Schedule (Subject to revision)

DateTopic 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 PhylogenySlides
Feb. 15 (4pm) Gene Myers lecture
Feb. 20 Holiday
Feb. 22Paper Presentation: CrystalN. 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 1Comparative Genome AssemblySlides. NOTE: Class meets in CIT 367 (joint with CS32)
March 6 Phylogeny: IntroductionSlides
March 8Phylogenetic Trees: Additive Trees and Neighbor Joining Slides
March 13Cancer Genomics Slides
March 15Models of Cancer Progression; Intro. to GeneticsSlides
March 20Paper 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 22Paper 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: RecombinationSlides
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 HaynesBansal 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

Last modified: Wed May 2 19:20:56 EDT 2007