lectures.yaml

lectures:
  - lecture_number: 1
    section: "Computational Biology I"
    date: 2024-02-12
    topic: Course overview and introduction to computational biology
    details: Course overview, history of computational biology, introduction to Bioconductor
    instructor: Nathan Sheffield
    links:
      - url: slides/introduction
        title: Lecture slides
      - url: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002050
        title: All biology is computational biology
        required: true
      - url: https://www.nature.com/articles/nbt.2740
        title: So you want to be a computational biologist?
      - url: https://www.degruyter.com/document/doi/10.7208/9780226080345/html?lang=en#contents
        title: "Life Out of Sequence: A Data-Driven History of Bioinformatics"
    assignments:
      - title: Quiz 0
        url: https://docs.google.com/forms/d/e/1FAIpQLSepqDRD2htGRLupXRybXMbDsfOu5ipQrFU4pkgKeAVPWxl6nA/viewform?usp=sf_link
  - lecture_number: 2
    date: 2024-02-14
    topic: Statistics and probability review
    details: Random Variables, Probability Distributions, Central Limit Theorem, Hypothesis Testing, P-value, Type I and Type II Errors, Multiple Testing Correction, FDR
    instructor: Chongzhi Zang
    links:
      - url: resources/2 Statistics review.pdf
        title: Lecture slides
      - url: https://www.nature.com/articles/506150a
        title: Statistical errors
        required: true
      - url: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004961
        title: Ten Simple Rules for Effective Statistical Practice
        required: true
      - url: https://www.nature.com/articles/nbt1209-1135
        title: How does multiple testing correction work?
        required: true
      - url: https://www.nature.com/articles/s41587-023-01794-9
        title: How the Monty Hall problem is similar to the false discovery rate in high-throughput data analysis
        required: true
      - 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
    assignments:
      - title: Assignment 1
        url: resources/Assignment1.pdf
  - lecture_number: 3
    date: 2024-02-19
    topic: Sequence alignment
    details: Local vs. global alignment, Dynamic programming, Heuristic approaches, BLAST, Short-read alignments
    instructor: Aakrosh Ratan
    assignments:
      - title: Quiz 1
        url: https://forms.gle/Led6u86Fq7NnemWr8
      - title: Assignment 1 due
      - title: Assignment 2
        url: https://github.com/cphg/sequence_alignment
    links:
      - url: slides/alignments
        title: Lecture slides
      - url: https://www.nature.com/articles/nbt0509-455
        title: How to map billions of short reads onto genomes
        required: true
      - url: https://samtools.github.io/hts-specs/SAMv1.pdf
        title: Sequence Alignment/Map Format Specification
        required: true
  - lecture_number: 4
    date: 2024-02-21
    topic: Sequence alignment lab
    details: Smith-Waterman algorithm
    instructor: Aakrosh Ratan
    links:
      - url: slides/alignments_lab
        title: Lecture slides
      - url: https://www.ncbi.nlm.nih.gov/books/NBK464187/
        title: Chapter on Sequence Alignment 
      - url: https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
        title: The Statistics of Sequence Similarity Scores
  - lecture_number: 5
    date: 2024-02-26
    topic: Genome assembly
    details: Pairwise overlaps, Overlap-layout-consensus strategy, De Bruijn graphs
    instructor: Aakrosh Ratan
    links:
      - url: slides/assembly
        title: Lecture slides
      - url: https://www.nature.com/articles/nmeth.1935
        title: What every biologist should know about genome assembly
        required: true
    assignments:
      - title: Quiz 2
        url: https://forms.gle/NV6rLBURAt4YJrdv5
      - title: Assignment 2 due
      - title: Assignment 3
        url: https://github.com/cphg/genome_assembler
  - lecture_number: 6
    date: 2024-02-28
    topic: Genome assembly lab
    details: Shortest superstring problem, Removal of transitive edges, Eulerian walks
    instructor: Aakrosh Ratan
    links:
      - url: slides/assembly_lab
        title: Lecture slides
      - url: https://www.annualreviews.org/doi/10.1146/annurev-genom-090314-050032
        title: The Theory and Practice of Genome Sequence Assembly
  - lecture_number: 7
    date: 2024-03-04
    topic: Molecular evolution and phylogenetics
    details: History of molecular evolution, Sequence divergence and models of sequence evolution, Tree-building, UPGMA, Neighbor-joining, parsimony, maximum likelihood.
