Schedule (Subject to revision)
Date
Topic
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 Hybridization
Slides
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 11
Paper 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