lectures.yaml

lectures:
  - lecture_number: 1
    date: 02/15/22
    topic: Course overview and introduction to computational genomics
    details: Course overview, git/GitHub, history of genomics and sequencing technology, genomic data scale, popular topics in genomics, computing in genomics
    instructor: Nathan Sheffield
    links:
      - url: slides/introduction
        title: Lecture slides
      - url: https://www.sciencedirect.com/science/article/pii/S0012160604008231
        title: Friedrich Miescher and the discovery of DNA
      - url: https://kbroman.org/github_tutorial/
        title: Karl Broman's guide to git and GitHub
  - lecture_number: 2
    date: 02/17/22
    topic: Statistics and probability review 1
    details: Random Variables, Probability Distributions, Expectation, Variance, Moment-Generating Functions, Central Limit Theorem
    instructor: Stefan Bekiranov
    links:
      - url: slides/statistics1
        title: Lecture slides
      - url: resources/BIMS_8601_Homework1.pdf
        title: Statistics assignment
      - url: https://books.google.com/books?id=7SI8AAAAQBAJ&source=gbs_book_other_versions
        title: Mathematical Statistics and Data Analysis      
  - lecture_number: 3
    date: 02/22/22
    topic: Statistics and probability review 2
    details: statistical tests, p-value, type I and type II errors, multiple testing corrections, FDR, ROC
    instructor: Chongzhi Zang
    links:
      - url: slides/statistics2
        title: Lecture slides
      - url: https://amstat.tandfonline.com/doi/pdf/10.1080/00031305.2016.1154108
        title: ASA Statement on Statistical Significance and P-Values
      - url: https://www.nature.com/articles/nbt1209-1135.pdf
        title: How does multiple testing correction work?
  - lecture_number: 4
    section: "Unit 1: Genome"
    date: 02/24/22
    topic: Fundamental string matching algorithms
    details: Local vs. global alignment, Dynamic programming, Heuristic approaches, BLAST 
    instructor: Aakrosh Ratan
    links:
      - url: slides/fundamental_string.html
        title: Lecture slides
      - url: resources/BLAST.pdf
        title: Basic Local Alignment Search Tool
      - url: https://github.com/cphg/sequence_alignment
        title: Alignment assignment

  - lecture_number: 5
    date: 03/01/22
    topic: Suffix trees, Suffix arrays, and Burrows-wheeler transform
    details: Short-read alignments
    instructor: Aakrosh Ratan
    links:
      - url: slides/short_read.html
        title: Lecture slides
      - url: resources/ShortReadAlignment.pdf
        title: Survey of sequence alignment algorithms
  - lecture_number: 6
    date: 03/03/22
    topic: Bayes theorem, Likelihood, and Expectation-Maximization
    details: Variant calling, Structural Variants
    instructor: Aakrosh Ratan
    links:
      - url: slides/variant_calling.html
        title: Lecture slides
      - url: https://stephens999.github.io/fiveMinuteStats/beta.html
        title: Beta distribution
      - url: https://stephens999.github.io/fiveMinuteStats/dirichlet.html
        title: Dirichlet distribution
      - url: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1828-7
        title: Structural variant detection
  - lecture_number: null
    date: 03/08/22
    topic: Spring Recess
    details: 
    instructor: 
  - lecture_number: null
    date: 03/10/22
    topic: Spring Recess
    details: 
    instructor: 
  - lecture_number: 7
    date: 03/15/22
    topic: De-bruijn graphs and String graphs
    details: Genome assembly
    instructor: Aakrosh Ratan
    links:
      - url: slides/genome_assembly.html
        title: Lecture slides
      - url: https://github.com/cphg/genome_assembler
        title: Assembler assignment
      - url: https://academic.oup.com/bib/article/19/1/23/2339783?login=false
        title: Review of de novo whole-genome assembly
  - lecture_number: 8
    date: 03/17/22
    topic: Hidden Markov Models (HMMs)
    details: Gene-finding, CpG islands and Chromatin states, Gibbs sampling, Expectation maximization
    instructor: Aakrosh Ratan
    links:
      - url: slides/hmm.html
        title: Lecture slides
      - url: resources/RABINER1989.pdf
        title: Rabiner 1989 tutorial on HMMs
      - url: https://www.nature.com/articles/nbt1004-1315
        title: What is a hidden Markov model?
