1 |
29-Aug |
Mon |
Introduction |
* Biological data sciences in genome research (Schatz, 2015, Genome Research) * Big Data: Astronomical or Genomical? (Stephens et al, 2015, PLOS Biology) |
Sign Up for Piazza |
2 |
31-Aug |
Wed |
Genomic Technologies |
* Molecular Structure of Nucleic Acid (Watson and Crick, 1953, Nature) * Coming of age: ten years of next-generation sequencing technologies (Goodwin et al, 2016, Nature Reviews Genetics) * Piercing the dark matter: bioinformatics of long-range sequencing and mapping (Sedlazeck et al, 2018, Nature Reviews Genetics) |
Assignment 1: Genomic Fundamentals |
* |
5-Sep |
Mon |
Labor Day |
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3 |
7-Sep |
Wed |
Whole Genome Assembly |
* Velvet: Algorithms for de novo short read assembly using de Bruijn graphs (Zerbino and Birney, 2008, Genome Research) * Quake: quality-aware detection and correction of sequencing errors (Kelley et al, 2010, Genome Biology) * Allpaths-LG: High-quality draft assemblies of mammalian genomes from massively parallel sequence data (Gnerre et al, 2011, PNAS) * FALCON-unzip: Phased diploid genome assembly with single-molecule real-time sequencing (Chin et al, 2016, Nature Methods)
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4 |
12-Sep |
Mon |
Whole Genome Assembly and Alignment |
* Toward simplifying and accurately formulating fragment assembly. (Myers, 1995, J. Comp. Bio.) * MHAP: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing (Berlin et al, 2015, Nature Biotech) * Genome assembly forensics: finding the elusive mis-assembly (Phillippy et al, 2008, Genome Biology) * MUMmer: Alignment of Whole Genomes (Delcher et al, 1999, NAR) |
Assignment 2: Assembly |
5 |
14-Sep |
Wed |
The human genome and intro to long reads |
* Piercing the dark matter: bioinformatics of long- range sequencing and mapping (Sedlazeck et al, 2018, Nature Reviews Genetics) * Nanopore sequencing and assembly of a human genome with ultra-long reads (Jain et al, 2018, Nature Biotech) * The complete sequence of a human genome (Nurk et al, 2022, Science) |
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6 |
19-Sep |
Mon |
Genomics in the Cloud |
* Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) (Schatz et al, 2022, Cell Genomics) |
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7 |
21-Sep |
Wed |
Read Mapping |
* How to map billions of short reads onto genomes (Trapnell and Salzberg, 2009, Nature Biotech) * Bowtie: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (Langmead et al, 2009, Genome Biology) * BWA-MEM: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (Li, 2013, arXiv) * Sapling: Accelerating Suffix Array Queries with Learned Data Models (Kirsche et al, 2020, bioRxiv |
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8 |
26-Sep |
Mon |
Variant Analysis |
* Haplotype-based variant detection from short-read sequencing (Garrison and Marth, arXiv, 2012) * The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data (McKenna et al, 2010, Genome Research) * A universal SNP and small-indel variant caller using deep neural networks (Poplin et al, 2018, Nature Biotechnology * SAM/BAM/Samtools: The Sequence Alignment/Map format and SAMtools (Li et al, 2009, Bioinformatics) * IGV: Integrative genomics viewer (Robinson et al, 2011, Nature Biotech) |
Assignment 3: Mappability and Mapping |
9 |
28-Sep |
Wed |
Structural Variant Analysis and Pangenomics |
* Accurate detection of complex structural variations using single-molecule sequencing (Sedlazeck et al, 2018, Nature Methods) * Characterizing the Major Structural Variant Alleles of the Human Genome (Audano et al, 2019, Cell) * Resolving the complexity of the human genome using single-molecule sequencing (Chaisson et al, 2015, Nature) |
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10 |
3-Oct |
Mon |
Genome Arithmetic and Plane Sweep |
* BEDTools: a flexible suite of utilities for comparing genomic features (Quinlan & Hall, 2010, Bioinformatics) * A Parallel Algorithm for N-Way Interval Set Intersection (Layer & Quinlan, 2016, IEEE Proceedings) |
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11 |
5-Oct |
Wed |
Machine Learning Primer |
* What are decision trees? (Kingsford and Salzberg, 2008, Nature Biotechnology) * What is a hidden Markov model? (Eddy, 2004, Nature Biotechnology) * Deep learning in biomedicine (Wainberg et al, 2018, Nature Biotechnology) * Visualizing Data Using t-SNE |
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12 |
10-Oct |
Mon |
Functional Analysis 1: Annotation |
* BLAST: Basic Local Alignment Search Tool * Glimmer: Microbial gene identification using interpolated Markov models * MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
