Unit 8: RNA Structure Prediction

Material

• slides

• lecture notes

• Video 8-1 (2026-01-29, 15:08): Noncoding RNA
  
• Video 8-2 (2026-01-29, 20:41): RNA secondary structure
  
• Video 8-3 (2026-01-29, 18:19): Pseudoknot-free secondary structures, Nussinov algorithm
  
• Video 8-4 (2026-01-29, 8:58): Refined energy model, Zuker algorithm
  
• Video 8-5 (2026-01-29, 9:24): Grammar based secondary structure prediction
  
• Video 8-6 (2026-02-05, 23:23): Probabilistic context-free grammars
  
• Video 8-6 (2026-02-05, 20:00): Probabilistic Parsing
  
• Video 8-6 (2026-02-05, 34:58): RNA Grammar
  

Further sources

Further reading on RNA structure and prediction:

• Manolis Kellis et al., Computational Biology - Genomes, Networks, and Evolution, Chapter 10

Background on non-coding RNA:

• Pyle, RNA Structure, Function, and Recognition (online talk series)
  chemical details of what dictates RNA folding and structure
• Munzenmaier, Introduction to Non-Coding RNA
  3D printed models of RNA structures, using kits for teachers

In depth documentary about X-ray crystallography:

• The Royal Institution, Understanding Crystallography

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Unit 7  ⋅  Syllabus