Скачать или смотреть MIT CompBio Lecture 17 - Comparative Genomics (Fall 2019)

MIT Computational Biology: Genomes, Networks, Evolution, Health
http://compbio.mit.edu/6.047/
Prof. Manolis Kellis

Full playlist with all videos in order is here:    • Machine Learning in Genomics - Fall 2019  

All slides from Fall 2019 are here: https://stellar.mit.edu/S/course/6/fa...

Outline for this lecture:
1. Nucleotide conservation: evolutionary constraint
Purifying selection, neutral branch length, discovery power
Detect constrained elements: nucleotides, windows, HMM
Estimate fraction constrained: signal vs. background
2. Evolutionary signatures: focus on pattern of change
Different functions == Characteristic patterns of evolution
3. Signatures of protein-coding genes
Reading-frame conservation, codon-substitution frequency
Likelihood ratio framework: Estimating QCQN, scoring
Revise genes, read-through, excess constraint regions
4. Signatures of RNAs, motifs, TFBS, microRNAs
RNAs: Phylo-SCFGs. Motifs: MCS. TFBS: branch length
miRNAs: Struct/evo. Comb: decision trees, random forests
Sense/anti-sense miRNAs, mature/star arm cooperation
5. Measuring selection within the human lineage