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Epigenomics and Hidden Markov Models in Computational Biology - Lecture 5
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- 1 Logistics
- 2 Lecture Overview
- 3 Introduction to Epigenomics
- 4 Three types of Epigenomic Modifications
- 5 Q1: Non-standard modifications
- 6 Q2: Epigenetic inheritance
- 7 Q3: Developmental memory establishment
- 8 Diversity of Histone modifications
- 9 Methylation Bisulfite and DNase Profiling
- 10 Antibodies, ChIP-Seq, data generation projects, raw data
- 11 Read mapping: Hashing, Suffix Trees, Burrows-Wheeler Transform
- 12 Quality Control, Cross-correlation, Peak calling, IDR similar to FDR
- 13 Discovery and characterization of chromatin states
- 14 HMM Foundations, Generating, Parsing, Decoding, Learning
- 15 Two Sets of HMM parameters: Emissions, Transitions
- 16 Example 2-state HMM, observations, scoring, inference
- 17 Viterbi algorithm: Find best parse π*= argmaxπPx,π
- 18 Posterior Decoding: Most likely state πiover all paths
- 19 Summary
