Schedule: Fall 2010



(Slides available only from Brown IP addresses)


(Some available only from Brown IP addresses)

September 2

Lecture: Introduction: Genomes, Networks, and Cancer.

DNA Sequencing

Slides Molecular Biology Primer (Chapter 3 of Jones & Pevzner)
September 7 Lecture: Sequence Alignment & Fragment Assembly Slides
September 9 Lecture: Fragment Assembly Slides
September 14 Lecture: Fragment Assembly: EULER Slides
September 16 No class    
September 21 Lecture: Resequencing and Structural Variation Slides  
September 23 No class  
September 28 Paper Presentation: Ben Maximum Likelihood Genome Assembly
September 30 Paper Presentation: Soumya Genovo: De Novo Assembly for Metagenomes
October 5 Lecture Slides


October 7 Paper Presentation: Jonathan  

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

Background reading: An MCMC algorithm for haplotype assembly from whole-genome sequence data

October 12

Lecture: Interaction Networks: Introduction. Biology of signalling and regulatory networks.


Slides (Biology introduction)

Analysis and Principles of Biological Networks
October 14

Lecture: Interaction Networks: Gene Expression and Integration


October 19

Paper Presentation: Layla

Paper Presentation: Steve


Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles

Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways

October 21

Paper presentation: Dae Il

Paper Presentation: Edward

An integrative approach for causal gene identification and gene regulatory pathway inference

eQED: an efficient method for interpreting eQTL associations using protein networks

October 26 Lecture: Interaction Networks: Network Alignment and Color Coding Slides Network comparison
October 28 Lecture: Interaction Networks: Network Querying and Motifs Slides
November 2Lecture: Interaction Networks: Network Motifs and Inference


November 4 Guest lecture: Fabio Vandin  
November 9

Paper presentation: Layla

Paper presentation: Jonathan

RAPID detection of gene–gene interactions in genome-wide association studies

Pathway-Based Approaches for Analysis of Genomewide Association Studies

November 11 Work on projects
November 16

Paper presentation: Steve

Paper presentation: Edward

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments

Structural variation analysis with strobe reads

November 18

Paper presentation: Ben

Bayesian Rose Trees
November 23

Paper presentation: Dae Il

Paper presentation: Soumya

Inference of Population Structure Using Multilocus Genotype Data [Read up to "Applications to data" p.949. Appendix is alow useful to understand model.]

MMG: a probabilistic tool to identify submodules of metabolic pathways

November 25 NO CLASS: Thanksgiving
November 30 Lecture: Phylogenetic Tree Reconstruction Slides
December 2 Project updates

December 7