Difference between revisions of "BCH364C BCH394P 2017"

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* '''Office hours:'''  Wed 11 AM – 12 noon in MBB 3.148BA<br>
 
* '''Office hours:'''  Wed 11 AM – 12 noon in MBB 3.148BA<br>
 
'''TA:''' Azat Akhmetov, azat @ utexas.edu<br>
 
'''TA:''' Azat Akhmetov, azat @ utexas.edu<br>
*'''TA Office hours:''' Mon/Wed 3 PM - 4 PM in MBB 3.128A '''Phone:''' on syllabus<br>
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*'''TA Office hours:''' Mon/Wed 3 PM - 4 PM in MBB 3.204 '''Phone:''' on syllabus<br>
  
 
== Lectures & Handouts ==
 
== Lectures & Handouts ==
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'''May 2 - May 4, 2017 - Final Project Presentations'''
'''Apr 28 - May 5, 2016 - Gene Presentations'''
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* Note: There are some great [http://ccbb.biosci.utexas.edu/summerschool.html short summer courses in computational biology] being offered at UT. Of particular note, introductions to [http://ccbb.biosci.utexas.edu/summerschool.html#ngs core NextGen sequencing tools], [http://ccbb.biosci.utexas.edu/summerschool.html#rna RNA-seq], and [http://ccbb.biosci.utexas.edu/summerschool.html#proteomics proteomics].
* Note: There are some great [http://ccbb.biosci.utexas.edu/summerschool.html short summer courses in computational biology] being offered at UT. Of particular note, introductions to [http://ccbb.biosci.utexas.edu/summerschool.html#corengs core NextGen sequencing tools].
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* Here's an assortment of final class projects (with permission to be posted):
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** [https://sites.google.com/view/viralpeptides Fishing in Oceanic Virus: A Search for Novel Peptides, by Austin Cole, Shaunak Kar, and Raghav Shroff]
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** [https://pailnguyen.github.io/jackal/ jackal: a cell phenotype image classification using a convolutional neural network, by Paul Nguyen and Steven Tran]
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** [https://sites.google.com/a/utexas.edu/proteinspace/home Protein chemical space, by Xun Wang, Cory D Dubois, and Viviana M June]
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** [https://sites.google.com/a/utexas.edu/pks_iii_annotation_bch364c_final Bioinformatic Analysis of KAS III, by Yu-Hsuan Lee, Geng-Min Lin, and Daan Ren]
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** [https://sites.google.com/a/utexas.edu/high-coverage-prediction-of-protein-levels/ High-coverage prediction of protein levels, by Eric A Brenner]
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** [https://github.com/dvanderwood/AltProteome/wiki Detection of Translation Products from Alternative Open Reading Frames, by Drew Vander Wood and Riddhiman K Garge]
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'''April 27, 2017 - Synthetic Biology II'''
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* '''UPDATE: Projects are now due by Saturday, midnight, April 29'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR. 
 +
* We'll be finishing the slides from Apr. 20.
 +
 
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'''Apr 25, 2017 - Genome Engineering'''
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* Guest speaker: [https://www.researchgate.net/profile/Aashiq_Kachroo Dr. Aashiq Kachroo]. Here's a link to [https://www.sciencenews.org/article/swapping-analogous-genes-no-problem-among-species some of his recent work.]
  
'''April 26, 2016 - Synthetic Biology'''
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'''April 20, 2017 - Synthetic Biology I'''
* '''Reminder: All gene projects are due by midnight, April 27'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
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* '''Reminder: All projects are due by midnight, April 27'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_SyntheticBio-Spring2016.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_SyntheticBio_Spring2017.pdf Today's slides]
 
A collection of further reading, if you're so inclined:
 
A collection of further reading, if you're so inclined:
* [http://www.marcottelab.org/users/BCH339N_2016/MinimalMycoplasma.pdf Minimal Mycoplasma]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/MinimalMycoplasma.pdf Minimal Mycoplasma]
* [http://www.marcottelab.org/users/BCH339N_2016/GenomeTransplantation.pdf Genome Transplantation]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/GenomeTransplantation.pdf Genome Transplantation]
* [http://www.marcottelab.org/users/BCH339N_2016/JCVI-1.0.pdf JCVI-1.0]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/JCVI-1.0.pdf JCVI-1.0]
* [http://www.marcottelab.org/users/BCH339N_2016/OneStepAssemblyInYeast.pdf One step genome assembly in yeast]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/OneStepAssemblyInYeast.pdf One step genome assembly in yeast]
* [http://www.marcottelab.org/users/BCH339N_2016/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
* [http://www.marcottelab.org/users/BCH339N_2016/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH339N_2016/NewCellFromChemicalGenome.SOM.pdf SOM]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH364C_394P_2017/NewCellFromChemicalGenome.SOM.pdf SOM]
* [http://www.marcottelab.org/users/BCH339N_2016/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
* & the latest: [http://www.marcottelab.org/users/BCH339N_2016/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome]  
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome]
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* [http://science.sciencemag.org/content/355/6329/1040.long Sc 2.0, as of 2017], with the [http://science.sciencemag.org/content/355/6329/1038 computational genome design]
 
* [http://en.wikipedia.org/wiki/Gillespie_algorithm The Gillespie algorithm]
 
* [http://en.wikipedia.org/wiki/Gillespie_algorithm The Gillespie algorithm]
 
* [https://www.igem.org/Main_Page iGEM], and an example part ([http://parts.igem.org/Featured_Parts:Light_Sensor the light sensor])
 
* [https://www.igem.org/Main_Page iGEM], and an example part ([http://parts.igem.org/Featured_Parts:Light_Sensor the light sensor])
 
* [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]
* [http://www.marcottelab.org/users/BCH339N_2016/repressilator.pdf The infamous repressilator]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/repressilator.pdf The infamous repressilator]
* [http://www.marcottelab.org/users/BCH339N_2016/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry]
* [http://www.marcottelab.org/users/BCH339N_2016/EdgeDetector.pdf Edge detector]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/EdgeDetector.pdf Edge detector]
* [http://www.marcottelab.org/users/BCH339N_2016/nbt.2510.pdf A more recent example of digital logic]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/nbt.2510.pdf A nice 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]
Food for thought:<br>
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[http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells Food for thought]
[http://www.nationalgeographic.com/deextinction De-extinction I], [http://science.kqed.org/quest/video/reawakening-extinct-species/ II], and [http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells III]
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'''April 21, 2016 - Phenologs'''
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'''April 18, 2017 - Phenologs'''
* You should have started mini-assignment 5.  The web page is due by midnight April 27, 2016.   
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* '''Remember: The final project web page is due by midnight April 27, 2017, turned in as a URL emailed to the TA+ProfessorPlease indicate in the email if you are willing to let us post the project to the course web site.'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Phenologs_Spring2016.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Phenologs_Spring2017.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'll discuss in class
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* [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. This is a fun example of the power of opportunistic data mining aka [http://researchparasite.com/ "research parasitism"] in biomedical research.
 
