Date | Topic | Notes (Slides available only from Brown IP addresses) | Readings (Some available only from Brown IP addresses) |
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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 The impact of next-generation sequencing technology on genetics. E. Mardis |
September 17 | Fragment Assembly | Slides | Genome Sequencing Technology and Algorithms [Ch. 7] |
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. |
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October 20 |
Interaction Networks: Introduction |
Slides (Biology introduction) |
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October 22 | Interaction Networks: Network Alignment | Slides |
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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 | |
November 10 | Paper presentation: Carleton | SPINE: A framework for signaling-regulatory pathway inference from cause-effect experiments |
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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 |
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November 17 | Paper presentation: | ||
November 19 | |||
December 8 |
FINAL PROJECT PRESENTATIONS |