 2015 - SPRING BREAK
Mar 12, 2015 - Motifs
- Today's slides
- NBT Primer - What are motifs?
- NBT Primer - How does motif discovery work?
- The biochemical basis of a particular motif
- Gibbs Sampling
- AlignAce
Mar 10, 2015 - Genomes II, Gene Expression
- Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is due by 11:59PM March 24.
- Science news of the day: Genome engineering vs. HIV
- We're finishing up the slides from Mar. 5. Note: we'll increasingly be discussing primary papers in the lectures
- An overview of the current state of DNA sequencing and applications
& on to RNA expression!
- Gene expression by ESTs
- Gene expression by SAGE
- Affy microarrays 1 & Affy microarrays 2
- cDNA microarrays
- RNA-Seq
- Clustering by gene expression
- Cell cycle data
- Clustering
Mar 5, 2015 - Genome Assembly
Mar 3, 2015 - Gene finding II
- We're finishing up the slides from Feb. 26. A gentle reminder that HW2 is due by 11:59PM tonight...
- Due March 12 by email - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators. This assignment will account for 5 points out of your 25 total points for your course project.
- Here are a few examples of final projects from previous years: 1, 2, 3, 4, 5 6 7 8 9 10 11 12 13 14
News of the day, regarding the application of next gen sequencing to fetal diagnostics:
- Timely article in the New York Times
- Official recommendations for doctors
- Detecting fetal aneuploidy by NGS of maternal blood
- A recent fetal aneuploidy trial
Feb 26, 2015 - Gene finding
Reading:
Feb 24, 2015 - HMMs II
- We're finishing up the slides from Feb. 19.
Feb 19, 2015 - Hidden Markov Models
- re: our discussion of databases, the remarkable growth of data, e.g. UniProt
- Today's slides
Problem Set 2, due before midnight Mar. 3, 2015:
- Problem Set 2.
- You'll need these 3 files: State sequences, Soluble sequences, Transmembrane sequences
Reading:
- HMM primer and Bayesian statistics primer, Wiki Bayes
- Care to practice your regular expressions? (In python?)
Feb 17, 2015 - Next-generation Sequencing (NGS)
- Guest speaker: Dr. Scott Hunicke-Smith, director of the Genome Sequencing and Analysis Facility.-->
- Illumina/Solexa Sequencing (Youtube Video)
- Genome Analyzer (Youtube Video)
Feb 12, 2015 - 3D Protein Structure Modeling
- Guest speaker: Dr. Kevin Drew
- The Rosetta software suite for 3D protein modeling, and what it can do for you
Feb 10, 2015 - Biological databases
- Just a note that we'll be seeing ever more statistics as go on. Here's a good primer from Prof. Lauren Myers to refresh/explain basic concepts.
- Today's slides
Feb 5, 2015 - Guest lecture: Intro to Appsoma
- We'll have a guest lecture by Zack Simpson, a Fellow of the UT Center for Systems and Synthetic Biology. For the curious, Science magazine wrote a nice feature on Zack several years ago (posted here). Zack co-founded the bioinformatics startup company Traitwise (full disclosure: I'm on their scientific advisory board) and is the lead developer of Appsoma, a web-based scientific cloud computing platform that has a number of enhancements (and dedicated computer clusters) specifically for UT students.
Feb 3, 2015 - BLAST
- Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is due by 11:59PM February 12.
- Our slides today are modified from a paper on Teaching BLAST by Cheryl Kerfeld & Kathleen Scott.
- The original BLAST paper
- 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.
- Repeats in the human genome, tallied here
Jan 29, 2015 - Sequence Alignment II
- We're finishing up the slides from Jan. 27.
- Dynamic programming primer
- An example of dynamic programming using Excel, created by Michael Hoffman (a former UT undergraduate who took the prior incarnation of this class)
- A few examples of proteins with internally repetitive sequences: 1, 2, 3
Jan 27, 2015 - Sequence Alignment I
- One of my favorite news items last year: China cloning on an 'industrial scale'. Favorite quote: "If it tastes good you should sequence it..." BGI is one of the biggest (the biggest?) genome sequencing centers in the world and employs >2,000 bioinformatics researchers.
