Lectures
- 8/27/2019 (Tue): Lecture 1 - Course introduction, policies and prospective topics & basic sequence searching (Lec1 Slides)
- 8/29/2019 (Thu): Lecture 2 - Pseudocode, intro to algorithms (Lec2 Slides)
- Class Prep 1: Ch. 1, pp. 3-9, 53-57
- Class Prep 2: Algorithms Introduction
- 9/03/2019 (Tue): Lecture 3 - Algorithm complexity (Lec3 Slides)
- 9/05/2019 (Thu): Lecture 4 - Approch to Bioinformatics Problems (Lec4 Slides)
- 9/10/2019 (Tue): Lecture 5 - String Match: Naive and KMP algorithms (Lec5 Slides)
- 9/12/2019 (Thu): Lecture 6 - String Match: KMP algorithms (Lec6 Slides)
- 9/17/2019 (Tue): Lecture 7 - Motif Finding algorithms (Lec7 Slides)
- 9/19/2019 (Thu): Lecture 8 - Motif Finding algorithms (Lec8 Slides)
- 9/24/2019 (Tue): Lecture 9 - Greedy algorithms (Lec9 Slides)
- 9/26/2019 (Thu): Lecture 10 - Genome Assembly (Lec10 Slides)
- Class Prep : Watch Chap3 videos and skim Chap. 3 textbook
- 10/1/2019 (Tue): Lecture 11 - Genome Assembly (Lec11 Slides)
- 10/3/2019 (Thu): Lecture 12 - Genome Assembly (Lec12 Slides)
- 10/8/2019 (Tue): Lecture 13 - Sequence Alignment (Dynamic Programming) (Lec13 Slides)
- 10/10/2019 (Thu): Lecture 14 - Sequence Alignment (Dynamic Programming) (Lec14 Slides)
- 10/15/2019 (Tue): Lecture 15 - Midterm Prep Day (Lec15 Slides)
- 10/17/2019 (Thu): Midterm Exam
- 10/22/2019 (Tue): Fall Break (No Class)
- 10/24/2019 (Thu): Midterm review
- 10/29/2019 (Tue): Lecture 16 - Sequence Alignment (Lec16 Slides)
- 10/31/2019 (Thu): Lecture 17 - Sequence Alignment (Lec17 Slides)
- 11/5/2019 (Tue): Lecture 18 - Genome Rearrangement (Lec18 Slides)
- 11/7/2019 (Thu): Lecture 19 - Genome Rearrangement (Lec19 Slides)
- 11/12/2019 (Tue): Lecture 20 - Evolutionary Tree (Lec20 Slides)
- 11/14/2019 (Thu): Lecture 21 - Evolutionary Tree (Lec21 Slides)
- 11/19/2019 (Tue): Lecture 22 - Evolutionary Tree (Lec22 Slides)
- 11/21/2019 (Thu): No Class
- 11/26/2019 (Tue): Homework 8 recap
- 11/28/2019 (Thu): No Class (Thanksgiving Break)
- 12/3/2019 (Tue): Lecture 23 - Trie, Suffix Tree (Lec23 Slides)
- 12/5/2019 (Thu): Lecture 24 - BWT (Lec24 Slides)
- 12/9/2019 (Mon): Take Home Final Exam Due (11:59 PM) (Final Exam)
Other links
Algorithms is free electronic version of Algorithms by Jeff Erickson (CS at UIUC).
Assignments
- HW1 (Due: Thu, 8/29/2019 2:15pm) : Rosalind SLU BCB5300 Num 1-2 (points: 10)
- HW2 (Due: Tue, 9/10/2019 2:15pm) : Rosalind SLU BCB5300 Num 3-7 (points: 10)
- HW3 (Due: Thu, 9/19/2019 2:15pm) : KMP problem (points: 10 + 2)
- HW4 (Due: Fri, 9/28/2019 11:59pm) : Rosalind SLU BCB5300 Num 8-10 (points: 10)
- HW5 (Due: Tue, 10/8/2019 11:59pm) : Rosalind SLU BCB5300 Num 11-15 (points: 10)
- HW6 (Due: Mon, 11/4/2019 11:59pm) : Rosalind SLU BCB5300 Num 16-19 (points: 10)
- HW7 (Due: Mon, 11/11/2019 11:59pm) : Rosalind SLU BCB5300 Num 20-21 (points: 10)
- HW8 (Due: Tue, 11/26/2019 2:15pm) : Rosalind SLU BCB5300 Num 22-26 (points: 20)