Week 1
27,29 Aug. |
Introduction Slides
Exact Matching
Gusfield Chapters 1, 5, & 6 |
Exact Matching
Homework 1 (due 18 Sept.) |
Week 2
3,5 Sept. |
Exact Matching
Gusfield Chapter 7 |
Inexact Matching (Alignment)
Wing-Kim Sung Chapter 2
Myers & Miller 1988
Example Homework Solution |
Week 3
10,12 Sept. |
Inexact Matching (Alignment)
Video |
Inexact Matching (Alignment)
In Class Exercises (key)
|
Week 4
18,20 Sept. |
Inverse Parametric Alignment
Gusfield Chapter 13
Homework 2 (due 2 Oct.) |
Inverse Parametric Alignment |
Week 5
24,26 Sept. |
Sequence Database Search
Sung Chapter 5 |
Sequence Database Search |
Week 6
1,3 Oct. |
Multiple Sequence Alignment
Sung Chapter 6
Project Description (due 13 Dec., check-in due 13 Nov.)
Homework 1 Solution |
Multiple Sequence Alignment |
Week 7
8,10 Oct. |
Phylogenetics |
Phylogenetics
Gusfield Chapter 17 (part) Sung Chapter 7 (part)
|
Week 8
15,17 Oct. |
Midterm Exam Review
Homework 2 Solutions
Midterm Practice Questions
Homework 3 |
Midterm Exam
|
Week 9
22,24 Oct. |
Introcution to Sequencing
Mäkinen, Belazzougui, Cunial, & Tomescu Chapter 1
Gibson & Muse Chapter 2
|
Burroughs-Wheeler Transform
Mäkinen, Belazzougui, Cunial, & Tomescu Chapter 9
|
Week 10
29,31 Oct. |
Burroughs-Wheeler Transform
Read Alignment
Homework 4
|
Read Alignment
BWA In Class Exercise (key)
|
Week 11
5,7 Nov. |
Bowtie
Langmead, et al. 2009 (external link) |
RNA-Seq Alignment
Dobin, et al. 2012 (external link)
Kim, et al. 2013 (external link) |
Week 12
12,14 Nov. |
de Brujin Graphs and de novo Sequence Assembly
Li et al. 2010 (external link) |
de Brujin Graphs and de novo Sequence Assembly
Hashing and Sketching |
Week 13
19,21 Nov. |
Long-read (third generation) assembly
MashMap
Canu |
Long-read (third generation) assembly |
Week 14
26,28 Nov. |
Protein-Protein Interation Networks
No office hours Wednesday
PathLinker
NetBox |
Thanksgiving Holiday
(no class) |
Week 15
3,5 Dec. |
Protein-Protein Interation Networks |
Final Exam Review
Extra office hours Thursday and Friday (times TBD) |
Week 16
10 Dec. |
Final Exam
Extra office hours Monday (times TBD)
No office hours Tuesday or Wednesday |
Friday:
Project Due |