* 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.
 
Tools for finding orthologs:<br>
 
Tools for finding orthologs:<br>
* 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. Or, just link there from [http://www.uniprot.org/ Uniprot]. InParanoid tends towards higher recall, lower precision for finding orthologs. Approaches with higher precision include [http://omabrowser.org/oma/home/ OMA] (introduced in [http://www.marcottelab.org/users/BCH339N_2016/OMA.pdf this paper]), [http://phylomedb.org/ PhylomeDB], and just released, [http://pythonhosted.org/bio-MOSAIC/ MOSAIC]
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* 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. Or, just link there from [http://www.uniprot.org/ Uniprot]. InParanoid tends towards higher recall, lower precision for finding orthologs. Approaches with higher precision include [http://omabrowser.org/oma/home/ OMA] (introduced in [http://www.marcottelab.org/users/BCH364C_394P_2017/OMA.pdf this paper]), [http://phylomedb.org/ PhylomeDB], and just released, [http://pythonhosted.org/bio-MOSAIC/ MOSAIC]
* [http://www.marcottelab.org/users/BCH339N_2016/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
  
'''April 19, 2016 - Networks'''
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'''April 13, 2017 - Networks II'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Networks_Spring2016.pdf Today's slides]
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* We're finishing up the slides from Apr. 11.
* 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/BCH339N_2016/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], and older but still relevant review of [http://www.marcottelab.org/users/BCH339N_2016/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/BCH339N_2016/vonmering.pdf protein interaction extent and quality] whose lessons still hold.
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'''April 11, 2017 - Networks'''
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Networks_Spring2017.pdf Today's slides]
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* 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/BCH364C_394P_2017/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], and older but still relevant review of [http://www.marcottelab.org/users/BCH364C_394P_2017/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/BCH364C_394P_2017/vonmering.pdf protein interaction extent and quality] whose lessons still hold.
 
* Useful gene network resources include:
 
* Useful gene network resources include:
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** [http://www.reactome.org/ Reactome]), which we've seen before, links human genes according to reactions and pathways, and also calculated functional linkages from various high-throughput data.
 
** [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.  
 
** [http://string-db.org/ STRING] is available for many organisms, including large numbers of prokaryotes. Try searching on the <i>E. coli</i> enolase (Eno) as an example.
 
** [http://string-db.org/ STRING] is available for many organisms, including large numbers of prokaryotes. Try searching on the <i>E. coli</i> enolase (Eno) as an example.
 
** [http://www.genemania.org/ GeneMania], which aggregates many individual gene networks.
 
** [http://www.genemania.org/ GeneMania], which aggregates many individual gene networks.
 
** [http://func.mshri.on.ca/ MouseFunc], a collection of network and classifier-based predictions of gene function from [http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseFunc_2008.pdf an open contest to predict gene function in the mouse].
 
** [http://func.mshri.on.ca/ MouseFunc], a collection of network and classifier-based predictions of gene function from [http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseFunc_2008.pdf an open contest to predict gene function in the mouse].
** The best interactive tool for network visualization is [http://www.cytoscape.org/ 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 [http://www.inetbio.org/yeastnet/ YeastNet]).
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** The best interactive tool for network visualization is [http://www.cytoscape.org/ 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 [http://www.inetbio.org/yeastnet/ YeastNet]).  Here's an example file to visualize, the [http://proteincomplexes.org/static/downloads/human_protein_complex_map.cys latest version] of the [http://proteincomplexes.org/ human protein complex map].
 
Reading:<br>
 
Reading:<br>
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/YeastSGA-2016.pdf The Yeast SGA map]
 
* [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/BCH339N_2016/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
  
'''Apr 14, 2016 - Genome Engineering'''
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'''Apr 6, 2017 - Principal Component Analysis (& the curious case of European genotypes)'''
* Go ahead and start mini-assignment 4, and try to finish it within a week. 
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_PCA_Spring2017.pdf Today's slides]
* Problem Set 3 deadline has been pushed to midnight April 18, 2016.
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
* Guest speaker: [http://www.yeastgenome.org/cgi-bin/colleague/colleagueSearch?rm=colleague_page&id=12102 Dr. Chris Yellman]
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* [http://projector.tensorflow.org/ The tSNE interactive visualization tool also performs PCA]
 
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'''Apr 12, 2016 - Mass spectrometry proteomics'''
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* Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz]
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'''Apr 7, 2016 - IMPORTANT : PLAGIARISM'''
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* [http://www.marcottelab.org/users/BCH339N_2016/PlagiarismInClass-Spring2016.pdf Plagiarism in the course and what we're going to do about it.]  I refer you to the [http://deanofstudents.utexas.edu/sjs/acadint_whatis.php official policies of UT Austin].
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* Go ahead and start mini-assignment 3. 
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'''Apr 5, 2016 - Principal Component Analysis (& the curious case of European genotypes)'''
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* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_PCA_Spring2016.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH339N_2016/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
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* Relevant to today's discussion for his eponymous distance measure: [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis]
 
* Relevant to today's discussion for his eponymous distance measure: [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/BCH339N_2016/NBT_primer_PCA.pdf NBT Primer on PCA]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBT_primer_PCA.pdf NBT Primer on PCA]
* [http://www.marcottelab.org/users/BCH339N_2016/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/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/BCH339N_2016/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH339N_2016/2001967Slides-FINAL.ppt slides])
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* Science Signaling (more specifically, Neil R. Clark and Avi Ma’ayan! '''Check out Avi's talk today, 4:00 p.m., NHB 1.720''') 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/BCH364C_394P_2017/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH364C_394P_2017/2001967Slides-FINAL.ppt slides])
 
* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]
 
* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]
  
'''Mar 31, 2016 - Classifiers I'''
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'''Apr 4, 2017 - Classifiers I'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Classifiers_Spring2016.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Classifiers_Spring2017.pdf Today's slides]
* [http://www.marcottelab.org/users/BCH339N_2016/AMLALLclassification.pdf Classifying leukemias]
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* [http://www.marcottelab.org/users/BCH364C_394P_2017/AMLALLclassification.pdf Classifying leukemias]
* For those of you interesting in trying out classifiers on your own, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka]
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* For those of you interesting in trying out classifiers on your own, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka].  There is a great introduction to using Weka in this book chapter [http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_17 Introducing Machine Learning Concepts with WEKA], as well as the very accessible Weka-produced book [http://www.cs.waikato.ac.nz/ml/weka/book.html Data Mining: Practical Machine Learning Tools and Techniques].
  
