Bio 451 - Genome Analysis

	Lecture Topics (principles)	Lab Activities
Week 1 8/30 – 9/3	Introduction to large-scale, integrative, systems biology. Science -11 April 2003; 300 (5617) Special Issue: Building on the DNA Revolution Pennisi, E., DNA’s Cast of Thousands. Collins, F.S. et al., The Human Genome Project: Lessons from Large-Scale Biology. Frazier, M.E., Realizing the Potential of the Genome Revolution: The Genomes to Life Program. Snyder, M. & Gerstein, M., Defining Genes in the Genomics Era.	GCAT Assessment Isolation of pCOS110, pBS. Partial Digestion with Sau3A, Gel purify 0.8 -2 kb fragments.
Week 2 9/6 – 9/10	Methods of sequencing, assembly, annotation. CAP3 A DNA Sequence Assembly Program -- Huang and Madan. 1999. Genome Research 9:868	Ligate gel purified fragments into pBS, transform into E. coli.
Week 3 9/13 – 9/17	Microbial genomes (COGs) A genomic perspective on protein families. Tatusov et al. 1997 Science. 278:631 Gene families: the taxonomy of protein paralogs and chimeras. Henikoff S et al., 1997 Science 278:609 The COG database a tool for genome-scale analysis of protein functions and evolution - Tatusov et al. 2000, - Nucleic Acids Research 28:33	COG Database at the National Center for Biotechnology Information (NCBI) Ligate gel purified fragments into pBS, transform into E. coli.
Week 4 9/20 – 9/24	Microbial genomes (metabolic reconstruction) Whole-Genome Analysis of Photosynthetic Prokaryotes. Raymond et al. 2002. Science 298:1616 Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network. Forster et al. 2003 Genome Res. 13:244-253 In Silico Organisms - Yeast KEGG: Kyoto Encyclopedia of Genes and Genomes CYGD:Comprehensive Yeast Genome Database SGD: Saccharomyces Genome Database ExPASy database	Plasmid preps of transformants, restriction enzyme digestion, gel electrophoresis. Send samples for sequencing.
Week 5 9/27 – 10/1	Unicellular Eukaryote Genomes (Endosymbiosis) Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii	Assemble contigs, annotate sequence (computer lab) CAP3 Sequence Assembly Program
Week 6 10/4 – 10/8	Plant genomes (Synteny) The Rice Genome Science v. 296 n. 5565 (5 April 2002) Structural Dynamics of Eukaryotic Chromosome Evolution. Eichler and Sankoff. (2003) Science 301:793-797	Microbial genome presentations Microarrays: Grow yeast cells
Week 7 10/11 – 10/15 (long weekend)	Fungal genomes (Protein Interaction Networks) A comprehensive two-hybrid analysis to explore the yeast protein interactome -- Ito et al., 2001. PNAS 98:4569 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae -- Uetz et al., 2000, Nature 403:623	Microarrays: Isolate, quantify RNA
Week 8 10/18 – 10/22	catch up, review, Mid-term exam (10/22)	Microarrays: Make cDNA
Week 9 10/25 – 10/29	Insect genomes (Gene expression clustering) The Genome Sequence of the Malaria Mosquito Anopheles gambiae. (2002) Holt et al.. Science 298:129-149. Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster. (2002) Zdobnov et al., Science 298:149-159.	Microarrays: Hybridization, send for scanning
Week 10 11/1 – 11/5	Vertebrate genomes (gene duplication) The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins. (2002) Dehal et al. Science 298:2157-2167. Tunicate Genome Shows a Little Backbone. (2002) Pennisi Science. 298: 2111-2112 Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. (2004) Jaillon et al., Nature 431:946-957	Microarray Data Analysis (computer lab)
Week 11 11/8 – 11/12	Mammal genomes (evolutionary genomics) The Mouse Genome (2002) Nature 420:520-562 Genome sequence of the Brown Norway rat yields insights into mammalian evolution (2004) Nature 428:493-521 The Chimpanzee Genome (2004) Nature 429:382-388	Microarray Data Analysis (computer lab)
Week 12 11/15 – 11/19	Human genome (proteomics) Human genome: End of the beginning. Stein (2004) Nature 431:916-917 Finishing the euchromatic sequence of the human genome. (2004) Nature 431:931-945 NHGRI Human Genome Draft (2001) Nature Celera Human Genome Draft (2001) Science	Microarray Data Analysis – Produce final reports (computer lab)
Week 13+ 11/22 – 12/3	SNPs, Individualized Medicine	More NCBI Databases
Week 14 12/6 – 12/10	Advanced Integrative & Systems Biology	Eukaryote genome presentations

Structural Dynamics of Eukaryotic Chromosome Evolution. Eichler and Sankoff. (2003) Science 301:793-797

Tunicate Genome Shows a Little Backbone. (2002) Pennisi Science. 298: 2111-2112