CISC-471: Computational Biology(also known as: CMPE-471) |
(Fall 2019) |
Monday | 8:30-9:30 | JEFFERY RM 102 |
Tuesday | 10:30-11:30 | JEFFERY RM 102 |
Thursday | 9:30-10:30 | JEFFERY RM 102 |
Monday | Tuesday | Thursday | |
Week 0 Introduction. |
September 2 First Class is on Thursday, Sept. 5. |
September 3 First Class is on Thursday, Sept. 5. |
September 5 Introduction/ Finding most frequent k-mers Watch this video: The Search for Hidden Messages in the Replication Origin (Part 1). In particular near the 10 minute mark he discusses different approaches to solve the most frequent k-mer problem. Homework 1. |
Week 1 Introduction. |
September 9 Introduction/ Finding most frequent k-mers |
September 10 Review of complexity analysis, recursive algorithms. |
September 12 Today we will go over solutions of HWK 1. Homework 2. |
Week 2 Exhaustive Search. The Partial Digest Problem (Chapter 4, sections 4.1, 4.2, 4.3) |
September 16 Restriction Mapping. See section 4.1-4.3 of the text. |
September 17 Restriction Mapping. See section 4.1-4.3 of the text. |
September 19 Solutions to Homework #2 Homework 3. |
Week 3 Exhaustive Search. Motifs in DNA Sequences. (Chapter 4, sections 4.4-4.9) |
September 23 Scoring k-mers, to find Motifs in DNA sequences. |
September 24 Hamming distance and Median strings in DNA sequences. | September 26 Solutions to Homework #3 Sorting by reversals see Chapter 5. Homework 4. Be prepared to share your solutions with classmates in class on Thursday Oct. 3. |
Week 4 Greedy Algorithms (Chapter 5) |
September 30 |
October 1 | October 3 Solutions to Homework #4 Introduction to dynamic programming algorithms. |
Week 5 Dynamic Programming Algorithms (Chapter 6) |
October 7 |
October 8 | October 10 Quiz #1 base on homework 1, 2, 3, and 4 |
Week 6 Dynamic programming algorithms for sequence alignment (Chapter 6) |
October 14 Thanksgiving no class. |
October 15 Sequence alignment. |
October 17 Homework 5. Due October 28. Solutions to quiz #1. |
Week 7 Dynamic Programming Sequence Alignment (Chapter 6) |
October 21 |
October 22 |
October 24 FALL BREAK. No class. |
Week 8 Divide and Conquer. (Space efficient Sequence Alignment, Chapter 7) |
October 28 Solutions to Homework #5 Homework 5 submit. This is a programming homework that must be submitted by Nov.8 for participation credit. |
October 29 Homework 6. Due November 4. |
October 31 |
Week 9 Graph Algorithms. (Chapter 8) |
November 4 Be prepared to share your homework #6 solutions in class. |
November 5 Homework 7. Due November 11. |
November 7 |
Week 10 Pattern Matching. (Chapter 9) |
November 11 Be prepared to share your homework #7 solutions in class. |
November 12 Homework 8. Due November 18. |
November 14 |
Week 11 |
November 18 Be prepared to share your homework #8 solutions in class. |
November 19 |
November 21 Quiz #2 Based on homework 5,6,7,8. |
Week 12 |
November 25 |
November 26 Guest Lecture by Professor Amber Simpson who is cross appointed to the School of Computing and Dept of Biomedical & Molecular Sciences. |
November 28 |
Numeric Range | Letter Grade | GPA |
90-100 | A+ | 4.3 |
85-89 | A | 4.0 |
80-84 | A- | 3.7 |
77-79 | B+ | 3.3 |
73-76 | B | 3.0 |
70-72 | B- | 2.7 |
67-69 | C+ | 2.3 |
63-66 | C | 2.0 |
60-62 | C- | 1.7 |
57-59 | D+ | 1.3 |
53-56 | D | 1.0 |
50-52 | D- | 0.7 |
0-49 | F | 0 |