| 1. | Mo 1/25 | 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. | We 1/27 | 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 |
| 3. | Mo 2/1 | 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)
| |
| 4. | We 2/3 | 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 |
| 5. | Mo 2/8 | 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) | |
| 6. | We 2/10 | 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 |
| 7. | Mo 2/15 | 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) | |
| 8. | We 2/17 | 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 | Assignment 4 |
| 9. | Mo 2/22 | Structural Variant Analysis | * 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) | |
| 10. | We 2/24 | 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 | |
| 11. | Mo 3/1 | Nanopore Signal Analysis | * Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED (Kovaka et al, 2020, bioRxiv)
* Detecting DNA cytosine methylation using nanopore sequencing (Simpson et al, 2017, Nature Methods) | |
| 12. | We 3/3 | 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
| Assignment 5 |
| 13. | Mo 3/8 | 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) | Project Proposal |
| 14. | We 3/10 | 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) | |
| 15. | Mo 3/15 | 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) | |
| 16. | We 3/17 | 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 (Lähnemann et al, Genome Biology, 2020) | |
| * | Mo 3/22 | Spring Break! | | |
| 17. | We 3/24 | Midterm Review | | Preliminary Project Report |
| 18. | Mo 3/29 | Midterm Exam | | Take home exam |
| 19. | We 3/31 | 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) | |
| 20. | Mo 4/5 | 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) | |
| 21. | We 4/7 | 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) | Project Presentations |
| 22. | Mo 4/12 | 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) | |
| * | We 4/14 | Spring Break! | | |
| 23. | Mo 4/19 | Genomic 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) | Project Report |
| 24. | We 4/21 | Project Presentations | | |
| 25. | Mo 4/26 | Project Presentations | | |
| 26. | We 4/28 | Project Presentations | | |
| Wed 5/12 | Final Project Report Due! | | |