Schedule (Subject to revision)

Date	Topic	Notes (Slides available only from Brown IP addresses)	Readings (Some available only from Brown IP addresses)
September 4	Introduction: Genomes, Networks, and Cancer	Slides
September 9	DNA Sequencing and Fragment Assembly	Slides
September 11	DNA Sequencing and Fragment Assembly	Slides	EULER assembler Euler-DB Myers EW. The fragment assembly string graph.
September 16	Genome Rearrangements	Slides	Sorting by Reversals
September 18	Guest Lecture: Crystal Kahn	Slides	Duplication Distance
September 23	Genome Rearrangements	Slides
September 25	Paper Presentation: Selim	Slides	Computability of Models for Sequence Assembly
September 30	Paper Presentation: Elena	Slides	Velvet
October 2	Paper Presentation: Fabio	Slides	Gene Duplications
October 7	Paper Presentation: Derek	Slides	Multi-break rearrangements
October 9	Phylogeny	Slides
October 14	Phylogeny	Slides	Notes (from M. Singh)
October 16	Cancer Genomics	Slides	Aberrations in Cancer Chromsome Aberrations in Solid Tumors The Cancer Genome Atlas (pp. 22-29)
October 21	Cancer Genomics	Slides	Comparative Genomic Hybridization Identifying Common Aberrations
October 23	Cancer Genomics	Slides	STAC: Common Aberrations Oncogenetic Trees
October 28	Paper Presentation: Eric	Slides	Orthologous Repeats
October 30	Guest Lecture
November 4	:Paper Presentation: Hsin-Ta	Slides	Genome-wide reconstruction of phylogenetic trees Gene duplication in fungi (for discussion)
November 6	Paper Presentation: Elena	Slides	Cancer Cell Lineages Cell Lineages (methods for above)
November 11	PROJECT PROPOSALS
November 13	Paper Presentation: Derek	Slides	Copy number and expression
November 18	:Networks	Slides	Network comparison Protein networks in disease Analysis and Principles of Biological Networks Network Research
November 20	:Networks	Slides
November 25	Paper Presentation: Kamran	Slides	Signal Transduction Network Inference
November 27	THANKSGIVING HOLIDAY
December 2	NO CLASS: Work on projects		Suggested papers for presentation: Multiple network alignment Orienting graphs Network motif discovery using subgraph enumeration and symmetry-breaking.
December 4	Paper Presentation: Selim Paper Presentation: Hsin-Ta	Slides Slides	Network priors Activity Motifs
December 5	Paper Presentation: Kamran Paper Presentation: Eric	Class meets: 11am-12:20 (CIT 241)	Disease genes in networks miRNA in Prostate Cancer
December 9	NO CLASS: Work on projects
December 11	FINAL PROJECT PRESENTATIONS

Last modified: Sat Nov 3 20:21:10 EDT 2007