  - lecture_number: 9
    date: 03/22/22
    topic: Linear Regression, Chi-Squared Test of Independence 
    details: Genome Wide Association Studies, eQTLs
    instructor: Stefan Bekiranov
    links:
      - url: slides/linear_models.html
        title: Lecture slides
  - lecture_number: 10
    section: "Unit 2: Epigenome"
    date: 03/24/22
    topic: Regulatory DNA, Transcription factors, Sequence motifs 
    details: PWMs, information entropy, motif finding algorithms
    instructor: Chongzhi Zang
    links:
      - url: slides/epigenomics1.pdf
        title: Lecture slides
      - url: https://www.nature.com/articles/nbt0406-423.pdf
        title: What are DNA sequence motifs?
      - url: resources/10.1.1.121.7056.pdf
        title: Bailey & Elkan MEME paper
      - url: https://github.com/cphg/compgen/tree/master/resources/motif_assignment
        title: Motif assignment
      - url: resources/motif_assignment/motif%20assignment.pdf
        title: Motif assignment (pdf)
  - lecture_number: 11
    date: 03/29/22 
    topic: ChIP-seq, Epigenome profiles, Peak detection
    details: ChIP-seq, read mapping, epigenomic profile construction, narrow peak calling 
    instructor: Chongzhi Zang
    links:
      - url: slides/epigenomics2.pdf
        title: Lecture slides
      - url: resources/Computational%20methodology%20for%20ChIP-seq%20analysis.pdf
        title: ChIP-seq computational methodology review
      - url: https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2008-9-9-r137.pdf
        title: MACS paper
  - lecture_number: 12
    date: 03/31/22
    topic: Epigenomic domains, Hierarchy and scales of genome structure
    details: Histone modifications, broad peak calling, chromatin domains, 3D genome basics
    instructor: Chongzhi Zang
    links:
      - url: slides/epigenomics3.pdf
        title: Lecture slides
      - url: resources/btp340.pdf
        title: SICER paper
      - url: resources/TheHitchhikersGuideToHiCAnalysis.pdf
        title: The Hitchhiker's Guide to Hi-C Analysis
  - lecture_number: 13
    date: 04/05/22
    topic: "Genomic intervals: formats, data structures and algorithms"
    details: Genomic intervals; genomic interval file formats; interval operations; interval data structures (R-trees, B+ trees, NCList); interval search
    instructor: Nathan Sheffield
    links:
      - title: Lecture slides
        url: slides/interval-data-structures
      - title: Interval basics assignment
        url: https://github.com/cphg/interval_basics
      - title: Orchestrating high-throughput genomic analysis with Bioconductor 
        url: https://doi.org/10.1038/nmeth.3252
      - title: "BigWig and BigBed: enabling browsing of large distributed datasets"
        url: https://doi.org/10.1093/bioinformatics/btq351
  - lecture_number: 14
    date: 04/07/22
    topic: ATAC-seq diagnostics and harmonization
    details: ATAC-seq count data; data diagnostics; clip functions; consensus peaks; tests of normality; quantile normalization; Q-Q plots; batch correction
    instructor: Nathan Sheffield
    links:
      - url: slides/data-diagnostics
        title: Lecture slides
      - url: resources/Smith2020.pdf
        title: Review of ATAC-seq data analysis
  - lecture_number: 15
    date: 04/12/22
    topic: Scalable computing in genomics
    details: Parallelization, workflow management, optimization, Big-Oh complexity, Efficiently processing large sequencing data
    instructor: Nathan Sheffield
    links:
      - url: slides/scalable-computing-genomics
        title: Lecture slides
      - url: https://doi.org/10.1038/s41592-021-01254-9
        title: Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
  - lecture_number: 16
    date: 04/14/22
    section: "Unit 3: Transcriptome"
    topic: Genomic data standards and reference genomes
