Here is this semester's tentative schedule; I will update it as the semester progresses. The listed sections refer to the course textbook or the lecture notes (described on the Course Policies page); any external references will also be listed here.
Please note that all lectures notes are provided as a resource, not a substitution for attending class! In particular, my tablet will inevitably lose notes at least a few times this semester, and you should be prepared to do extra reading and/or meet with a friend to get notes that you missed if you are gone.
Date Topic Reading Lecture Notes Tuesday, Aug. 28 Syllabus, intro to algorithms Chapter 1 and sections 2.1, 2.3, and 2.4 of book
Section 0.5 (stable marriage problem)Lecture Notes Thursday, Aug. 30 More intro to algorithms Rest of chapter 2, brief discussion of chapter 3
Section 1.3 (Towers of Hanoi)Lecture Notes Tuesday, Sept. 4 Partial digest problem Chapter 4 of book
Lecture Notes Thursday, Sept. 6 Motifs and medians Chapter 4 of book Lecture Notes Tuesday, Sept. 11 Greedy algorithms: rearrangements and motifs Chapter 5 of book Lecture Notes Thursday, Sept. 13 Greedy: shortest common superstrings Ben Langmead's slides
(and older version)Lecture Notes Tuesday, Sept. 18 Dynamic Programming: intro, and edit distance Sections 6.2 and 6.4 of book
Additional reference (5.5 and 5.1)Lecture Notes Thursday, Sept. 20 Dynamic Programming: LCS and sequence alignment Sections 6.5 to 6.8 of book
Also, go read 6.3Lecture Notes Tuesday, Sept. 25 Dynamic Programming: more alignment Rest of chapter 6 Lecture Notes Tuesday, Oct. 2 Divide and Conquer Chapter 7 Lecture Notes Thursday, Oct. 4 Graph algorithms: Assembly Sections 8.1 and 8.2
Ben Langmead's notes on assemblyLecture Notes Tuesday, Oct. 9 Exact pattern matching part 1 Chapter 9 Lecture Notes Thursday, Oct. 11 Exact matching part 2 Chapter 9
Ben Langmead's notesLecture Notes Tuesday, Oct. 16 Inexact pattern matching part 1 Ben Langmead's notes
Chapter 9Lecture Notes Thursday, Oct. 18 Inexact matching part 2 Chapter 9
Extra book: "Algorithms on Strings, Trees, and Sequences" (available at library)Lecture Notes Thursday, Oct. 25 Inexact matching part 3 Chapter 9
Extra book: "Algorithms on Strings, Trees, and Sequences" (available at library)Lecture Notes Tuesday, Oct. 30 Clutering part 1 Chapter 10 Lecture Notes Thursday, Nov. 1 Clutering part 2 Chapter 10
Lecture Notes by Frederic Chazal
Paper on k-means and approximationsLecture Notes Tuesday, Nov. 6 Clutering and persistent homology Lecture Notes by Frederic Chazal Slides Thursday, Nov. 8 Evolutionary trees and parsimony Chapter 10 Lecture Notes Thursday, Nov. 15 Hidden Markov Models Chapter 11 Slides Tuesday, Nov. 20 More HMMs Chapter 11
Article on bioinformatics and HMMsLecture Notes Tuesday, Nov. 27 MinHash Chapter 3 of this book
Mash paper
Code and implementation
Assembly with MinHashSlides Thursday, Nov. 29 Randomized algorithms Chapter 12
Nice slides on Gibbs samplingLecture Notes Tuesday, Dec. 4 Burrows-Wheeler Transform Notes from Langmead lab
Additional notesLecture Notes Thursday, Dec. 6 Burrows-Wheeler Transform (cont) Notes from Langmead lab
Nice tutorialLecture Notes