'''Mar 29, 2016 - Clustering II'''
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'''Mar 30, 2017 - 3D Protein Structure Modeling'''
* We're finishing up the slides from Mar.  24.<br>
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* Guest speaker: [https://scholar.google.com/citations?hl=en&user=zJ8L0GcAAAAJ&view_op=list_works Dr. Kevin Drew], formerly of New York University and now at the UT Center for Systems and Synthetic Biology
* [http://www.marcottelab.org/users/BCH339N_2016/FuzzyK-Means.pdf Fuzzy k-means]
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<!--
* [http://www.marcottelab.org/users/BCH339N_2016/SOM-geneexpression.pdf SOM gene expression]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/structbio_lecture_BCH364C-394P_2016.pptx Today's slides]<br>
** 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 from problem set 3 with the '-s' option, or GUI option. See [http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM the manual] for details. (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).
+
-->
 +
* The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH364C_394P_2017/RosettaOverview.pdf what it can do for you]
 +
* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]
  
'''Mar 24, 2016 - Functional Genomics & Data Mining - Clustering I'''
+
'''Mar 28, 2017 - Mass spectrometry proteomics'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_LargeScaleExperiments_Spring2016.pdf Today's slides]
+
* Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz]
 +
 
 +
'''Mar 23, 2017 - Clustering II'''
 +
* Fun article: [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002050 All biology is computational biology]
 +
* We're finishing up the slides from Mar.  21.<br>
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/FuzzyK-Means.pdf Fuzzy k-means]
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/SOM-geneexpression.pdf SOM gene expression]
 +
** Links to various applications of SOMs: [http://en.wikipedia.org/wiki/Self-organizing_map 1], [http://vizier.u-strasbg.fr/kohonen.htx 2], [http://wn.com/Self_Organizing_Maps_Application 3]. 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 [http://bonsai.hgc.jp/~mdehoon/software/cluster Open Source Clustering package] with the '-s' option, or GUI option (here's the [http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM manual]). (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/BCH364C_394P_2017/t-SNE.pdf t-SNE]
 +
** Links to various applications of t-SNE: [https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding 1], [http://lvdmaaten.github.io/tsne/ 2], [https://www.youtube.com/watch?v=RJVL80Gg3lA 3], [http://distill.pub/2016/misread-tsne/ 4]. You can run t-SNE on the [http://projector.tensorflow.org/ following web site].
 +
 
 +
[http://www.marcottelab.org/users/BCH364C_394P_2017/ProblemSet3_2017.pdf '''Problem Set 3], due before midnight Apr. 10, 2017'''.  You will need the following software and datasets:<br>
 +
* The clustering software is available [https://software.broadinstitute.org/morpheus/ here]. There is an alternative package [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm here] that you can download and install on your local computer if you prefer.<br>
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_aaseqs Yeast protein sequences]
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_cofractionationdata.txt Yeast protein fractionation/mass spectrometry profiles].  These additionally have common gene names (LocusID_commonname_location) which may help with the interpretation. These data come from [http://www.marcottelab.org/paper-pdfs/Nature_AnimalComplexes_2015.pdf this paper].
 +
 
 +
'''Mar 21, 2017 - Functional Genomics & Data Mining - Clustering I'''
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_LargeScaleExperiments_Spring2017.pdf Today's slides]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
* [http://www.marcottelab.org/users/BCH339N_2016/nature_review_2000.pdf Review of phylogenetic profiles]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nature_review_2000.pdf Review of phylogenetic profiles]
* [http://www.marcottelab.org/users/BCH339N_2016/Bcelllymphoma.pdf B cell lymphomas]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Bcelllymphoma.pdf B cell lymphomas]
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
* [http://www.marcottelab.org/users/BCH339N_2016/K-means-Example.ppt K-means example (.ppt)]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/K-means-Example.ppt K-means example (.ppt)]
  
[http://www.marcottelab.org/users/BCH339N_2016/ProblemSet3_2016.pdf '''Problem Set 3], due before midnight Apr. 14, 2016'''.  You will need the following software and datasets:<br>
+
'''Mar 14-16, 2017 - SPRING BREAK'''
* The clustering and treeview software is available [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm here].<br>
+
* Finish HW3 and turn in the proposal for your course project.
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_aaseqs Yeast protein sequences]
+
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
+
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_microarraydata2.txt Yeast mRNA expression profiles]
+
  
'''Mar 22, 2016 - Motifs'''
+
'''Mar 9, 2017 - Motifs'''
* Homework #3 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM tonight'''.  There were apparently problems with the [http://meme-suite.org/ Meme web server], but it appears to working now. Also, a [http://alternate.meme-suite.org/ mirror Meme server] has been set up as an alternative.
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Motifs_Spring2017.pdf Today's slides]
* Go ahead and start mini-assignment 2, and try to finish it within a week.   
+
* '''Due March 21 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>
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Motifs_Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
* [http://www.marcottelab.org/users/BCH339N_2016/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
* [http://www.marcottelab.org/users/BCH339N_2016/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/BCH339N_2016/GibbsSampling.pdf Gibbs Sampling]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/GibbsSampling.pdf Gibbs Sampling]
* [http://www.marcottelab.org/users/BCH339N_2016/AlignAce.pdf AlignAce]
+
<!--
 
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/AlignAce.pdf AlignAce] -->
'''Mar 15-17, 2016 - SPRING BREAK'''
+
* Finish HW3 and and the first mini-assignment (#1) for your gene project.
+
  
