Overview
Syllabus
Logistics
Lecture Overview
Introduction to Epigenomics
Three types of Epigenomic Modifications
Q1: Non-standard modifications
Q2: Epigenetic inheritance
Q3: Developmental memory establishment
Diversity of Histone modifications
Methylation Bisulfite and DNase Profiling
Antibodies, ChIP-Seq, data generation projects, raw data
Read mapping: Hashing, Suffix Trees, Burrows-Wheeler Transform
Quality Control, Cross-correlation, Peak calling, IDR similar to FDR
Discovery and characterization of chromatin states
HMM Foundations, Generating, Parsing, Decoding, Learning
Two Sets of HMM parameters: Emissions, Transitions
Example 2-state HMM, observations, scoring, inference
Viterbi algorithm: Find best parse π*= argmaxπPx,π
Posterior Decoding: Most likely state πiover all paths
Summary
Taught by
Manolis Kellis