| 1 |
28-Aug |
Mon |
Introduction |
Sign Up for Piazza |
* Biological data sciences in genome research (Schatz, 2015, Genome Research)
* Big Data: Astronomical or Genomical? (Stephens et al, 2015, PLOS Biology) |
| 2 |
30-Aug |
Wed |
Genomic Technologies |
Assignment 1: Genomic Fundamentals |
* 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) |
| * |
4-Sep |
Mon |
\({\color{red}\text{Labor Day}}\) |
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| 3 |
6-Sep |
Wed |
Whole Genome Assembly |
Assignment 2: Assembly |
* Toward simplifying and accurately formulating fragment assembly. (Myers, 1995, J. Comp. Bio.)
* Velvet: Algorithms for de novo short read assembly using de Bruijn graphs (Zerbino and Birney, 2008, Genome Research)
*SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing (Bankevich et al. 2012)
* Quake: quality-aware detection and correction of sequencing errors (Kelley et al, 2010, Genome Biology)
* MUMmer: Alignment of Whole Genomes (Delcher et al, 1999, NAR) |
| 4 |
11-Sep |
Mon |
The human genome and intro to long reads |
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* The complete sequence of a human genome (Nurk et al, 2022
* MHAP: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing (Berlin et al, 2015, Nature Biotech)
FALCON-unzip: Phased diploid genome assembly with single-molecule real-time sequencing (Chin et al, 2016, Nature Methods)
* Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (Rhie et al. 2020) |
| 5 |
13-Sep |
Wed |
Pan-Genomics |
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* Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing (Kovaka et al, 2023, Nature Methods
* Piercing the dark matter: bioinformatics of long- range sequencing and mapping (Sedlazeck et al, 2018, Nature Reviews Genetics)
* A draft human pangenome reference (Liao et al, 2023) |
| 6 |
18-Sep |
Mon |
Genomics in the Cloud |
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* 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) |
| 7 |
20-Sep |
Wed |
Read Mapping |
Assignment 3: Mappability and 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 |
| 8 |
25-Sep |
Mon |
Variant Analysis |
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* 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) |
| 9 |
27-Sep |
Wed |
Structural Variant Analysis |
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* 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 |
2-Oct |
Mon |
Sketching |
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* Mash: fast genome and metagenome distance estimation using MinHash (Ondov et al, 2016, Genome Biology) |
| 11 |
4-Oct |
Wed |
Genome Arithmetic and Plane Sweep |
Assignment 4: BWT and Modimizers |
* 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) |
| 12 |
9-Oct |
Mon |
Machine Learning Primer |
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* 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 |
| 13 |
11-Oct |
Wed |
Functional Analysis 1: Annotation |
Project Proposal |
* 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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| 14 |
16-Oct |
Mon |
Functional Analysis 2: RNA-seq |
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* 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) |
| 15 |
18-Oct |
Wed |
Functional Analysis 3: Methyl-seq, Chip-seq, and Hi-C |
Assignment 5: Functional Genomics |
* 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) |
| 16 |
23-Oct |
Mon |
Functional Analysis 4: Regulatory States, ENCODE, GTEx, RoadMap |
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* 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) |
| 17 |
25-Oct |
Wed |
Functional Analysis 5: Single Cell Genomics |
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* 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) |
| 18 |
30-Oct |
Mon |
Human Evolution |
Preliminary Project Report |
* 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) |
| 19 |
1-Nov |
Wed |
\({\color{blue}\text{Midterm review}}\) |
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| 20 |
6-Nov |
Mon |
\({\color{blue}\text{Midterm}}\) |
*In class exam* |
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| 21 |
8-Nov |
Wed |
Human Genetic Diseases |
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* 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) |
| 22 |
13-Nov |
Mon |
Cancer Genomics |
Prelim Report Due |
* 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) |
| 23 |
15-Nov |
Wed |
Microbiome and Metagenomics |
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* Kraken: ultrafast metagenomic sequence classification using exact alignments (Wood and Salzberg, 2014, Genome Biology)
* Chapter 12: Human Microbiome Analysis (Morgan and Huttenhower) |
| * |
20-Nov |
Mon |
\({\color{red}\text{Thanksgiving Break}}\) |
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| * |
22-Nov |
Wed |
\({\color{red}\text{Thanksgiving Break}}\) |
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| 24 |
27-Nov |
Mon |
\({\color{blue}\text{In class project presentation}}\) |
Project presentation |
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| 25 |
29-Nov |
Wed |
\({\color{blue}\text{In class project presentation}}\) |
Project presentation |
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| 26 |
4-Dec |
Mon |
\({\color{blue}\text{In class project presentation}}\) |
Project presentation |
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| * |
6-Dec |
Wed |
\({\color{red}\text{No Class}}\) |
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| * |
17-Dec |
Sun |
\({\color{blue}\text{Final Report Due}}\) |
Final Report |
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