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Assignment 4: Variants and Bedtools |
13 |
12-Oct |
Wed |
Functional Analysis 2: RNA-seq |
* RNA-Seq: a revolutionary tool for transcriptomics (Wang et al, 2009. Nature Reviews Genetics) * Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (Trapnell et al, 2012, Nature Protocols) * Salmon provides fast and bias-aware quantification of transcript expression (Patro et al, 2017, Nature Methods) * Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications (Krueger and Andrews, 2011, Bioinformatics) |
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14 |
17-Oct |
Mon |
Functional Analysis 3: Methyl-seq, Chip-seq, and Hi-C |
* ChIP-seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions (Furey, 2012, Nature Reviews Genetics) * PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls (Rozowsky et al. 2009. Nature Biotech) * Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome (Lieberman-Aiden et al, 2009, Science) |
Project Proposal |
15 |
19-Oct |
Wed |
Functional Analysis 4: Regulatory States, ENCODE, GTEx, RoadMap |
* An integrated encyclopedia of DNA elements in the human genome (The ENCODE Project Consortium, Nature, 2012) * Genetic effects on gene expression across human tissues (GTEx Consortium, Nature, 2017) * Integrative analysis of 111 reference human epigenomes (Roadmap Epigenome Consortium, Nature, 2015) * ChromHMM: automating chromatin-state discovery and characterization (Ernst & Kellis, 2012, Nature Methods) * Segway: Unsupervised pattern discovery in human chromatin structure through genomic segmentation (Hoffman et al, 2012, Nature Methods) |
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16 |
24-Oct |
Mon |
Functional Analysis 5: Single Cell Genomics |
* Ginkgo: Interactive analysis and assessment of single-cell copy-number variations (Garvin et al, 2015, Nature Methods) * The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells (Trapnell et al, Nature Biotech, 2014) * Eleven grand challenges in single-cell data science (Lahnemann et al, Genome Biology, 2020) |
Assignment 5: Functional Genomics |
17 |
26-Oct |
Wed |
Human Evolution |
* An integrated map of genetic variation from 1,092 human genomes (1000 Genomes Consortium, 2012, Nature) * Analysis of protein-coding genetic variation in 60,706 humans (Let et al, 2016, Nature) * A Draft Sequence of the Neandertal Genome (Green et al. 2010, Science) * Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals (Vernot et al. 2016. Science) |
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18 |
31-Oct |
Mon |
Midterm review |
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19 |
2-Nov |
Wed |
Midterm |
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Take home exam |
20 |
7-Nov |
Mon |
Human Genetic Diseases |
* Genome-Wide Association Studies (Bush & Moore, 2012, PLOS Comp Bio) * The contribution of de novo coding mutations to autism spectrum disorder (Iossifov et al, 2014, Nature) |
Preliminary Project Report |
21 |
9-Nov |
Wed |
Cancer Genomics |
* The Hallmarks of Cancer (Hanahan & Weinberg, 2000, Cell) * Evolution of Cancer Genomes (Yates & Campbell, 2012, Nature Reviews Genetics) * Comprehensive molecular portraits of human breast tumours (TCGA, 2012, Nature) |
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22 |
14-Nov |
Mon |
Microbiome and Metagenomics |
* Kraken: ultrafast metagenomic sequence classification using exact alignments (Wood and Salzberg, 2014, Genome Biology) * Chapter 12: Human Microbiome Analysis (Morgan and Huttenhower) |
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23 |
16-Nov |
Wed |
Genomics Futures |
* Snyderome: Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes (Chen et al, 2012, Cell) * Identifying Personal Genomes by Surname Inference (Gymrek et al, 2013, Science) |
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* |
21-Nov |
Mon |
Thanksgiving Break |
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* |
23-Nov |
Wed |
Thanksgiving Break |
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24 |
28-Nov |
Mon |
In class project presentation |
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Presentations |
25 |
30-Nov |
Wed |
In class project presentation |
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Presentations |
26 |
5-Dec |
Mon |
In class project presentation |
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Presentations |
27 |
7-Dec |
Wed |
In class project presentation |
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Presentations |
* |
21-Dec |
Wed |
Final Report Due |
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Final Report |