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MutPredDatetopicReadingDetailsadditional linksDetailsHomework
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123-JanIntroduction to the class
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Discussion - how to make a bad presentation - OR - how to give a good talk (you pick)https://www.youtube.com/watch?v=Pbdo-ozuOugA talk by David Patterson. View the first 20 minutes (part 1), although the entire talk is highly recommended.http://www.craftofscientificpresentations.com
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230-JanNext generation sequencing
https://www.youtube.com/watch?annotation_id=annotation_1533942809&feature=iv&src_vid=HMyCqWhwB8E&v=fCd6B5HRaZ8
Illumina Sequencing by Synthesis
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Sequencing output: format and basic QChttps://www.youtube.com/watch?v=SZ6suqu-eLAFastq format
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https://www.youtube.com/watch?v=bz93ReOv87YFastQC tutorial
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36-FebRead alignment (1): Exact string matching with the Burrows Wheeler transform, handling mismatches with Bowtiehttp://link.springer.com/book/10.1007/978-0-387-78909-5/page/1Chapters 2 and 7.2.4https://www.youtube.com/watch?v=4n7NPk5lwbIBurrows-Wheeler Transform tutorialHW1
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https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25Bowtie
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http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.htmlBowtie2
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413-FebRead alignment (2): the case of mRNA sequencinghttps://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r36TopHat2http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8A survey of best practices for RNA-seq data analysis
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/STARhttps://www.nature.com/articles/nmeth.3317HiSat
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http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4106.html?WT.feed_name=subjects_biotechnologySimulation based benchmarking of RNA-seq alignershttp://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2722.htmlevaluation of spliced alignment programs for RNA-seq data
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520-FebGroup 1 presentation: ChIPseq
https://www.ncbi.nlm.nih.gov/pubmed/22955616; https://www.nature.com/articles/nrg2905
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Group 2 presentation: ATACseqhttps://www.ncbi.nlm.nih.gov/pubmed/24097267
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Group 3 presentation: MPRAhttps://www.nature.com/articles/ng.2713
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Group 4 presentation: CRISPRhttps://www.nature.com/articles/s41467-018-04252-2
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627-FebPrediction methods: Basic concepts in classification
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76-MarClassification Workshop
Make sure to bring your laptop, and install R studio with R notebook. To install R notebook, see: http://rmarkdown.rstudio.com/r_notebooks.htmlHW2
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Group 5 presentation: Hi-Chttps://www.ncbi.nlm.nih.gov/pubmed/22652625
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Group 6 presentation: Ribosome profiling
http://science.sciencemag.org/content/324/5924/218 ; https://www.sciencedirect.com/science/article/pii/S0092867411011925
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813-MarSpotlight on computational interpretation of noncoding and coding genetic variartion with Nilah Ioannidis (Berkeley EECS, starting fall '19)https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065685/Predicting pathogenicity of nonsynonymous coding variants (REVEL)
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https://www.ncbi.nlm.nih.gov/pubmed/28961785Predicting efects (coding and non coding) on gene expression (FIRE)
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Journal club: Predicting the clinical impact of human mutation with deep neural networkshttps://www.nature.com/articles/s41588-018-0167-z
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920-MarSpotlight on interpreting genetic variartion with CRISPR with Stacia Wyman (IGI)https://www.biorxiv.org/content/early/2019/01/08/432716Editing pathogenic variants in Sickle Cell Disease
http://stm.sciencemag.org/content/8/360/360ra134.full
Earlier study from the IGI on Sickle Cell Disease
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https://www.biorxiv.org/content/early/2018/11/14/469635An assay for unbiased identification of CRISPR off-target sites
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Journal club: Predicting the mutations generated by repair of Cas9-induced double-strand breakshttps://www.nature.com/articles/nbt.4317 and https://www.biorxiv.org/content/early/2018/11/28/481069.
https://www.biorxiv.org/content/early/2018/11/28/481069
Another recent manuscript on prediction of CRISPR/Cas9-mediated double-strand break repair
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103-AprGroup Presentations 1: Comparative reading of computational Methods
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1110-AprDimensonality Reduction / Data Visualizationhttp://www.cs.toronto.edu/~hinton/absps/tsne.pdftSNE manuscripthttps://liorpachter.wordpress.com/2014/05/26/what-is-principal-component-analysis/Lior Pachter's blog entry about PCAHW3
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Visualisation excercise with R notebookMake sure to bring your laptop, and install R studio with R notebook. To install R notebook, see: http://rmarkdown.rstudio.com/r_notebooks.htmlhttps://www.youtube.com/watch?v=RJVL80Gg3lAtSNE
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1217-AprSpotlight on single cell genomics with Nirhttp://www.jimmunol.org/content/200/1_Supplement/163.21Metabolic modeling
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https://www.nature.com/articles/s41592-018-0230-9?WT.feed_name=subjects_software
Probablistic representation with VAE
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https://www.biorxiv.org/content/early/2018/09/28/403055Visualization and interpretation
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Journal club: the Human Cell Atlashttps://elifesciences.org/articles/27041https://www.humancellatlas.orgThe human cell atlas
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1324-AprilGroup Presentations 2: Comparative reading of computational Methods
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141-MaySpotlight on interpreting genetic variartion with MPRA with Katie Pollard (UCSF)https://www.biorxiv.org/content/early/2018/01/29/256313Design principles of regulatory sequenceshttp://www.nature.com/nrg/journal/v15/n7/full/nrg3684.htmlReview on trasncriptional grammar
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Journal club: Massively parallel decoding of mammalian regulatory sequenceshttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4024068/BIORXIV/2019/527887MPRAnalyze - A statistical framework for Massively Parallel Reporter Assays
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