Bioinformatics Schedule
BH = The Bedford Handbook
CG = Cartoon Guide to Genetics
IBA = Introduction to Bioinformatics Algorithms
| Wk | Day | Date | Topic | Reading | Homework |
| 1 | M | Aug 27 | What is bioinformatics? | ||
| W | Aug 29 | Basic genetics | CG 1-96 | ||
| R | Aug 30 | DNA structure and replication | CG 97-128 | ||
| F | Aug 31 | DNA transciption and translation | CG 129-143, IBA 3.1-3.7, 3.11 | ||
| 2 | M | Sep 3 | Introduction to algorithms and Python | IBA Ch 1, 2.1-2.2 | |
| W | Sep 5 | More Python | |||
| R | Sep 6 | Even more Python | |||
| F | Sep 7 | Gene hunting (locating long ORFs) | |||
| 3 | M | Sep 10 | Review HW 1 | HW 1 | Solutions | |
| W | Sep 12 | Example: Making change | IBA 2.3-2.4 | ||
| R | Sep 13 | Regulatory motifs | IBA 4.4-4.5 | ||
| F | Sep 14 | Regulatory motif search | IBA 4.6-4.8 | ||
| 4 | M | Sep 17 | Brute force motif search | HW 2 | Solutions | |
| W | Sep 19 | Consensus scoring in python | Paper 1 topic | ||
| R | Sep 20 | Library research instruction (go to Library e-classroom, room 102) | |||
| F | Sep 21 | No class | |||
| 5 | M | Sep 24 | Scientific writing | ||
| W | Sep 26 | Conducting research | BH p. 528-571 | HW 3 | Solutions | |
| R | Sep 27 | Managing sources | BH p. 572-585, 698-753 | ||
| F | Sep 28 | No class | |||
| 6 | M | Oct 1 | Branch and bound motif search | Paper 1 draft | |
| W | Oct 3 | Dynamic programming: making change, revisited | IBA 6.1-6.2 | ||
| R | Oct 4 | Manhattan tourist problem | IBA 6.3 (to p. 160) | ||
| F | Oct 5 | MT problem, continued | HW 4 | Solutions | ||
| 7 | M | Oct 8 | Edit distance problem | IBA 6.4 | |
| W | Oct 10 | Longest common subsequence (LCS) | IBA 6.5 | ||
| R | Oct 11 | Exam 1 | |||
| F | Oct 12 | LCS algorithm | |||
| 8 | M | Oct 15 | Review exam | ||
| W | Oct 17 | Intro to recursion | |||
| R | Oct 18 | Global sequence alignment | IBA 6.6 | ||
| F | Oct 19 | Local sequence alignment (Smith-Waterman algorithm) |
IBA 6.8, handout | Paper 1 final | |
| 9 | M | Oct 22 | Exact pattern matching | IBA 9.3-9.4 | |
| W | Oct 24 | Suffix trees | IBA 9.5 | HW 5 | Solutions Paper 2 topic |
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| R | Oct 25 | Heuristic pattern matching | IBA 9.6-9.7 | ||
| F | Oct 26 | BLAST | IBA 9.8, handouts | ||
| 10 | M | Oct 29 | BLAST | HW 6 | Solution to #2 | |
| W | Oct 31 | Exam 2 | |||
| R | Nov 1 | Review exam 2 | |||
| F | Nov 2 | BLAST with Dr. Jeff Thompson | |||
| 11 | M | Nov 5 | No class | Paper 2 draft | |
| W | Nov 7 | Graphs | IBA 8.1-8.2 | ||
| F | Nov 9 | Shotgun sequencing | IBA 8.3-8.4, 8.9 | ||
| 12 | M | Nov 12 | Sequencing by hybridization | IBA 8.5-8.8 | |
| W | Nov 14 | Sequencing by hybridization | |||
| F | Nov 16 | Human Genomics: A New Guide for Medicine (video) | |||
| Nov 19-23 | Thanksgiving Break | ||||
| 13 | M | Nov 26 | Phylogenetic trees | IBA 10.5 | Paper 2 final |
| W | Nov 28 | Distance-based trees (UPGMA algorithm) | IBA 10.6-10.8 | Probs 8.6 and 8.9 on p. 302-303 | Solutions | |
| F | Nov 30 | Exam 3 | |||
| 14 | M | Dec 3 | Review exams | ||
| W | Dec 5 | Character-based trees | IBA 10.9-10.11 | ||
| F | Dec 7 | Wrap-up | HW 8 | Solution | ||
| R | Dec 13 | Final paper |