Table of Contents
Bio 101: Genomics & Computational Biology
DNA2: Last week's take home lessons
RNA1: Today's story & goals
Discrete & continuous bell-curves
“Significant” distributions
Primary to tertiary structure
Non-watson-crick bps
Modified bases & bps in RNA
Covariance
Mutual Information
RNA secondary structure prediction
Stacked bp & ss
Initial 1981 O(N2) DP methods: Circular Representation of RNA Structure
RNA pseudoknots, important biologically, but challenging for structure searches
Dynamic programming finally handles RNA pseudoknots too.
CpG Island + in a ocean of - First order Markov Model
Small nucleolar (sno)RNA structure & function
SnoRNA Search
Performance of RNA-fold matching algorithms
Putative Sno RNA gene disruption effects on rRNA modification
RNA1: Today's story & goals
RNA (array) & Protein/metabolite (MS) quantitation
8 cross-checks for regulon quantitation
Check regulons from conserved operons (chromosomal proximity)
Predicting the PurR regulon by piecing together smaller operons
(Whole genome) RNA quantitation objectives
(Sub)cellular inhomogeneity
Fluorescent in situ hybridization (FISH)
RNA1: Today's story & goals
Steady-state population-average RNA quantitation methodology
PPT Slide
Most RNAs < 1 molecule per cell.
Microarray data analyses (web)
Statistical models for repeated array data
“Significant” distributions
Independent Experiments
RNA quantitation
PPT Slide
(Whole genome) RNA quantitation methods
Microarray to Northern
Genomic oligonucleotide microarrays
Random & Systematic Errors in RNA quantitation
Spatial Variation in Control Intensity
Detection of Antisense and Untranslated RNAs
Mapping deviations from expected repeat ratios
RNA1: Today's story & goals
Independent oligos analysis of RNA structure
Predicting RNA-RNA interactions
Experimental annotation of the human genome using microarray technology.
RNA1: Today's story & goals
Time courses
Beyond steady state: mRNA turnover rates (rifampicin time-course)
TimeWarp: pairs of expression series, discrete or interpolative
TimeWarp: cell-cycle experiments
TimeWarp: alignment example
RNA1: Today's story & goals
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