    details: Standards and interoperability; GA4GH; Reference genomes; refget; sequence collections; APIs; other standards
    instructor: Nathan Sheffield
    links:
      - url: slides/genomic-data-standards
        title: Lecture slides
      - title: "GA4GH: International policies and standards for data sharing across genomic research and healthcare"
        url: http://dx.doi.org/10.1016/j.xgen.2021.100029
  - lecture_number: 17
    date: 04/19/22
    topic: K-mer analysis
    details: RNA pseudoalignment; membership testers; Bloom filters
    instructor: Nathan Sheffield
    links:
      - url: slides/k-mer-analysis
        title: Lecture slides
      - url: https://github.com/cphg/kmer-counting
        title: K-mer assignment
      - title: Efficient counting of k-mers in DNA sequences using a bloom filter
        url: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-333
  - lecture_number: 18
    date: 04/21/22
    topic: Dimensionality reduction
    details: Curse of Dimensionality, PCA, NMF, t-SNE, UMAP
    instructor: Stefan Bekiranov
    links:
      - url: slides/dim_red
        title: Lecture slides
      - url: https://dx.doi.org/10.1038/44565
        title: Learning the parts of objects by non-negative matrix factorization
      - url: https://lvdmaaten.github.io/tsne/
        title: t-SNE
      - url: https://umap-learn.readthedocs.io/en/latest/
        title: UMAP
      - url: https://doi.org/10.1101/2021.08.25.457696
        title: Picasso       
  - lecture_number: 19
    date: 04/26/22
    topic: Differential expression analysis
    details: Mircoarray and Bulk RNA-seq Analysis
    instructor: Stefan Bekiranov
    links:
      - url: slides/diff_exp
        title: Lecture slides
      - url: https://doi.org/10.1186/s13059-014-0550-8
        title: "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2"  
  - lecture_number: 20
    date: 04/28/22
    topic: Spatial omics, Encoding of genomic data
    details: MERFISH, spatial transcriptomics, simplex encoding, Hamming codes
    instructor: Chongzhi Zang
    links:
      - url: slides/transcriptomics5.pdf
        title: Lecture slides
      - url: resources/BMGseminar0428
        title: BMG seminar by Siyuan Wang on 4/28
      - url: https://www.science.org/doi/10.1126/science.aaa6090
        title: MERFISH Chen 2015 Science paper
      - url: https://www.nature.com/articles/s41592-020-01033-y.pdf
        title: Spatially resolved transcriptomics
      - url: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02653-7
        title: Statistical and machine learning methods for spatially resolved transcriptomics data analysis
      - url: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4
        title: Exaggerated false positives by popular differential expression methods when analyzing human population samples
  - lecture_number: 21
    date: 05/03/22
    topic: Clustering, transcriptomic data integration
    details: Clustering algorithms, regulatory networks, transcriptional regulation
    instructor: Chongzhi Zang
    links:
      - url: slides/transcriptomics6.pdf
        title: Lecture slides
      - url: https://onlinelibrary.wiley.com/doi/10.1111/j.0006-341X.2005.031032.x
        title: Tight Clustering Tseng & Wong 2005
      - url: https://academic.oup.com/bioinformatics/article/25/22/2906/180866
        title: iCluster Shen et al 2009
      - url: https://arxiv.org/pdf/0803.0476.pdf
        title: Louvain method Blondel et al 2008
      - url: https://academic.oup.com/bioinformatics/article/34/16/2867/4956015
        title: BART Wang et al 2018
  - lecture_number: 22
    section: Final presentations
    date: 05/05/22
    topic: Final Presentations
    details: 
    instructor: 
  - lecture_number: 23
    date: 05/10/22
    topic: Final Presentations
    details: 
    instructor: