CSCI 8610 Topics in Theoretical Computer Science (Spring 2014)

Computational Linguistics of Biomolecules


Instructor : Liming Cai
Office: 544 Boyd
Phone : 2-6081
Email : cai@cs.uga.edu
Lecture hours: 12:20 - 1:10M and 12:30 - 1:45 TR
Classrooms: 306 Boyd (M) and 326 Boyd (TR)
Office Hours: 9:30-10:30 TR or by appointment


Scope of the course:

Reading Materials
  1. Papers 4, 5, 6 and 7 following this link [Eddy]
  2. Pioneer work in SCFG for RNA secondary structure prediction [UCSC group]
  3. Lightweight SCFGs for RNA secondary structure prediction [Eddy group]
  4. The language of RNA: a formal grammar that includes pseudoknots [Eddy and Rivas]
  5. Complex probabilistic models for RNA secondary structure prediction [Eddy group]
  6. Subclasses of tree-adjoining grammars for RNA secondary structure [Uemura group]
  7. Tree adjoining grammars for RNA pseudoknots [Uemura group]
  8. Parallel grammar systems for RNA pseudoknots [Cai and Malmberg group]
  9. Computational linguistics of biological sequences [Searls group]
  10. Grammatical representations of Macromolecular structure [Chiang and Searls]
  11. Computational linguistics for biopolymer structures and statistical mechanics [Dill et al]
  12. Routes are trees: parsing perspectives on protein folding [Dill group]
  13. Graph grammar modeling RNA tertiary structure motifs [Major group]
  14. Stochastic k-tree grammar for biomolecular structure modeling [Cai and Malmberg group]
  15. PPT in non-coding RNA structure, modeling, prediction, and search [Cai's presentation]
  16. A ppt presentation in SCFG [from the web]

Projects

Table of content:

Schecule and format: Grading policy: Prerequisites: Academic Dishonesty: