| 1. |
Mo 1/28 |
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 1/30 |
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)
* High‐throughput sequencing for biology and medicine (Soon et al, 2013, Molecular Systems Biology) |
Assignment 1 |
| 3. |
Mo 2/4 |
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. |
We 2/6 |
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 2/11 |
Long Read Technologies |
* 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)
* Characterizing the Major Structural Variant Alleles of the Human Genome (Audano et al, 2019, Cell) |
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| 6. |
We 2/13 |
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)
* 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) |
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| 7. |
Mo 2/18 |
FM Index & BWT Lecture Notes |
* PolyBayes: A general approach to single-nucleotide polymorphism discovery (Marth et al, 1999, Nature Genetics)
* GATK: A framework for variation discovery and genotyping using next-generation DNA sequencing data (Depristo et al, 2011, Nature Genetics)
* Scalpel: Accurate de novo and transmitted indel detection in exome-capture data using microassembly (Narzisi et al, 2014, Nature Methods) |
Assignment 3 |
| 8. |
We 2/20 |
Variant Analysis |
* Genome structural variation discovery and genotyping (Alkan et al, 2011, Nature Reviews Genetics)
* LUMPY: a probabilistic framework for structural variant discovery (Layer et al, 2014, Genome Biology)
* Assembly Reconciliation (Zimin et al, 2008, Bioinformatics)
* Resolving the complexity of the human genome using single-molecule sequencing (Chaisson et al, 2015, Nature) |
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| 9. |
Mo 2/25 |
Genome Arithmetic |
* 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) |
Assignment 4 |
| 10. |
We 2/27 |
Genome 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
* What is a hidden Markov model? |
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| 11. |
Mo 3/4 |
Functional Analysis 1: 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) |
Assignment 5 |
| 12. |
We 3/6 |
Functional Analysis 2: Methyl-seq & Chip-seq |
* 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) |
Project Proposal |
| 13. |
Mo 3/11 |
Functional Analysis 3: Regulatory States |
* 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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| 14. |
We 3/13 |
Functional Analysis 4: 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) |
Assignment 6 |
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Mo 3/18 |
Spring Break! |
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We 3/20 |
Spring Break! |
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| 15. |
Mo 3/25 |
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) |
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| 16. |
We 3/27 |
Functional Analysis 6: Scalable methods for genomics |
* Cloud computing and the DNA data race (Schatz et al, Nature Biotech, 2010)
* Reproducible RNA-seq analysis using recount2 (Collado-Torres et al, Nature Biotech, 2017)
* Fast search of thousands of short-read sequencing experiments (Solomon et al. Nature Biotech, 2016) |
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| 17. |
Mo 4/1 |
Midterm Review |
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| 18. |
We 4/3 |
Midterm Exam |
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In class exam |
| 19. |
Mo 4/8 |
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)
* Visualizing Data Using t-SNE |
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| 20. |
We 4/10 |
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) |
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| 21. |
Mo 4/15 |
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) |
Preliminary Project Report |
| 22. |
We 4/17 |
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. |
Mo 4/22 |
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) |
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| 24. |
We 4/24 |
Project Presentations |
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Project Presentations |
| 25. |
Mo 4/29 |
Project Presentations |
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Project Presentations |
| 26. |
We 5/1 |
Project Presentations |
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Project Presentations |
| 27. |
Wed 5/15 |
Final Project Report Due! |
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Final Project Report |