'''Mar 10, 2016 - Genomes II'''<br>
+
'''Mar 7, 2017 - Genomes II'''<br>
* For those of you interested in doing your homework/research with more experienced coders in the room, there is a weekly Open Coding Hour in the CCBB conference room / collaboratorium (GDC 7.514) each Tuesday from 5-6 PM. [http://ccbb.biosci.utexas.edu/community.html#opencoding].
+
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 20'''.
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 22'''.
+
* We're finishing up the slides from Mar. 2, then on to motif-finding. Note that we give short shrift to read mapping/alignment algorithms, of which there are now [https://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment a very long list]. Here's a nice discussion by Lior Pachter of the [https://liorpachter.wordpress.com/2015/11/01/what-is-a-read-mapping/ major developments in that field.]
* We're finishing up the slides from Mar. 8, then on to motif-finding. Note: we'll increasingly be discussing primary papers in the lectures.  Here are a few classics and reviews that will come up after Spring Break if you want to start looking ahead.<br>
+
* In response to questions after class today about how the Burrows–Wheeler transform is used to construct an index, here's a very clear explanation for the [http://www.marcottelab.org/users/BCH364C_394P_2017/BWApaper.pdf BWA read mapping algorithm].
* [http://www.marcottelab.org/users/BCH339N_2016/ESTs.pdf Gene expression by ESTs]
+
* Note #2: we'll increasingly be discussing primary papers in the lectures.  Here are a few (old) classics and reviews that will come up after Spring Break if you want to start looking ahead.<br>
* [http://www.marcottelab.org/users/BCH339N_2016/SAGE.pdf Gene expression by SAGE]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/ESTs.pdf Gene expression by ESTs]
* [http://www.marcottelab.org/users/BCH339N_2016/Affy2.pdf Affy microarrays 1] & [http://www.marcottelab.org/users/BIO337_2014/Affy1.pdf Affy microarrays 2]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/SAGE.pdf Gene expression by SAGE]
* [http://www.marcottelab.org/users/BCH339N_2016/DeRisi.pdf cDNA microarrays]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Affy2.pdf Affy microarrays 1] & [http://www.marcottelab.org/users/BIO337_2014/Affy1.pdf Affy microarrays 2]
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/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/BCH339N_2016/eisen.pdf Clustering by gene expression]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/eisen.pdf Clustering by gene expression]
* [http://www.marcottelab.org/users/BCH339N_2016/Spellman.pdf Cell cycle data]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Spellman.pdf Cell cycle data]
  
'''Mar 8, 2016 - Genome Assembly'''
+
'''Mar 2, 2017 - Genome Assembly'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_GenomeAssembly_Spring2017.pdf Today's slides]
* A gentle reminder that Problem Set 2 is '''due by 11:59PM tonight'''<br>
+
* A gentle reminder that Problem Set 2 is '''due by 11:59PM March 6'''<br>
* [http://www.marcottelab.org/users/BCH339N_2016/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH339N_2016/DeBruijnSupplement.pdf Supplement]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH364C_394P_2017/DeBruijnSupplement.pdf Supplement]
 
* Here are a few explanations of using the BWT for indexing: [http://blog.avadis-ngs.com/2012/04/elegant-exact-string-match-using-bwt-2/ 1] [http://www.di.unipi.it/~ferragin/Libraries/fmindexV2/index.html 2]
 
* Here are a few explanations of using the BWT for indexing: [http://blog.avadis-ngs.com/2012/04/elegant-exact-string-match-using-bwt-2/ 1] [http://www.di.unipi.it/~ferragin/Libraries/fmindexV2/index.html 2]
 +
* Here are some [http://www.marcottelab.org/images/5/5a/Annotated_peptides.txt example yeast protein sequences], annotated with their transmembrane and soluble regions (according to UniProt).
  
'''Mar 3, 2016 - Gene finding II'''
+
'''Feb 28, 2017 - Next-generation Sequencing (NGS)'''
* We're finishing up the slides from Feb. 25, then moving on into [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Genome Assembly]
+
* Guest speaker: [https://www.linkedin.com/in/scott-hunicke-smith-6081767 Dr. Scott Hunicke-Smith], former director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility], and current VP, Molecular R&D at [http://www.sonichealthcareusa.com/ Sonic Reference Laboratory].
 
+
'''Mar 2, 2016''' - TA office hours canceled due to illness, rescheduled tomorrow, Mar 3, 3-4PM
+
 
+
'''Mar 1, 2016 - Next-generation Sequencing (NGS)'''
+
* Guest speaker: [http://cssb.utexas.edu/members/scott-hunicke-smith/ Dr. Scott Hunicke-Smith], former director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility], and current director of commercial NextGen sequencing diagnostics.
+
 
* [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)]
  
'''Feb 25, 2015 - Gene finding'''
+
'''Feb 23, 2017 - Gene finding II'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-GeneFinding-Spring2016.pdf Today's slides]
+
* We're finishing up the slides from Feb. 21, then moving on into [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_GenomeAssembly_Spring2017.pdf Genome Assembly]
 +
 
 +
'''Feb 21, 2017 - Gene finding'''
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-GeneFinding-Spring2017.pdf Today's slides]
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A61755389-61788517&hgsid=477602291_ccTRfcOcZIQHnMkBKGzbQLBRc6HL The UCSC genome browser]
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A61755389-61788517&hgsid=477602291_ccTRfcOcZIQHnMkBKGzbQLBRc6HL The UCSC genome browser]
 +
Problem Set 2, due before midnight Mar. 6, 2017:<br>
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_ProblemSet2_Spring2017.pdf '''Problem Set 2''']. 
 +
* You'll need these 3 files: [http://www.marcottelab.org/users/BCH364C_394P_2017/state_sequences State sequences], [http://www.marcottelab.org/users/BCH364C_394P_2017/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH364C_394P_2017/transmembrane_sequences Transmembrane sequences]
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH339N_2016/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH339N_2016/BurgeKarlin-main.pdf GENSCAN]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH364C_394P_2017/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH364C_394P_2017/BurgeKarlin-main.pdf GENSCAN]
  
'''Feb 23, 2016 - HMMs II'''
+
'''Feb 16, 2017 - HMMs II'''
 
* We're finishing up the slides from Feb. 18.  
 
