Manolis Kellis
@manoliskellis1·24.9K subscribers·255 videos
MIT CompBio Lecture 07 - RNA world, RNA-seq, RNA folding (Fall '19)
Posted
September 26, 2019
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4,250
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September 26, 2019
4,250
63
1
1.51%
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1:16:22Now PlayingMIT Computational Biology: Genomes, Networks, Evolution, Health
Prof. Manolis Kellis
Full playlist with all videos in order is here
All slides from Fall 2019 are here
Outline for this lecture:
1. Functional diversity of RNA molecules
- Ancient housekeeping ncRNAs and the RNA world hypothesis
- Young ncRNAs as regulatory layer in complex organisms
2. RNA transcript reconstruction
a) Map to Genome Methods: (e.g. Tuxedo suite and Cufflinks)
- Individual reads. Spliced reads. Transcript abundance
b) Align-de-novo approaches (e.g. Trinity)
- Linear contigs. Group contigs. Transcript resolving.
c) Differential expression analysis
- Variability: Technical, biological, uncertainty.
3. RNA folding
a) Introduction and representation
b) Biophysical energy constraints
- Finding the optimal structure: Nussinov’s algorithm (DP)
- Biophysically realistic folding using loop-based energy model
- Structural ensemble and base-pairing 'posterior probability’
c) Parsing Approach: Stochastic context free grammars
d) Combining phylogenetic and biophysical information
e) Advanced problems (kinetics, pseudoknots, RNA-RNA interactions
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