lecture_1

lecture_1 - Key Goals This Term How can we choose an...

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Unformatted text preview: Key Goals This Term How can we choose an appropriate model or algorithm to interpret biological data? What biological questions can we hope to answer with the data that we observe? How can we design better experiments? When can our conclusions be viewed as mechanistic? Course Team Prof. Tommi Jaakkoa Prof. David Gifford Tim Danford Lectures Sequence models (Lectures 1 4) Sequence alignment DNA sequence element discovery Single data source models (Lectures 5 12) Microarray data binding models Proteomic data models Classification and clustering Integrated models (Lectures 13 22) Network models Functional modules Dynamic models Requirements Team Project Topic chosen by you in consultation with us Roughly four person teams Intermediate (10 minute) and final presentation (20 minute) in-class presentation Problem Sets (4 5) One Final Quiz You must register even if you are a listener Structure and Function of the Genome Chromosomes Human Genome Comparative Genomics Genes and their Products Stem Cells Diagram removed for copyright reasons. Structure of chromosomes, genes, DNA double helix and base pairs. DNA is Packaged into Nucleosomes Nucleosomes consist of 140 bp DNA wrapped around 8 histone proteins 2 X (H2A, H2B, H3, H4) Histones Diagram removed for copyright reasons. Chromosomes are Arrays of Nucleosomes Alberts et al., Molecular Biology of the Cell Diagram removed for copyright reasons. Alberts et al., Molecular Biology of the Cell tructure of the Nucleus hromatin-contains DNA and proteins formed into chromosomes ucleolus-manufactures ribosomes uclear envelope-allows the nucleus to control entry and exit of molecules Diagram removed for copyright reasons. Structure and Function of the Genome Chromosomes Human Genome Comparative Genomics Genes and their Products Stem Cells Image removed for copyright reasons. Shows relative size and shape of 23 human chromosome pairs. Human Gene Content: Surprisingly Few Genes Only 1% of genome is genes Protein-coding Gene Number: 30,000? Human Genes: Tend to live in GC-rich regions Few new protein domains, many new domain architectures Big expansions of some families . . . Smell receptors Immunoglobulins Growth Factors Human Genome Overview Size of the genome 2.91 Gbp Percent of genome classified as repeats 35 Number of annotated genes 26,383 Percent of annotated genes with unknown function 42 Number of genes (hypothetical and annotated-2001) 39,114 Gene with the most exons Titin (234 exons) Average gene size 27 kbp Most gene-rich chromosome Chr. 19 (23 genes/Mb) Least gene-rich chromosomes Chr. Y (5 genes/Mb) Percent of base pairs spanned by genes 25.5 Percent of base pairs spanned by exons 1.1 Percent of base pairs spanned by introns 24.4 Percent of base pairs in intergenic DNA 74.5 Longest intergenic region Chr. 13 (3,038,416 bp) Rate of SNP variation 1/1250 bp Venter et al., Science (2001) National Center for Biotechnology Information (NCBI)...
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lecture_1 - Key Goals This Term How can we choose an...

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