Schedule (Subject to revision)



(Slides available only from Brown IP addresses)


(Some available only from Brown IP addresses)

September 10 Introduction: Genomes, Networks, and Cancer Slides Molecular Biology Primer (Chapter 3 of Jones & Pevzner)
September 15 DNA Sequencing and Fragment Assembly Slides

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 17 Fragment Assembly Slides

Genome Sequencing Technology and Algorithms [Ch. 7]

Myers EW. The fragment assembly string graph.

EULER assembler

September 22 Fragment Assembly and Resequencing Slides
September 24 Resequencing Slides Haplotyping: Genome Sequencing Technology and Algorithms [Ch.10, pp. 151-154]
September 29 Paper Presentation: Aparna Maximum Likelihood Genome Assembly. P. Mendevev and M. Brudno
October 1 Paper Presentation: Adrian HapCUT: an efficient and accurate algorithm for the haplotype assembly problem V. Bansal and V. Bafna
October 6 Structural Variation Slides
October 8 Paper Presentation:Lauren Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. F. Hormozdiari C. Alkan E. E. Eichler and S. C. Sahinalp.
October 13 Copy Number Variation and Segmentation Slides Comparative Genomic Hybridization
October 15

Guest lecture: Doron Lipson, Helicos Biosciences

Quantification of the yeast transcriptome by single-molecule sequencing.

Single-molecule sequencing of an individual human genome

October 20


Interaction Networks: Introduction


Slides (Biology introduction)

Analysis and Principles of Biological Networks

October 22 Interaction Networks: Network Alignment Slides

Network comparison


October 27 NO CLASS
October 29 Guest lecture: Fabio Vandin
November 3 Interaction Networks: Alignment and Color Coding Slides
November 5 Interaction Networks: Function Prediction Slides

Protein networks in disease

Network Research

November 10 Paper presentation: Carleton

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

Orienting graphs

November 12 Paper presentation: Luan

Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. M. Lavallée-Adam, B. Coulombe and M. Blanchette

November 17 Paper presentation:
November 19  

December 8