CSE 5095:  Research Topics in Bioinformatics, Spring 2012,  Instructor: Yufeng Wu
Tentative Class Schedule (subject to change)

Week
Lectures
Readings
1
Algorithms for next-generation sequencing data analysis
1/17. Inroduction to string matching, suffix array construction.
1/19. Basic string algorithms and Burrows-Wheeler transform
Notes and papers.
2
1/24. Burrows-Wheeler transform
1/26. Short sequence reads mapping
Papers.
3
1/31: More short reads mapping
2/2: Genetic variants detectionfrom sequence reads.
Papers
4
2/7. Genome assembly from sequence reads: Introduction.
2/9. Genome assembly with short reads: current approaches.
Papers
5
Coalescent theory and Population Genetics
2/14. Probability theory for coalescent models.
2/16. Introduction to coalescent theory.
Book chapters
6
2/21. Probability computation on coalescent models.
2/23. More probabilty computation on coalescent models.
Book chapters.
7
2/28. Population genetics and DNA forensics.
Recombination
3/1. 
Recombination: concept and coalescent models.
Papers
8
3/6. Lower bounds for the minimum recombination.
3/8. 
Ancestral recombination graph (ARG).
Papers
9
3/20. Algorithms for reconstructing ARGs.
Phylogenetic networks and more
3/22.
Comparision of phylogenetic trees. Subtree prune and regraft (SPR).
Papers
10
3/27. Algorithms for computing SPR distance.
3/29. Phylogenetic network models
Papers.
11
4/3. More phylogenetic network models
4/5. Incomplete lineage sorting and phylogenetics
Papers.
12
Student presentations
4/10.
Student paper presentation 1.
4/12. Student paper presentation 2.

13
4/17. Student paper presentation 3.
4/19. Student paper presentation 4.

14
4/24. Student paper presentation 5.
4/26. Student paper presentation 6.

15
Project presentation