* We're finishing up the slides from Feb. 18.  
Problem Set 2, due before midnight Mar. 8, 2016:<br>
+
* News of the day: [https://www.washingtonpost.com/news/speaking-of-science/wp/2017/02/15/broad-institute-scientist-prevails-in-epic-patent-fight-over-crispr/?utm_term=.ab548bb221c4 CRISPR patent! #1] [http://www.sciencemag.org/news/2017/02/how-battle-lines-over-crispr-were-drawn #2], [http://www.nature.com/news/broad-institute-wins-bitter-battle-over-crispr-patents-1.21502 and #3]. I recommend reading the [http://www.marcottelab.org/users/BCH364C_394P_2017/Broad-Cal-Decision-on-Motions.pdf actual decision].
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_ProblemSet2_Spring2016.pdf '''Problem Set 2''']
+
* You'll need these 3 files: [http://www.marcottelab.org/users/BCH339N_2016/state_sequences State sequences], [http://www.marcottelab.org/users/BCH339N_2016/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH339N_2016/transmembrane_sequences Transmembrane sequences]
+
  
'''Feb 18, 2015 - Hidden Markov Models'''
+
'''Feb 14, 2017 - Hidden Markov Models'''
* Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM today'''.
+
* Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM February 20'''.
* It's also time to get started with our major class project.  [http://www.marcottelab.org/users/BCH339N_2016/GeneDossierAssignment.pdf Here] are the instructions.  Go ahead and start mini-assignment 1, and try to finish it within a week. There will be 5 of these from now until the end of the semester. '''By classtime Tuesday, Feb. 23, email the TA the name of the gene you selected and a link to the web page you are creating for your project.'''  (You can find instructions for how to create a google web site at the bottom of this page.)
+
* Linking out to [http://www.uniprot.org/ UniProt], discussed last time
* Another view of the remarkable growth of data, e.g. [http://www.ebi.ac.uk/uniprot/TrEMBLstats/ UniProt]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-HMMs-Spring2017.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-HMMs-Spring2016.pdf Today's slides]<br>
+
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-Bayes.pdf Bayesian statistics primer], [http://en.wikipedia.org/wiki/Bayes'_theorem Wiki Bayes]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-Bayes.pdf Bayesian statistics primer #1], [http://www.marcottelab.org/users/BCH364C_394P_2017/BayesPrimer-NatMethods.pdf Bayesian statistics primer #2], [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 16, 2016 - Biological databases'''
+
'''Feb 9, 2017 - Biological databases'''
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH339N_2016/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/BCH364C_394P_2017/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/BCH339N_2016/BCH339N-BiologicalDatabases-Spring2016.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-BiologicalDatabases-Spring2017.pdf Today's slides]<br>
  
'''Feb 11, 2016 - 3D Protein Structure Modeling'''
+
'''Feb 7, 2017 - BLAST'''
* Guest speaker: [https://scholar.google.com/citations?hl=en&user=zJ8L0GcAAAAJ&view_op=list_works Dr. Kevin Drew], formerly of New York University and now at the UT Center for Systems and Synthetic Biology
+
* News of the day: [https://www.genomicsengland.co.uk/the-100000-genomes-project-by-numbers/ The UK 100K genomes project is up to 19,072 human genomes sequenced!] Such data are extremely valuable for learning about human variation and gene function. For example, [http://www.marcottelab.org/users/BCH364C_394P_2017/Study-2017-Nature.pdf exome sequences of >4,000 families] are revealing [http://www.marcottelab.org/users/BCH364C_394P_2017/DDD-Figure2.jpg critical genes for developmental disorders].
* [http://www.marcottelab.org/users/BCH339N_2016/structbio_lecture_BCH339N_2016.pptx Today's slides]<br>
+
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 20'''.
* The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH339N_2016/RosettaOverview.pdf what it can do for you]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-BLAST-Spring2017.pdf Our slides today] are modified from a paper on [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] by Cheryl Kerfeld & Kathleen Scott.
* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLAST.pdf The original BLAST paper]
 
+
'''Feb 9, 2016 - BLAST'''
+
* News of the day: [http://www.nature.com/nbt/journal/v34/n2/full/nbt0216-117.html?WT.ec_id=NBT-201602&spMailingID=50636844&spUserID=MTc3MTg5MDc0MQS2&spJobID=860630483&spReportId=ODYwNjMwNDgzS0 ''farmaceuticals'' from transgenic chickens]
+
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 18'''.
+
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-BLAST-Spring2016.pdf Our slides today] are modified from a paper on [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] by Cheryl Kerfeld & Kathleen Scott.
+
* [http://www.marcottelab.org/users/BCH339N_2016/BLAST.pdf The original BLAST paper]
+
 
* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art.  
 
* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art.  
  
'''Feb 4, 2016 - Guest lecture: Homologs, orthologs, and evolutionary trees'''  
+
'''Feb 2, 2017 - Guest lecture: Homologs, orthologs, and evolutionary trees'''  
* '''*** HEADS UP FOR THE PROBLEM SET ***'''  If you're trying to use the Python string.count function to count dinucleotides, Python counts '''non-overlapping''' instances, not '''overlapping''' instances.  So, ''AAAA'' is counted as 2, not 3, dinucleotides.  You want '''overlapping''' dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
+
 
* We'll have a guest lecture by [http://bliebeskind.github.io/ Ben Liebeskind], a postdoctoral fellow in the Center for Systems and Synthetic Biology, on decoding the evolutionary relationships among genes.  
 
