Date | Topic | Notes (Slides available only from Brown IP addresses) |
---|---|---|
January 30 | Introduction, Genome Sequencing, and Fragment Assembly | Slides |
Feb. 2 | Genome Rearrangements: Sorting by Reversals | Slides |
Feb. 6 | Genome Rearrangements II: Duplications | Slides |
Feb. 8 | Thesis Proposal: Planar Graph Algorithms | Lubrano (4th floor CIT) |
Feb. 13 | Paper Presentation: Zach | Myers EW. The fragment assembly string graph. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii79-ii85 |
Feb. 15 | Phylogeny | Slides |
Feb. 15 (4pm) | Gene Myers lecture | |
Feb. 20 | Holiday | |
Feb. 22 | Paper Presentation: Crystal | N. El-Mabrouk. Reconstructing an ancestral genome using minimum segments duplications and reversals. Journal of Computer and System Sciences, Vol. 65, pp. 442-464, 2002. |
Feb. 27 | Paper Presentation: Haynes | Bourque G, Pevzner PA. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 2002 Jan;12(1):26-36. |
March 1 | Comparative Genome Assembly | Slides. NOTE: Class meets in CIT 367 (joint with CS32) |
March 6 | Phylogeny: Introduction | Slides |
March 8 | Phylogenetic Trees: Additive Trees and Neighbor Joining | Slides |
March 13 | Cancer Genomics | Slides |
March 15 | Models of Cancer Progression; Intro. to Genetics | Slides |
March 20 | Paper Presentation: Anna | Beerenwinkel, N., et al. Learning Multiple Evolutionary Pathways from Cross-Sectional Data J. Computational Biology, Vol. 12, No.6: 584-598, 2005. |
March 22 | Paper Presentation: Eric | Ben-Dor A. et al. Framework for Identifying Common Aberrations in DNA Copy Number Data RECOMB 2007. |
Spring Break! | ||
April 3 | Population Genetics: Recombination | Slides |
April 5 | Guest Lecture: Alkes Price (Harvard Genetics) | Population genetics and whole-genome disease association studies |
April 10 | Structural Variation | Slides |
April 12 | Paper Presentations: Zach and Haynes | Bansal V, Bashir A, Bafna V. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res. 2007 Feb;17(2):219-30. Corona, Raphael, and Eskin. Identification of Deletion Polymorphisms from Haplotypes. RECOMB 2007. |
April 17 | Paper Presentation: Peter | J. Comp. Bio. Vol.13 (2): 481-500, 2006. Halperin, E. and Eskin, E. Haplotype Reconstruction from Genotype Data using Imperfect Phylogeny. Bioinformatics 2003. |
April 19 | Paper Presentation: Crystal | Halperin, E. and Hazan, E. HAPLOFREQ - Estimating Haplotype Frequencies Efficiently |
April 24 | Guest Lecture: Art Salomon (Brown MCB) | |
April 26 | Networks | Slides |
May 1 | CCMB Poster Session | |
May 3 | Networks | Slides |
May 8 | Projects Discussion |