Genomics, Proteomics, and Systems Biology
Reading Schedule: Spring 2012
Discovering Genomics, Proteomics and Bioinformatics 2nd edition - by A. Malcolm Campbell and Laurie J. Heyer. (ISBN 0-8053-4722-4; jointly published by Cold Spring Harbor Laboratory Press and Benjamin Cummings)
| Dates | Day | Chapter | Read Before Class | Discovery Questions |
| Jan 18 | W | Intro.; email your thoughts | ||
| Jan 20 | F | 1.1: & 1.2 Stop at "How can they have..." | ix - xiii & 1 - 14 |
8, 10, 13, (MM 1 & 2), 17 |
| Jan 23 | M | 1.2: What's wrong with my child? | 14 - 29 | 26, 27, 29, 36, 38, 39, 45 |
| Jan 25 | W | 2.1: How are genomes sequenced? | 34 - 45 454 and pyrosequenicng, Illumina, SOLiD, Ion Torrent, single molecule |
5, 9, (MM2.1:1, 2, 5), (MM2.2:1, 2), 12, 15 basic elements, typical read lengths |
| Jan 27 | F | 2.1: cont. |
45 - 59 |
(MM2.3:2, 3), 22, 28, 30, 33, 38 |
| first draft |
M |
Put it online | Due Monday Jan 30, 12:30 pm | |
| Jan 30 | M | 2.2: What have we learned from unicelluar genomes? | 59 - 74 | 40, 51, 52, 58 |
| Feb 1 | W | 2.3: What have we learned from multicelluar genomes? | 90 - 109 | 88, (MM2.5:2), 94 |
Feb 3 |
F |
3.1: Comparative Genomics human biome |
114 - 123 |
4, 5, 6, 8, 14 summarize paper |
revised page |
M
|
First Web Page | Trait and Gene | Due Mon Feb 6, 12:30 pm |
| Feb 6 | M | 3.2 Human Evolution | 138 - 145 and Queen Bee Paper |
38, 39, 41 - summarize paper |
| Feb 8 | W | 3.3: Genomic Identifications | 145 - 155 | 47, 50, 53 |
| Feb 10 | F | Family of four | Read Paper | discusss figures and conclusions |
| Feb 10 | F |
1st Exam |
DUE Wed Feb 15, 12:30
pm |
|
| Feb 13 | M | 4.1: What drives environmental diversity? | 178 - 186 | No DQ's |
| Feb 15 | W | EXAM RECOVERY DAY |
Turn In Exam |
DUE Wed Feb 15, 12:30
pm |
| Feb 17 | F | 4.2: What are SNPs? Cancer genomics |
186 - 198 |
17, 28, 32, 37, 39 summarize review |
| Feb 20 | M | 4.4: What are the ethical implications? | 203 - 214 | 48, 52, (MM4.4:1, 2), 57, 63, 69 |
| Feb 22 | W | Copy Number Variation (News & Paper) | News & Paper | Synthetic Biology Seminar 23 February |
| Feb 24 | F |
Copy Number Variation (continued) | Paper | |
Review Paper #1 |
Choose paper A or B or C | Summarize Paper & Every Figure | Due Friday Mar 2, 1:30 pm | |
| Feb 27 | M | 5: Why can't I lose weight? Gut bacteria |
219 - 231 |
2, 9, 14, 20, 22, 27 summarize information |
| Feb 29 | W | Flying to U of AK Fairbanks |
no class | no questions |
| Mar2 | F | Work on Paper Review | Summarize Paper & Every Figure | Due Friday Mar 2, noon |
| Mar 5 | M | Spring Break |
ZZZZZZZ |
No Class |
| Mar 7 | W | Spring Break |
flip |
No Class |
| Mar 9 | F | Spring Break |
ZZZZZZZ |
No Class |
| Mar 12 | M | 6.1: What are DNA microarrays? Log transform data |
234 - 250 |
4, 6, 9, 11, 12, 17, 20, 25 |
| Mar 14 | W | 6.2: Any alternative uses of chips? | 250 - 261 | 31, 36, 51 (compare UniGene EST profile vs GEO Explorer) |
| Mar 16 | F | 7.1: Can microarrays diagnose cancer? | 264 - 269 | 2, 6, 12, 19, 26 |
| Mar19 | M | Salmon Microarray Paper | Paper | discusss figures and conclusions |
| Mar 21 | W | Sins of our Fathers (News and Paper) | News & Paper | discusss figures and conclusions |
| Mar 23 | F | Finish papers.. | discusss figures and conclusions | |
| Mar 23 | F |
2nd Exam |
DUE Wed March 28, 12:30
pm |
|
| Mar 26 | M | 8.1: What do all these
proteins do? 8.2: Does a protein's shape reveal its function? |
286 - 299 |
No DQs |
| Mar 28 | W | EXAM RECOVERY DAY |
Turn In Exam |
DUE Wed March 28, 12:30
pm |
| Mar 30 | F | SNP Proteomics (News and Paper) | News & Paper | discusss figures and conclusions |
| Apr 2 | M | Finish Paper | Paper & Correction | discusss figures and conclusions |
| Apr 4 | W | 8.3: Which proteins interact with each other? | 299 - 307 | 33, 40, 44 |
| Apr 6 | F | 8.4: How do we measure and ID proteins? |
307-19 | 48, 51, 52, 54, 55, 56 |
| Apr 9 | M | Easter Break |
no class | no questions |
| Apr 11 | W |
10.1: Are genes hardwired? Lunch with seminar speaker after class? |
342 - 355 | 3, 5, 9, 10 Seminar 4:30 on proteomics |
| Apr 13 | F | 10.1: What controls amount, location and timing? | 355 - 366 | 15, 16, (MM10.1:1, 3) |
| Apr 16 | M | 11.1: How do genes regulate each other? | 370 - 378 | 1, 2, 7, 8 |
| Apr 18 | W | Guest Speaker, Dr. Sallie Permar, MD, Ph.D. Lunch with seminar speaker after class? |
career advice |
Q & A Seminar 4:30: maternal and fetal vaccines |
| Apr 20 | F | 11.1: How are memories formed? | 378 - 391 | 9, 13, 14, 19, 21, 25, 26, 27 |
| Apr 23 | M | 11.1: Can we learn about cancer through circuits? 11.2: Synthetic Biology |
391 - 400 | 35, 39, 41, 43, 44 |
| Review Paper #2
|
M |
Summarize Paper & Every Figure | Due Friday, April 27, 2 pm | |
| Apr 25 | W | 11.2: Synthetic cont. | 400 - 407 | 44, 52, 53, 57, 58b&c |
| Apr 27 | F | RNA Regulators of Cells (News and Paper) |
||
| Apr 30 | M | 12: Can systems biology reveal new properties? | 410 - 419 | 1, 4, 5, 9 |
| May 2 | W | Fly Systems Biology (News and Paper) |
discusss figures and conclusions |
|
| May 4 | F | Fly Systems Biology | Paper | discusss figures and conclusions |
| May 7 |
M | Fly Systems Biology |
Paper | discusss figures and conclusions |
| May 9 | W | Last class & distribute final exam | Course Evaluation Fellowships Teacher Training |
Course Evaluations! |
| May 9 - 14 | F - M |