- Today's slides
Problem Set I, due before midnight Feb. 3, 2015:
- Problem Set 1
- T. volcanium genome
- 3 mystery genes (for Problem 5): Mgene1, Mgene2, Mgene3
Reading:
- BLOSUM primer
- The original BLOSUM paper (hot off the presses from 1992!)
- BLOSUM miscalculations improve performance
Jan 22, 2015 - Intro to Python
Jan 20, 2015 - Introduction
- Today's slides
- Some warm-up videos to get you started on Python: Code Academy's Python coding for beginners
- We'll be conducting homework using the online environment Rosalind. Go ahead and register on the site, and enroll specifically for BCH364C/391L using this link. Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is due by 11:59PM January 27.
- A useful online resource if you get bogged down: Python for Biologists. (& just a heads-up that some of their instructions for running code relate to a command line environment that's a bit different from the default one you install following the Rosalind instructions. It won't affect the programs, just the way they are run or how you specific where files are located.) However, if you've never programmed before, definitely check this out!!!
- An oldie (by recent bioinformatics standards) but goodie: Computers are from Mars, Organisms are from Venus
Syllabus & course outline
An introduction to systems biology and bioinformatics, emphasizing quantitative analysis of high-throughput biological data, and covering typical data, data analysis, and computer algorithms. Topics will include introductory probability and statistics, basics of Python programming, protein and nucleic acid sequence analysis, genome sequencing and assembly, proteomics, synthetic biology, analysis of large-scale gene expression data, data clustering, biological pattern recognition, and gene and protein networks.
Open to graduate students and upper division undergrads (with permission) 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, esp. in high-throughput biology.
Most of the lectures will be from research articles and slides posted online, with some material from the...
Optional text (for sequence analysis): Biological sequence analysis, by R. Durbin, S. Eddy, A. Krogh, G. Mitchison (Cambridge University Press),
For biologists rusty on their stats, The Cartoon Guide to Statistics (Gonick/Smith) is very good. A reasonable online resource for beginners is Statistics Done Wrong.
Some online references:
An online bioinformatics course
Assorted bioinformatics resources on the web: Assorted links
Beginning Python for Bioinformatics
Online probability texts: #1, #2, #3
No exams will be given. Grades will be based on online homework (counting 30% of the grade), 3 problem sets (given every 2-3 weeks and counting 15% each towards the final grade) and a course project (25% of final grade), which will be collaborative. Cross-discipline collaborations will be encouraged. The course project will consist of a research project on a bioinformatics topic chosen by the students (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.
Online homework will be assigned and evaluated using the free bioinformatics web resource Rosalind.
All projects and homework will be turned in electronically and time-stamped. No makeup work will be given. Instead, all students have 5 days of free “late time” (for the entire semester, NOT per project, and counting weekends/holidays). For projects turned in late, days will be deducted from the 5 day total (or what remains of it) by the number of days late (in 1 day increments, rounding up, i.e. 10 minutes late = 1 day deducted). Once the full 5 days have been used up, assignments will be penalized 10 percentage points per day late (rounding up), i.e., a 50 point assignment turned in 1.5 days late would be penalized 20%, or 10 points.
Homework, problem sets, and the project total to a possible 100 points. There will be no curving of grades, nor will grades be rounded up. We’ll use the plus/minus grading system, so: A= 92 and above, A-=90 to 91.99, etc. Just for clarity's sake, here are the cutoffs for the grades: 92% ≤ A, 90% ≤ A- < 92%, 88% ≤ B+ < 90%, 82% ≤ B < 88%, 80% ≤ B- < 82%, 78% ≤ C+ < 80%, 72% ≤ C < 78%, 70% ≤ C- < 72%, 68% ≤ D+ < 70%, 62% ≤ D < 68%, 60% ≤ D- < 62%, F < 60%.
Students are welcome to discuss ideas and problems with each other, but all programs, Rosalind homework, and written solutions should be performed independently (except the final collaborative project).
The final project is due by midnight May 4, 2015.
- How to make a web site for the final project
- Google Site: https://support.google.com/sites/answer/153197?hl=en
