Syllabus and Course Schedule (tentative)

Date Lectures    Topics    Readings    Assignments
   Introduction
Week 1: Mon 8/26 Course overview
[slides]
  • Brief history: from Human Genome Sequencing Project to 1000 Genome Project
Week 1: Wed 8/28 Introduction to genetics
[slides]
  • Mendel's law, recombination
Week 1: Fri 8/30 Introduction to molecular biology
[slides]
  • DNA, RNA, protein, and central dogma
Week 2: Mon 9/2
  • Labor Day (no class)
Week 2: Wed 9/4 Introduction to statistics
[slides]
  • Mean, variance, covariance, fundamentals of probability
Week 2: Fri 9/6 Human genome sequencing project (Dr. Thickman)
[slides]
  • Shot-gun sequencing, Sanger sequencing
Week 3: Mon 9/9 Human genome sequencing project: what did we learn?
[slides]
  • Gene-finding, gene annotation
   Genetic variations and what can we learn from them?
Week 3: Wed 9/11 Genetic diversity, genetic variation
[slides]
  • Alleles, genotypes, phenotypes
  • Different types of genetic variation: SNPs, CNVs, structured variations
  • [RH Chapter 5.4-5.6] Basic Mutations, CNVs, etc.
HW 1 out
Week 3: Fri 9/13 Genome browser (Note: Class will meet in Wean 5202)
  • UCSC genome browser and Watson's genome
  • UCSC genome browser
  • Week 4: Mon 9/16 International HapMap Project
    [slides]
    • SNP genotyping, genetic markers/map, linkage disequilibrium
    Week 4: Wed 9/18 Haplotypes I
    [slides]
    • What is a haplotype?
    • Phasing: finding haplotypes from SNPs
    Week 4: Fri 9/20 Haplotypes II
    • Haplotypes and linkage disequilibrium
    • What can we learn from haplotypes
    • Tag SNPs
    Week 5: Mon 9/23 Introduction to machine learning: clustering
    [slides]
    • Hierarchical clustering, K-means algorithm, mixture model
    • [DTW Chapter 10] Similarity, Distance, and Clustering
    Week 5: Wed 9/25 Population structure in genomes I
    [slides]
    • Evolution of human population
    • Hardy Weinberg equilibrium, genetic drift
    • Book chapter on Hardy-Weinberg Equilibrium
    HW 2 out HW 1 due
    Week 5: Fri 9/27 Population structure in genomes II
    • Genome structures of African/Caucasian/Asian populations
    • Admixture
       Genotype-phenotype relationship
    Week 6: Mon 9/30 Genome-wide Association Analysis
    [slides]
    • Introduction to genome-wide association analysis, case/control studies, chi-square test
    Week 6: Wed 10/2 Genome-wide Association Analysis for Quantitative Traits
    [slides]
    • Monogenic/multi-factorial diseases, univariate/multivariate regression, genotype imputation.
    • [LW Chapter 13 (pp. 210-218)] Linear and logistic regression (The book is available in the engineering library reserve.)
    Week 6: Fri 10/4 Population structure and diseases
    [slides]
    • Finding disease mutations under population subdivision
    • Genetics of lactose persistence
    Week 7: Mon 10/7 Gene-gene interaction I: epistasis
    • What is epistasis, and how can we detect it?
    Week 7: Wed 10/9 Gene-gene interaction II: pleiotropy
    • What is pleiotropy, and how can we detect it?

    HW 3 out, HW 2 due
       Genetics in Systems Biology
    Week 7: Fri 10/11 Measuring gene-expression levels
    [slides]
    • Microarray technology for measuring gene-expression levels
    • Single-channel/two-channel arrays
    Week 8: Mon 10/14 Analysis of gene expression data
    • Gene expressions of Leukemia patients
    • Hierarchical clustering
    Week 8: Wed 10/16 eQTL mapping
    • Genetic basis of variation in gene expression levels
    Week 8: Fri 10/18
    • Mid-semester break (no class)
    Week 9: Mon 10/21 Microarray (Dr. Thickman)
    [Tour Release Form]
    • Lab tour for microarray experiments
       Post GWAS and next generation sequencing
    Week 9: Wed 10/23 Limitation of genome-wide association studies
    [slides]
    • Missing heritability and why?
    • Rare genetic variants
    HW 4 out, HW 3 due
    [slides]
    Week 9: Fri 10/25 Next-generation sequencing technology (Dr. Thickman)
    [slides]
    • 1000 genome project
    • Other applications of next-generation sequencing technology: RNA-Seq, ChIP-Seq
    Week 10: Mon 10/28 Detecting structural variation
    [slides]
    • Computational methods for identifying structural variats in your genome from next generation sequencing data
    Week 10: Wed 10/30
    Week 10: Fri 11/1 Lab tour (Dr. Thickman)
    • Guided tour of lab for genome sequencing (The class will meet in Doherty Hall 2303)
    Week 11: Mon 11/4
    • Mid-term exam
       Evolving genomes
    Week 11: Wed 11/6 Natural selection
    [slides]
    • Signatures of natural selection in our genomes
    Week 11: Fri 11/8 Genomes of Neanderthals and humans
    [slides]
    • Analysis of Neanderthal genome sequence
    • Comparing Neanderthal genome with human genome
       Genomes in medicine
    Week 12: Mon 11/11 Case studies (Guest lecture: Dr. Wei Wu)
    • Asthma and auto-immune diseases
    Term-paper proposal due
    Week 12: Wed 11/13 Case studies: cancer I
    [slides]
    • Tumorigenesis
    • [Molecular Biology of the Cell Chapter 20] Cancer (copies available in blackboard)
    Week 12: Fri 11/15 Case studies: cancer II
    [slides]
    • Cancer genomes and personalized medicine
       Ethical issues
    Week 13: Mon 11/18 Social/ethical/legal issues in personal genomes
    [slides]
    • Personal genomes and policy making, ethical/legal/social issues in genome research
    Week 13: Wed 11/20 Genetic tests and genetic counselling
    [slides]
    • Ethical issues involved in genetic tests and genetic counseling
    HW 4 due
       Other fun topics
    Week 13: Fri 11/22 Genomes of microbiome
    • Microbiomes in human body
    • Metagenomics
    Week 14: Mon 11/25 Genomes of microbiome (Dr. Thickman)
    • Microbiomes in food
    Week 14: Wed 11/27
    • Thanksgiving Holiday (no class)
    Week 14: Fri 11/29
    • Thanksgiving Holiday (no class)
    Week 15: Mon 12/2
    • Student presentation
    Week 15: Wed 12/4
    • Student presentation
    Week 15: Fri 12/6
    • Student presentation