Week 
Lectures 
Readings 
1 
Algorithms for nextgeneration sequencing
data analysis 1/17. Inroduction to string matching, suffix array construction. 1/19. Basic string algorithms and BurrowsWheeler transform 
Notes and papers. 
2 
1/24. BurrowsWheeler
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 