Schedule (Subject to revision)

DateTopic Notes (Slides available only from Brown IP addresses) Readings
September 6 Introduction: Genomes, Networks, and Cancer Slides
  • The Cancer Genome Atlas
  • Sequencing Cancer Genomes
    • September 11 Duplications and Comparative Genomic Hybridization Slides
  • CGH Review
  • Lipson, Stepgram
  • Olshen, Circular Binary Segmentation
  • Fridlyand, Hidden Markov Models
    • September 13 Duplications and Comparative Genomic HybridizationSlides
  • Ben-Dor et al., Common Aberrations
  • Diskin et al., STAC
    • September 18 Guest Lecture: Crystal Kahn
    September 25 Genome Rearrangements Slides Sorting by Reversals
    September 27 Paper Presentation: Serdar Genomic Distances under Deletions and Insertions
    October 2 Paper Presentation: Brendan Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays
    October 4 Guest Lecture: Doron Lipson (Helicos Biosciences)
    October 9 Paper Presentation: Yuri New Probabilistic Network Models and Algorithms for Oncogenesis
    October 11Paper Presentation: E.J.Combined Analysis of Copy Number Changes and Structural Rearrangements in Cancer Genomes
    October 16
  • Paper Presentation: Lian
  • Wrap up: Genome Rearrangements
    		•  Reconstructing Tumor Genome Architectures
    October 18
  • Guest Lecture: Jan Korbel (Yale University)
  • PROJECT PROPOSALS DUE
    		• Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome
    October 23 Project Discussions (11:30-1pm or by appt.)
    October 25 No class
    October 30 Introduction: Networks Slides
  • Review article: Getting connected: analysis and principles of biological networks
  • Review (Ideker and Sharan)
  • PathBlast (supplement)
    • November 1 Networks: Alignment and Querying
  • Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data
  • QNet: A tool for querying protein interaction networks
    • November 6 Paper Presentation: Eric Representation and Simulation of Biochemical Processes using the Pi-calculus process algebra
    November 8 Paper Presentation: Anna PROJECT PROGRESS REPORTS DUE Markov chain Monte Carlo for Structural Inference with Prior Information
    November 13 Paper Presentation: Brendan Graemlin: General and robust alignment of multiple large interaction networks
    November 15 Paper Presentation: Anna SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
    November 20 No Class
    November 22 THANKSGIVING HOLIDAY
    November 27 Paper Presentation: Lian Network-based classification of breast cancer metastasis
    November 29 Paper Presentation: Serdar A network biology approach to prostate cancer
    December 4 Paper Presentation: Yuri Spontaneous evolution of modularity and network motifs
    December 6 Paper Presentation: Ed Network motif discovery using subgraph enumeration and symmetry-breaking.
    December 11 Paper Presentation: Eric Biological Networks: Comparison\ , Conservation, and Evolutionary Trees
    December 13 FINAL PROJECT PRESENTATIONS
    Last modified: Sat Nov 3 20:21:10 EDT 2007