* We'll have a guest lecture by [http://bliebeskind.github.io/ Ben Liebeskind], a postdoctoral fellow in the Center for Systems and Synthetic Biology, on decoding the evolutionary relationships among genes.  
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Orthology_Spring2016.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BioinformaticsClass_sp2017.pdf Today's slides]<br>
* For those of you pre-med or health-focused students, you might be interested in [https://oneheartsource.org/volunteer_programs/health-innovation/ volunteer opportunities in South Africa] ([https://oneheartsource.typeform.com/to/m79wDs?refcode=KMedero%28B%29 application])
+
  
'''Feb 2, 2016 - Sequence Alignment II'''
+
'''Jan 31, 2017 - Sequence Alignment II'''
* We're finishing up the slides from Jan. 28.  
+
* News of the day: [https://www.nytimes.com/2017/01/26/science/chimera-stemcells-organs.html?_r=0 pig-human chimeras not science fiction?]
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
+
* We're finishing up the slides from Jan. 26.  
* [http://www.marcottelab.org/users/BCH339N_2016/GALPAS.xls An example of dynamic programming using Excel], created by [http://www.thepmcf.ca/News-Media/Blog/The-PMCF-Blog/January-2014/Meet-Michael-Hoffman Michael Hoffman] (a former UT undergraduate who took a prior incarnation of this class)
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/GALPAS.xls An example of dynamic programming using Excel], created by [http://www.thepmcf.ca/News-Media/Blog/The-PMCF-Blog/January-2014/Meet-Michael-Hoffman Michael Hoffman] (a former U Texas undergraduate, now U Toronto professor, who took a prior incarnation of this class)
 
* A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3]
 
* A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3]
  
'''Jan 28, 2016 - Sequence Alignment I'''
+
'''Jan 26, 2017 - Sequence Alignment I'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-Spring2016-SequenceAlignmentI.pdf Today's slides]<br>
+
* [https://www.eurekalert.org/pub_releases/2017-01/sumc-rmp012517.php news of the day--growing a mouse pancreas in a rat!]  [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21070.html This] is the follow-up to [http://www.sciencedirect.com/science/article/pii/S0092867410008433 one of my favorite studies from the last few years], growing a rat pancreas in a mouse!
Problem Set I, due before midnight Feb. 4, 2016:<br>
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-Spring2017-SequenceAlignmentI.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_ProblemSet1_Spring2016.pdf Problem Set 1]
+
Problem Set I, due before midnight Feb. 6, 2017:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/Tvolcanium_genome.txt T. volcanium genome]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_ProblemSet1_Spring2017.pdf Problem Set 1]
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH339N_2016/Mgene1 Mgene1], [http://www.marcottelab.org/users/BCH339N_2016/Mgene2 Mgene2], [http://www.marcottelab.org/users/BCH339N_2016/Mgene3 Mgene3]<br>
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Hinfluenzae.txt H. influenzae genome]. [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenza] was the first free living organism to have its genome sequenced. '''NOTE: a few of you have pointed out that there are some additional characters in this file (from ambiguous sequence calls).  For simplicity's sake, when calculating your nucleotide and dinucleotide frequencies, you can just ignore anything other than A, C, T, and G.'''
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Taquaticus.txt T. aquaticus genome]. [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] helped spawn the genomic revolution as the source of heat-stable Taq polymerase for PCR.
 +
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH364C_394P_2017/MysteryGene1.txt MysteryGene1], [http://www.marcottelab.org/users/BCH364C_394P_2017/MysteryGene2.txt MysteryGene2], [http://www.marcottelab.org/users/BCH364C_394P_2017/MysteryGene3.txt MysteryGene3]<br>
 +
* '''*** HEADS UP FOR THE PROBLEM SET ***'''  If you try to use the Python string.count function to count dinucleotides, Python counts '''non-overlapping''' instances, not '''overlapping''' instances.  So, ''AAAA'' is counted as 2, not 3, dinucleotides.  You want '''overlapping''' dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
 +
* For those of you who could use more tips on programming, there's a peer-led open coding hour happening on Wednesdays 4-5pm in MBB 2.232 (2nd floor lounge). It's a very informal setting where you can ask questions of more experienced programmers.
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-BLOSUM.pdf BLOSUM primer]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-BLOSUM.pdf BLOSUM primer]
* [http://www.marcottelab.org/users/BCH339N_2016/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
* [http://www.marcottelab.org/users/BCH339N_2016/BLOSUM62Miscalculations.pdf BLOSUM miscalculations improve performance]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLOSUM62Miscalculations.pdf BLOSUM miscalculations improve performance]
 
* There is a good discussion of the alignment algorithms and different scoring schemes [http://www.bioinformaticsonline.org/ch/ch03/supp-all.html here]
 
* There is a good discussion of the alignment algorithms and different scoring schemes [http://www.bioinformaticsonline.org/ch/ch03/supp-all.html here]
  
'''Jan 26, 2016 - Rosalind help & programming Q/A'''
+
'''Jan 24, 2017 - Rosalind help & programming Q/A'''
* The TA office hours have changed to better accommodate conflicts. The new office hours have shifted forward 1 hour, to Wed/Thurs 3-4.
+
 
* [http://www.bbc.co.uk/news/science-environment-25576718 One of my favorite news items of the last few last years: 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.<br>
 
* [http://www.bbc.co.uk/news/science-environment-25576718 One of my favorite news items of the last few last years: 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.<br>
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
 
* We'll be finishing Python slides from last time.
 
* We'll be finishing Python slides from last time.
  
'''Jan 21, 2016 - Intro to Python'''
+
'''Jan 19, 2017 - Intro to Python'''
* News of the day/Science in action:  There's a huge ongoing debate raging about the development of CRISPR genome editing technology, stemming in part from an [https://www.washingtonpost.com/news/wonk/wp/2016/01/13/control-of-crispr-biotechs-most-promising-breakthrough-is-up-for-grabs/ ongoing patent contest] over who made key innovations in characterizing, engineering, and applying CRISPR. You can read some of the debate [http://www.the-scientist.com/?articles.view/articleNo/45072/title/Who-Owns-CRISPR--Cont-d/ here], [http://www.the-scientist.com/?articles.view/articleNo/45119/title/-Heroes-of-CRISPR--Disputed/ here], and [http://genotopia.scienceblog.com/579/landergate-a-link-list/ here], among many other sites.
+
* News of the day/Science in action:  There's a huge ongoing debate raging about the development of CRISPR genome editing technology, stemming in part from an [https://www.washingtonpost.com/news/wonk/wp/2016/01/13/control-of-crispr-biotechs-most-promising-breakthrough-is-up-for-grabs/ ongoing patent contest] over who made key innovations in characterizing, engineering, and applying CRISPR. You can read some of the debate [http://www.the-scientist.com/?articles.view/articleNo/45072/title/Who-Owns-CRISPR--Cont-d/ here], [http://www.the-scientist.com/?articles.view/articleNo/45119/title/-Heroes-of-CRISPR--Disputed/ here], and [http://genotopia.scienceblog.com/579/landergate-a-link-list/ here], among many other sites.  There's a good chance we'll hear the major CRISPR patents decided this semester.
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-PythonPrimer-Spring2016.pdf Today's slides]<br>
+
* REMINDER:  My email inbox is always fairly backlogged (e.g., my median time between non-spam emails yesterday was 11 minutes), so please copy the TA on any emails to me to make sure they get taken care of.
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Lecture2-Python_primer-Spring2016.pdf Python primer]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-PythonPrimer-Spring2017.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH339N_2016/Ecoli_genome.txt E. coli genome]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Lecture2-Python_primer-Spring2017.pdf Python primer]
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. For compatibility with Rosalind and other materials, we'll use version 2.7.
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Ecoli_genome.txt E. coli genome]
 
