Genomics, Proteomics, and Systems Biology
Reading Schedule: Fall 2008
Discovering Genomics, Proteomics and Bioinformatics - by A. Malcolm Campbell and Laurie J. Heyer. (ISBN 0-8053-4722-4; jointly published by Cold Spring Harbor Laboratory Press and Benjamin Cummings: September, 2002)
| Dates | Day | Chapter | Read Before Class | Discovery Questions |
| Aug 25 | M | Intro.; email your thoughts | N. A. | |
| Aug 27 | W | 1.1: What's wrong with my child? | ix - xiii & 1 - 9 |
8, 10, 12, 13, 14 + (MM 1 & 2) |
| Aug 29 | F | 1.2: What's wrong with my child? | 9 - 20 | 17, 20, 26, 27, 29, 31, 32 |
| Sep 1 | M | 1.2: What's wrong with my child? | 20 - 29 | 35, 36, 38, 39, 40, 42, 45, 46 |
| Sep 3 | W | 2.1: How are genomes sequenced? | 34 - 45 | 5, 8, 9, (MM2.1:1, 2, 5), (MM2.2:1, 2), 12, 15 |
| Sep 5 | F | 2.1: cont. |
45 - 59 |
(MM2.3:2, 3), 22, 28, 30, 33, 38 |
| first draft |
M |
Pilot Web Page | Put it online | Due Monday Sep 8, 11:30 am |
| Sep 8 | M | 2.2: What have we learned from unicelluar genomes? | 59 - 74 | 40, 42, 48, 51, 52, 56, 58, (MM2.4:1), 64 |
| Sep 10 | W | 2.3: What have we learned from multicelluar genomes? | 90 - 109 | 82, 87, 88, (MM2.5:2), 94, 96 |
Sep
12 |
F |
3.1: Comparative Genomics | 114 - 123 | 4, 5, 6, 8, 14 |
| Sep 15 | M | 3.2: Evolution of Genomes | 126 - 138 | 21, 23, 24, 29, 32, 34, 35 |
| revised page |
W
|
First Web Page | Trait and Gene | Due Wed Sep 17, 2:00 pm |
| Sep 17 | W | 3.2 Human Evolution | 138 - 145 | 38, 39, 41, 42, 43 |
| Sep 19 | F | 3.3: Genomic Identifications | 145 - 155 | 46, 47, 50, 53, 55, 56 |
| Sep 22 | M | 3.3: Genomic Identifications | 155 - 162 | 58, 59, 61, 62, 64, 65, 67 |
| Sep 24 | W | 3.4: Biomedical Genome Research | 162 - 172 | 69, 72, 73, 75, 80, 81 |
| Sep 26 | F | Buffer For First Exam | ||
| Sep 26 | F |
1st
Exam |
|
DUE Wed Oct 1; 11:30
am |
| Sep 29 | M | 4.1: What drives environmental diversity? | 178 - 186 | No DQ's |
| Oct 1 | W | EXAM RECOVERY |
Turn In Exam |
|
| Oct 3 | F |
4.2: What are SNPs? |
186 - 198 |
8, 10, 11, 17, 18, 28, 32,
37, 39 |
| Oct 6 | M | 4.3: Is death a genetically determined trait? | 198 - 203 | 40, 42, 43 |
| Oct 8 | W | 4.4: What are the ethical implications? | 203 - 214 | 48, 52, (MM4.4:1, 2), 57, 63, 69 |
| Oct 10 | F | Work on Paper Review | ||
Review Paper #1 |
F
|
Choose Paper A or Paper B | Summarize Paper & Every Figure | Due Fri. Oct 6, 5:00 pm |
| Oct 13 | M | Fall Break |
ZZZZZZZ |
No Class |
| Oct 15 | W | 5: Why can't I lose weight? | 219 - 231 | 2, 9, 14, 20, 22, 27 |
| Oct 17 | F | Christina Smolke Visits Class | Ask her questions! | |
| Oct 20 |
M | 6.1: What are DNA microarrays? | 234 - 245 | 4, 6, 7, (MM6.3:2,3), 9, 10, 11, 12 |
| Oct 22 | W | 6.1: Can chips reveal regulatory sequences? | 245 - 254 | 17-21, 25, 26, 31, 34, 35, 44 |
| Oct 24 | F | 6.2: Any alternative uses of chips? | 254 - 261 | 45, 51, 54, 55, 56, 61, 66, 74, 76, 77 |
| Oct 27 |
M | 7.1: Can microarrays diagnose
cancer? |
264 - 269 |
2, 4, 6, 10, 12, 15, 19, 20, 23, 24, 26 |
| Oct 29 | W | 7.2: Can microarrays analyze our health? | 273 - 282 | 41, 42, 45, 46, 53, 54, 56, 58, 62, 63, 67, 72, 79, 80 |
| Oct 31 | F | Buffer Day For Exam | ||
Oct 31 |
F |
2nd Exam |
DUE Wed. Nov. 5; 11:30
am |
|
| Nov3 | M | 8.1: What do all these proteins do? | 286 - 295 | No DQs |
| Nov 5 | W | EXAM RECOVERY |
Turn In Exam |
|
| Nov 7 | F | 8.2:
Does a protein's shape reveal its function? |
295 - 299 | 27, 29, 30, 32 |
| Nov 10 | M | 8.3: Which proteins interact with each other? | 299 - 307 | 33, 36, 38, 40, 44 |
| Nov 12 | W |
8.4: How do we measure and ID proteins? | 307-19 + 323-25 | 47, 48, (MM8.3:2), 51, 52, 54, 55, 56, 65, 66 |
| Nov 14 | F | 10.1: Are genes hardwired? | 342 - 355 | 3, 5, 8, 9, 10, 12 |
| Nov 17 | M | 10.1: What controls amount, location and timing? | 355 - 366 | 15, 16, 24, (MM10.1:1, 3), 25 |
| Nov 19 | W | 11.1: How do genes regulate each other? | 370 - 378 | 1, 2, 3, 5, 6, 7, 8 |
| Nov 21 | F | 11.1: How are memories formed? | 378 - 391 | 9, 13, 14, 17, 19, 21, 25, 26, 27 |
| Nov 24 | M | Work on Paper Review | ||
| Review Paper #2
|
Tu |
Choose Paper A or Paper B | Summarize Paper & Every Figure | Due Tuesday Nov 25, 2:00 pm |
| Nov 26 | W | Thanksgiving |
Eat |
No Class |
| Nov 28 | F | Thanksgiving |
Sleep |
No Class |
| Dec 1 |
M | 11.1: Can we learn about cancer through circuits? | 391 - 394 | 30, 31, 32, 33 |
| Dec 3 |
W | 11.2: Synthetic Biology | 394 - 400 | 34, 35, 37, 39, 41, 42, 43 |
| Dec 5 |
F | 11.2: Synthetic cont. | 400 - 407 | 44, 48, 52, 53, 55, 57, 58b&c |
| Dec 8 | M | 12: Can systems biology reveal new properties? | 410 - 419 | 1, 2, 4, 5, 6, 9 |
| Dec 10 | W | Course Evaluation Fellowships |
done! Take PostSurvey |