    instructor: Nathan Sheffield
    links:
      - title: Lecture slides
        url: slides/phylogenetics
      - title: Phylogenetic tree building in the genomic age
        url: https://doi.org/10.1038/s41576-020-0233-0
        required: true
      - title: Cases in which parsimony or compatibility methods will be positively misleading
        url: https://www.jstor.org/stable/2412923
        required: true
      - title: "Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach"
        url: http://nematodes.org/teaching/tutorials/phylogenetics/Bayesian_Workshop/PDFs/Felsenstein%20J%20Mol%20Evol%201981.pdf
      - title: "A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood"        
        url: https://doi.org/10.1080/10635150390235520
      - title: "MEGA11: Molecular Evolutionary Genetics Analysis Version 11"
        url: https://doi.org/10.1093/molbev/msab120
    assignments:
      - title: Quiz 3
        url: https://forms.gle/hjUGnwXHRHyKNNb6A
      - title: Assignment 4
        url: https://github.com/cphg/phylogenetics_lab
      - title: Assignment 3 due
  - lecture_number: 8
    date: 2024-03-06
    topic: Molecular evolution and phylogenetics lab, Perspective by Bill Pearson
    details: 
    instructor: Nathan Sheffield, Bill Pearson
    links:
      - title: Lecture slides
        url: slides/bims_wrp_persp2024.pdf
  - lecture_number: 9
    date: 2024-03-11
    topic: Differential expression analysis
    details: null
    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"
        required: true
      - url: https://doi.org/10.1186/gb-2010-11-10-r106
        title: "Differential expression analysis for sequence count data"
      - url: https://doi.org/10.1093/bib/bbx008
        title: "Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions"
      - title: Differential Expression Notes
        url: resources/Differential_Expression_Notes.pdf
    assignments:
      - title: Quiz 4
        url: https://forms.gle/RZNdprNFrapMoumj6
      - title: Assignment 5
        url: resources/Assignment_5.pdf
      - title: Assignment 4 due
  - lecture_number: 10
    date: 2024-03-13
    topic: Differential expression lab
    details: 
    instructor: Stefan Bekiranov
    links:
      - url: #
        title: Lecture slides
  - lecture_number: 11
    date: 2024-03-18
    topic: Transcription factors 
    details: 
    instructor: Chongzhi Zang
    links:
      - url: resources/11 Transcription factors.pdf
        title: Lecture slides
      - url: https://www.nature.com/articles/nbt0406-423
        title: What are DNA sequence motifs?
        required: true
    assignments:
      - title: Quiz 5
        url: https://forms.gle/WoShFjywgYCNRr1g9
      - title: Assignment 6
        url: resources/Assignment 6.pdf
      - title: Assignment 5 due
  - lecture_number: 12
    date: 2024-03-20
    topic: Transcription factor lab
    details: 
    instructor: Chongzhi Zang
    links:
      - url: #
        title: Lecture slides
  - lecture_number: 13
    date: 2024-03-25
    topic: Module I Review
    details:
    instructor: Aakrosh Ratan
    links: 
      - url: slides/review1
        title: Lecture slides
    assignments:
      - title: Quiz 6
        url: https://forms.gle/TgCmZEiYN83hhUVz6
      - title: Assignment 6 due
  - lecture_number: 14
    section: "Computational Biology II"
    date: 2024-03-27
    topic: Dimensionality reduction
    details: 
    instructor: Chongzhi Zang
    links:
      - url: resources/14 Dimensionality reduction.pdf
        title: Lecture slides
      - url: https://jmlr.org/papers/volume9/vandermaaten08a/vandermaaten08a.pdf
        title: t-SNE
      - url: https://arxiv.org/abs/1802.03426
        title: UMAP
      - url: https://www.nature.com/articles/s41467-019-13056-x
        title: The art of using t-SNE for single-cell transcriptomics
      - url: https://www.nature.com/articles/s41467-024-45891-y
        title: Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters
    assignments:
      - url: resources/Assignment 7.pdf
        title: Assignment 7
  - lecture_number: 15
    date: 2024-04-01
    topic: Dimensionality reduction lab
    details: null
    instructor: Chongzhi Zang
    links: null
  - lecture_number: 16
    date: 2024-04-03
    topic: Deep learning in biology
    details: null 
    instructor: Stefan Bekiranov
    links:
      - url: resources/Deep_Learning_1.pdf
        title: Deep Learning Lecture Notes 1
        required: true
      - url: resources/Deep_Learning_2.pdf
        title: Deep Learning Lecture Notes 2
        required: true
      - url: https://doi.org/10.1038/nature14539
        title: Deep learning
        required: true
      - url: https://www.deeplearningbook.org
        title: Deep Learning (book)
      - url: https://www.youtube.com/watch?v=CqOfi41LfDw&list=PLblh5JKOoLUIxGDQs4LFFD--41Vzf-ME1
        title: Neural Networks/Deep Learning StatQuest Video Series
      - url: https://www.youtube.com/watch?v=aircAruvnKk&list=PLZHQObOWTQDNU6R1_67000Dx_ZCJB-3pi
        title: Neural Networks (3Blue1Brown)
    assignments:
      - title: Quiz 7
        url: https://forms.gle/7HbocotR6Z1Qg5u68
      - title: Assignment 8
        url: https://pytorch.org/tutorials/beginner/basics/intro.html
      - title: Assignment 7 due
  - lecture_number: 17
    date: 2024-04-08
    topic: Deep learning lab
    details: null
    instructor: Stefan Bekiranov
    links: null
  - lecture_number: 18
    date: 2024-04-10
    topic: Genomic interval analysis
    details: Algorithms and data structures for genomic interval arithmetic, enrichment analysis.