+
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. For compatibility with Rosalind and other materials, we'll use version 2.7. The current plan is for Python 2.7 support to be halted in 2020, but there is some hope (wishful thinking?) that Python 4 will be backwards compatible, [http://astrofrog.github.io/blog/2016/01/12/stop-writing-python-4-incompatible-code/ unlike Python 3].
-->
+
  
'''Jan 19, 2016 - Introduction'''
+
'''Jan 17, 2017 - Introduction'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-IntroAndRosalind-Spring2016.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-IntroAndRosalind-Spring2017.pdf Today's slides]<br>
 
* Some warm-up videos to get you started on Python: [http://www.codecademy.com/tracks/python Code Academy's Python coding for beginners]<br>
 
* Some warm-up videos to get you started on Python: [http://www.codecademy.com/tracks/python Code Academy's Python coding for beginners]<br>
* We'll be conducting homework using the online environment [http://rosalind.info/faq/ Rosalind].  Go ahead and register on the site, and enroll specifically for BCH339N using [http://rosalind.info/classes/enroll/c5be9c4629/ ''this link''].  Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is '''due by 11:59PM January 28'''.
+
* We'll be conducting homework using the online environment [http://rosalind.info/faq/ Rosalind].  Go ahead and register on the site, and enroll specifically for BCH364C/BCH394P using [http://rosalind.info/classes/enroll/b22533ccd7/ ''this link''].  Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is '''due by 11:59PM January 26'''.
 
* A useful online resource if you get bogged down: [http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/ 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!!!'''<br>
 
* A useful online resource if you get bogged down: [http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/ 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!!!'''<br>
* An oldie (by recent bioinformatics standards) but goodie:  [http://www.marcottelab.org/users/BCH339N_2016/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus]
+
* An oldie (by recent bioinformatics standards) but goodie:  [http://www.marcottelab.org/users/BCH364C_394P_2017/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus]
  
 
== Syllabus & course outline ==
 
== Syllabus & course outline ==
  
[http://www.marcottelab.org/users/BCH339N_2016/BCH339N_2016_Syllabus.pdf Course syllabus]
+
[http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_2017_syllabus.pdf Course syllabus]
  
 
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.<br>
 
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.<br>
  
Open to biochemistry majors.  Prerequisites:  Biochemistry 339F or Chemistry 339K with a grade of at least C-. <br>
+
Open to graduate students and upper division undergrads (with permission) in natural sciences and engineering.
Requires basic familiarity with molecular biology & basic statistics, although varied backgrounds are expected. <br>
+
Prerequisites: Basic familiarity with molecular biology, statistics & computing, but realistically, it is expected that students will have extremely varied backgrounds. UGs have additional prerequisites, as listed in the catalog.<br>
  
 
''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.''<br>
 
''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.''<br>
Line 250: Line 266:
 
[http://lectures.molgen.mpg.de/ An online bioinformatics course]<br>
 
[http://lectures.molgen.mpg.de/ An online bioinformatics course]<br>
 
Assorted bioinformatics resources on the web: [http://zlab.bu.edu/zlab/links.shtml Assorted links]<br>
 
Assorted bioinformatics resources on the web: [http://zlab.bu.edu/zlab/links.shtml Assorted links]<br>
[http://onlamp.com/lpt/a/2727 Beginning Python for Bioinformatics]<br>
 
 
Online probability texts: [http://omega.albany.edu:8008/JaynesBook.html #1], [http://www-users.york.ac.uk/~mb55/pubs/pbstnote.htm #2], [http://www.dartmouth.edu/~chance/teaching_aids/books_articles/probability_book/pdf.html #3]<br>
 
Online probability texts: [http://omega.albany.edu:8008/JaynesBook.html #1], [http://www-users.york.ac.uk/~mb55/pubs/pbstnote.htm #2], [http://www.dartmouth.edu/~chance/teaching_aids/books_articles/probability_book/pdf.html #3]<br>
  
'''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 an independent course project (25% of final grade).'''  The course project will be focused on a specific gene & will involve bioinformatics research (e.g. calculation, programming, database analysis, etc.) developed over the semester in 5 mini-assignments, which will be turned in as a link to a web page that you will continue to expand over the semester. The completed final web site is due by midnight, April 27, 2016, and will be presented to the rest of the class on the last 3 class days. Each mini-assignment is 4% of the final grade; the presentation will be worth 5%.<br>
+
'''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 an independent course project (25% of final grade).'''  The course project will consist of a research 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 by midnight, April 27, 2017.  The last two classes will be spent presenting your projects to each other. (The presentation will account for 5% of the project.)'''<br>
  
 
Online homework will be assigned and evaluated using the free bioinformatics web resource [http://rosalind.info/faq/ Rosalind].<br>
 
Online homework will be assigned and evaluated using the free bioinformatics web resource [http://rosalind.info/faq/ Rosalind].<br>
Line 261: Line 276:
 
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%.
 
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'''.<br>
+
Students are welcome to discuss ideas and problems with each other, but '''all programs, Rosalind homework, and written solutions should be performed independently'''. Students are expected to follow the UT honor code. Cheating, plagiarism, copying, & reuse of prior homework or programs from CourseHero, Github, or other sources are all strictly forbidden and constitute breaches of academic integrity ([http://deanofstudents.utexas.edu/sjs/acint_student.php UT academic integrity policy]) and cause for dismissal with a failing grade.
  
'''The final project web site is due by midnight April 27, 2016.'''
+
'''The final project web site is due by midnight April 27, 2017.'''
  
