| 1 |
8/25/25 |
M |
Introduction |
Sign up for Piazza |
* Molecular Structure of Nucleic Acid (Watson and Crick, 1953, Nature)
* Biological data sciences in genome research (Schatz, 2015, Genome Research)
* Big Data: Astronomical or Genomical? (Stephens et al, 2015, PLOS Biology)
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| 2 |
8/27/25 |
W |
Genomics Technologies |
Ass1 |
* Coming of age: ten years of next-generation sequencing technologies (Goodwin et al, 2016, Nature Reviews Genetics)
* Guide to k-mer approaches for genomics across the tree of life (Jenike et al., 2024, arXiv)
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| * |
9/1/25 |
M |
$${\color{red}\text{Labor Day}}$$ |
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| 3 |
9/3/25 |
W |
Assembly and WGA |
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* 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, J Comput Biol)
* MUMmer: Alignment of Whole Genomes (Delcher et al, 1999, NAR)
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| 4 |
9/8/25 |
M |
The Human Genome |
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* The complete sequence of a human genome (Nurk et al, Science 2012)
* Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing (Kovaka et al, 2023, Nature Methods
* A draft human pangenome reference (Liao et al, 2023, Nature)
* Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References (Taylor et al., 2024, Annual Review of Genomics and Human Genetics)
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| 5 |
9/10/25 |
W |
Read Mapping |
Ass2 |
* How to map billions of short reads onto genomes (Trapnell and Salzberg, 2009, Nature Biotech)
* Sapling: Accelerating Suffix Array Queries with Learned Data Models (Kirsche et al, 2020, Bioinformatics)
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| 6 |
9/15/25 |
M |
BWT |
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* 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)
* Minimap2: pairwise alignment for nucleotide sequences (Li, Bioinformatics, 2018)
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| 7 |
9/17/25 |
W |
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)
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| 8 |
9/22/25 |
M |
Intro to ML |
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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
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| 9 |
9/24/25 |
W |
CNN + DeepVariant |
Ass3 |
* ImageNet Classification with Deep Convolutional Neural Networks (Krizhevsky et al., 2012, NIPS)
* A universal SNP and small-indel variant caller using deep neural networks (Poplin et al. 2018, Nature Biotech)
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| 10 |
9/29/25 |
M |
Populalation Genetics |
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* 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)
* 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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| 11 |
10/1/25 |
W |
Clinical Genomics |
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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)
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| 12 |
10/6/25 |
M |
Review 1 |
Project Proposal |
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| 13 |
10/8/25 |
W |
$${\color{orange}\text{Exam 1 (In class)}}$$ |
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| 14 |
10/13/25 |
M |
Functional Analysis 1: 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)
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| 15 |
10/15/25 |
W |
Functional Analysis 2: Single Cell Genomics |
Ass4 |
* 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)
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| 16 |
10/20/25 |
M |
Functional Analysis 3: Ab initiio gene finding |
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* 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
* BEDTools: a flexible suite of utilities for comparing genomic features (Quinlan & Hall, 2010, Bioinformatics)
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| 17 |
10/22/25 |
W |
Functional Analysis 4: Methyl-seq, Chip-seq, and Hi-C |
Prelim report assigned |
* 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)
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| 18 |
10/27/25 |
M |
Functional Analysis 5: 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)
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| 19 |
10/29/25 |
W |
Transformers |
Ass5 |
* Attention is all you need (Vaswani et al. 2017, arXiv)
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| 20 |
11/3/25 |
M |
Enformer + Other DL applications |
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* Effective gene expression prediction from sequence by integrating long-range interactions (Avsec et al., 2021, Nature Methods)
* Personal transcriptome variation is poorly explained by current genomic deep learning models
(Huang et al., 2023, Nature Genetics)
* Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings (Sasse et al., 2023, Nature Genetics)
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| 21 |
11/5/25 |
W |
AlphaGenome, Evo2, and related models |
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* AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model (Avsec et al, 2025, bioRxiv)
* Genome modeling and design across all domains of life with Evo 2 (Brixi et al, 2025, bioRxiv)
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| 22 |
11/10/25 |
M |
Review 2 |
Final Report Assigned |
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| 23 |
11/12/25 |
W |
$${\color{orange}\text{Exam 2 (In class)}}$$ |
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| 24 |
11/17/25 |
M |
Wrap up |
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* Deep Learning Sequence Models for Transcriptional Regulation (Sokolova et al., 2024, Annual Reviews of Genomics and Human Genetics)
* AlphaFold (Jumper et al, 2021, Nature)
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| 25 |
11/19/25 |
W |
In-class presentation |
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| * |
11/24/25 |
M |
$${\color{red}\text{Thanksgiving Break}}$$ |
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| * |
11/26/25 |
W |
$${\color{red}\text{Thanksgiving Break}}$$ |
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| 26 |
12/1/25 |
M |
In-class presentation |
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| 27 |
12/3/25 |
W |
In-class presentation |
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| * |
12/10/25 |
W |
Draft Report Due |
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| * |
12/11/25 |
Th |
Final project presentation |
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| * |
12/12/25 |
F |
Final project presentation |
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| * |
12/15/25 |
M |
Final project presentation |
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| * |
12/16/25 |
Tu |
Final Report Due |
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