Date | Topic | Notes (Slides available only from Brown IP addresses) | Readings (Some available only from Brown IP addresses) |
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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 |
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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 |
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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 |
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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 |
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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 |
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October 26 | Lecture: Interaction Networks: Network Alignment and Color Coding | Slides | Network comparison |
October 28 | Lecture: Interaction Networks: Network Querying and Motifs | Slides | |
November 2 | IntLecture: 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 |
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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 |
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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 |
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November 25 | NO CLASS: Thanksgiving | ||
November 30 | Lecture: Phylogenetic Tree Reconstruction | Slides | |
December 2 | Project updates | ||
December 7 |
FINAL PROJECT PRESENTATIONS |