Schedule: Fall 2011 (Subject to revision)



(Slides available only from Brown IP addresses)


(Some available only from Brown IP addresses)

September 12

Lecture: Introduction: Genomes, Networks, and Cancer.

DNA Sequencing

  • Slides Part 1
  • Slides Part 2
  • Molecular Biology Primer (Chapter 3 of Jones & Pevzner)
  • Sequencing technologies -- the next generation
  • September 19 Lecture: de Novo Assembly & Recurrent Somatic Mutations
  • Slides Part 1
  • Slides Part 2
  • Computer Assignment

  • Genome Sequencing Technology and Algorithms [Ch. 6]
  • Genome assembly reborn: recent
    computational challenges
    . M.Pop
  • The impact of next-generation sequencing technology on genetics. E. Mardis
  • September 26 Lecture: Resequencing and Structural Variation Slides
  • Genome structural variation discovery and genotyping
  • Genome Sequencing Technology and Algorithms [Ch. 7]
  • Structural Variation in Human and Cancer Genomes
  • October 3 Lecture: Combinations of Somatic Mutations: Pathway and Group-based Tests
  • Slides, Part 1
  • Slides, Part 2
  • Advances in understanding cancer genomes through second-generation sequencing
  • Algorithms for Detecting Significantly Mutated Pathways in Cancer
  • De novo Discovery of Mutated Driver Pathways in Cancer
  • October 10 NO CLASS: Fall weekend    
    October 17 Lecture: Mutation Progression Models, Genetic Association Studies Slides  
    October 24 Paper Presentations: David and Ahmad
  • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
  • Estimation of rearrangement phylogeny for cancer genomes
  • Inferring tumor progression from genomic heterogeneity
    October 31 Project Work
    November 7 Paper Presentations: Phong and Mike
  • Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction
  • Learning Multiple Evolutionary Pathways from Cross-sectional Data
  • November 14 PROJECT PROPOSALS DUE Proposal Description


    November 14 Paper Presentations: Alexandra and Hua
  • Mutual exclusivity analysis identifies oncogenic network modules
  • Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

    November 21 Paper Presentations: Kefei and Mainak
  • Inferring combined CNV/SNP haplotypes from genotype data
  • Viral Population Estimation Using Pyrosequencing
  • Background reading: Genotype and SNP calling from next-generation sequencing data
    November 28

    Paper Presentations: Russell and Ryan

  • Patient-oriented gene set analysis for cancer mutation data
  • Appendix for above
  • A multidimensional analysis of genes mutated in breast and colorectal cancers
  • Slides -- Brief introduction to Epigenetics
    December 5

    Paper Presentations: Bowei and Max

    Discovery and characterization of chromatin states for systematic annotation of the human genome
  • Genome-scale analysis of aberrant DNA methylation in colorectal cancer
  • Background reading
  • A statistical framework for Illumina DNA methylation arrays (Required:Read Introduction and first two paragraphs of Motivation.)
  • Cancer epigenomics: DNA methylomes and histone-modification maps
  • High-Throughput Assessments of Epigenomics in Human Disease, Chapter 12 of Genome Sequencing Technology and Algorithms.
  • December 9: 1-3pm


    December 19 FINAL PROJECT REPORT DUE Proposal Description