 
* How to make a web site for the final project  
 
* How to make a web site for the final project  

Latest revision as of 11:28, 2 May 2017

BCH364C/BCH394P Systems Biology & Bioinformatics

Course unique #: 55120/55210
Lectures: Tues/Thurs 11 – 12:30 PM in GDC 4.302
Instructor: Edward Marcotte, marcotte @ icmb.utexas.edu

  • Office hours: Wed 11 AM – 12 noon in MBB 3.148BA

TA: Azat Akhmetov, azat @ utexas.edu

  • TA Office hours: Mon/Wed 3 PM - 4 PM in MBB 3.204 Phone: on syllabus

Lectures & Handouts

May 2 - May 4, 2017 - Final Project Presentations

April 27, 2017 - Synthetic Biology II

  • UPDATE: Projects are now due by Saturday, midnight, April 29. Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.
  • We'll be finishing the slides from Apr. 20.

Apr 25, 2017 - Genome Engineering

April 20, 2017 - Synthetic Biology I

  • Reminder: All projects are due by midnight, April 27. Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.
  • Today's slides

A collection of further reading, if you're so inclined:

Food for thought

April 18, 2017 - Phenologs

  • Remember: The final project web page is due by midnight April 27, 2017, turned in as a URL emailed to the TA+Professor. Please indicate in the email if you are willing to let us post the project to the course web site.
  • Today's slides
  • Phenologs and the drug discovery story we'll discuss in class. This is a fun example of the power of opportunistic data mining aka "research parasitism" in biomedical research.
  • 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.

Tools for finding orthologs:

April 13, 2017 - Networks II

  • We're finishing up the slides from Apr. 11.

April 11, 2017 - 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:
    • Reactome), which we've seen before, links human genes according to reactions and pathways, and also calculated functional linkages from various high-throughput data.
    • 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). Here's an example file to visualize, the latest version of the human protein complex map.

Reading:

Apr 6, 2017 - Principal Component Analysis (& the curious case of European genotypes)

A smattering of links on PCA:

Apr 4, 2017 - Classifiers I

Mar 30, 2017 - 3D Protein Structure Modeling

Mar 28, 2017 - Mass spectrometry proteomics

Mar 23, 2017 - Clustering II

Problem Set 3, due before midnight Apr. 10, 2017. You will need the following software and datasets:

Mar 21, 2017 - Functional Genomics & Data Mining - Clustering I

Mar 14-16, 2017 - SPRING BREAK

  • Finish HW3 and turn in the proposal for your course project.

Mar 9, 2017 - Motifs

Mar 7, 2017 - Genomes II

Mar 2, 2017 - Genome Assembly

Feb 28, 2017 - Next-generation Sequencing (NGS)

Feb 23, 2017 - Gene finding II

  • We're finishing up the slides from Feb. 21, then moving on into Genome Assembly

Feb 21, 2017 - Gene finding

Problem Set 2, due before midnight Mar. 6, 2017:

Reading:

Feb 16, 2017 - HMMs II

Feb 14, 2017 - Hidden Markov Models

  • Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind by 11:59PM February 20.
  • Linking out to UniProt, discussed last time
  • Today's slides

Reading:

Feb 9, 2017 - Biological databases

Feb 7, 2017 - BLAST

Feb 2, 2017 - Guest lecture: Homologs, orthologs, and evolutionary trees

  • We'll have a guest lecture by Ben Liebeskind, a postdoctoral fellow in the Center for Systems and Synthetic Biology, on decoding the evolutionary relationships among genes.
  • Today's slides

Jan 31, 2017 - Sequence Alignment II

Jan 26, 2017 - Sequence Alignment I

Problem Set I, due before midnight Feb. 6, 2017:

  • Problem Set 1
  • H. influenzae genome. Haemophilus influenza was the first free living organism to have its genome sequenced. NOTE: a few of you have pointed out that there are some additional characters in this file (from ambiguous sequence calls). For simplicity's sake, when calculating your nucleotide and dinucleotide frequencies, you can just ignore anything other than A, C, T, and G.
  • T. aquaticus genome. Thermus aquaticus helped spawn the genomic revolution as the source of heat-stable Taq polymerase for PCR.
  • 3 mystery genes (for Problem 5): MysteryGene1, MysteryGene2, MysteryGene3
  • *** HEADS UP FOR THE PROBLEM SET *** If you try to use the Python string.count function to count dinucleotides, Python counts non-overlapping instances, not overlapping instances. So, AAAA is counted as 2, not 3, dinucleotides. You want overlapping dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
  • For those of you who could use more tips on programming, there's a peer-led open coding hour happening on Wednesdays 4-5pm in MBB 2.232 (2nd floor lounge). It's a very informal setting where you can ask questions of more experienced programmers.

Reading:

Jan 24, 2017 - Rosalind help & programming Q/A

Jan 19, 2017 - Intro to Python

  • News of the day/Science in action: There's a huge ongoing debate raging about the development of CRISPR genome editing technology, stemming in part from an ongoing patent contest over who made key innovations in characterizing, engineering, and applying CRISPR. You can read some of the debate here, here, and here, among many other sites. There's a good chance we'll hear the major CRISPR patents decided this semester.
  • REMINDER: My email inbox is always fairly backlogged (e.g., my median time between non-spam emails yesterday was 11 minutes), so please copy the TA on any emails to me to make sure they get taken care of.
  • Today's slides
  • Python primer
  • E. coli genome
  • Python 2 vs 3?. For compatibility with Rosalind and other materials, we'll use version 2.7. The current plan is for Python 2.7 support to be halted in 2020, but there is some hope (wishful thinking?) that Python 4 will be backwards compatible, unlike Python 3.

Jan 17, 2017 - 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/BCH394P 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 26.
  • 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

Course syllabus

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. UGs have additional prerequisites, as listed in the catalog.

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
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 an independent course project (25% of final grade). The course project will consist of a research 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 by midnight, April 27, 2017. The last two classes will be spent presenting your projects to each other. (The presentation will account for 5% of the project.)

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 percent 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. Students are expected to follow the UT honor code. Cheating, plagiarism, copying, & reuse of prior homework or programs from CourseHero, Github, or other sources are all strictly forbidden and constitute breaches of academic integrity (UT academic integrity policy) and cause for dismissal with a failing grade.

The final project web site is due by midnight April 27, 2017.