    instructor: Nathan Sheffield
    links:
      - url: slides/genomic-intervals
        title: Lecture slides
      - url: https://doi.org/10.1093/bioinformatics/btq351
        title: "BigWig and BigBed: enabling browsing of large distributed datasets"
        required: true
      - title: "Opportunities and challenges in sharing and reusing genomic interval data"
        url: https://doi.org/10.3389/fgene.2023.1155809 
    assignments:
      - title: Quiz 8
        url: https://docs.google.com/forms/d/e/1FAIpQLSf-2ECOUf2u2eee5ZDF_Yrto_djZgV5r2MltqsBwY83RXIiPg/viewform?usp=sf_link
      - title: Assignment 9
        url: https://github.com/cphg/interval_basics
      - title: Assignment 8 due
  - lecture_number: 19
    date: 2024-04-15
    topic: Genomic interval analysis lab
    instructor: Nathan Sheffield
    links:
      - url: #
        title: Lecture slides
  - lecture_number: 20
    date: 2024-04-17
    topic: Hidden Markov Models
    details: Markov chains, Hidden Markov Models, Viterbi, Baum-Welch, and forward-backward algorithms
    instructor: Nathan Sheffield
    links:
      - url: slides/hmm
        title: Lecture slides
      - url: resources/hmm.pdf
        title: Markov chains and hidden Markov models
        required: true
      - url: https://www.nature.com/articles/nbt1004-1315
        title: What is a hidden Markov model?
      - url: resources/RABINER1989.pdf
        title: A tutorial on Hidden Markov Models and Selected Applications in Speech Recognition
    assignments:
      - title: Quiz 9
        url: https://forms.gle/FFmsA9hRoUkzrVyq5
      - title: Assignment 10
        url: https://github.com/cphg/hmm_lab
      - title: Assignment 9 due
  - lecture_number: 21
    date: 2024-04-22
    topic: Hidden Markov Models lab
    instructor: Nathan Sheffield
    links:
      - url: #
        title: Lecture slides
  - lecture_number: 22
    date: 2024-04-24
    topic: Network analysis
    details: null
    instructor: Aakrosh Ratan
    links:
      - url: slides/networks
        title: Lecture slides
      - url: "https://barabasi.com/f/147.pdf"
        title: "Network Biology: Understanding the Cells Functional Organization"
        required: true
      - url: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007244
        title: Ten simple rules to create biological network figures for communication
      - url: "https://idekerlab.ucsd.edu/wp-content/uploads/publications/Cowen_NatReviews-Genetics_2017.pdf"
        title: "Network propagation: a universal amplifier of genetic associations"
      - url: "https://people.csail.mit.edu/dsontag/courses/ml14/notes/Luxburg07_tutorial_spectral_clustering.pdf"
        title: "A tutorial on Spectral Clustering"
    assignments:
      - title: Quiz 10
        url: https://docs.google.com/forms/d/e/1FAIpQLSdGeri9alyTxPy2MHaVtxsO1gZ0MNZC8Ht6HUYuoWVUNtr8_A/viewform?usp=sf_link
      - title: Assignment 11
        url: https://github.com/cphg/network_analysis
      - title: Assignment 10 due
  - lecture_number: 23
    date: 2024-04-29
    topic: Network analysis lab
    details: null
    instructor: Aakrosh Ratan
    links:
      - url: #
        title: Lecture slides
  - lecture_number: 24
    date: 2024-05-01
    topic: Protein structure prediction
    details: null
    instructor: Gloria Sheynkman
    links:
      - url: "https://pubmed.ncbi.nlm.nih.gov/28284537/"
        title: "Protein interactomes"
        required: true
      - url: "https://www.nature.com/articles/s41392-023-01381-z"
        title: "Overview of alphafold"
        required: true
    assignments:
      - title: Quiz 11
        url: https://docs.google.com/forms/d/e/1FAIpQLSc9vMqOh41xMz-H24-ZgiPfGG5VsZ6MyOLybuly1xUaHxw8rw/viewform?usp=sf_link
      - title: Assignment 12
        url: resources/StructuralBiologyAssignment.md
      - title: Assignment 11 due
  - lecture_number: 25
    date: 2024-05-06
    topic: Protein structure prediction lab
    details: null
    instructor: Gloria Sheynkman
  - lecture_number: 26
    date: 2024-05-08
    topic: Review
    details: null
    instructor: Nathan Sheffield
    assignments:
      - title: Quiz 12
        url: https://docs.google.com/forms/d/e/1FAIpQLSeqqnrh2HWzKW1YIv-fd5mQBer1wwvyGlAPkY8qq-TsPB7U4w/viewform?usp=sf_link
      - title: Assignment 12 due