Genomics, Proteomics, and Systems Biology
Reading Schedule: Spring 2013
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 14 | M | Intro.; entrance exam; email your thoughts | none | none |
| Jan 16 | W | 1.1: & 1.2 Stop at "How can they have..." | ix - xiii & 1 - 14 |
8, 10, 13, (MM 1 & 2), 17 |
| Jan 18 | F | 1.2: What's wrong with my child? | 14 - 29 | 26, 27, 29, 36, 38, 39, 45 |
| Jan 21 | M | MLK Celebration | none | none |
| Jan 23 | W | 2.1: How are genomes sequenced? | 34 - 45 454 and pyrosequenicng, Illumina, SOLiD, Ion Torrent, single molecule, Nanopore |
5, 9, (MM2.1:1, 2, 5), (MM2.2:1, 2), 12, 15 basic elements, typical read lengths |
| Jan 25 | F | 2.1: cont. |
45 - 59 |
(MM2.3:2, 3), 22, 28, 30, 33, 38 |
| first draft |
M |
Put draft online | Due Monday Jan 28, 10:30 am | |
| Jan 28 | M | 2.2: What have we learned from unicelluar genomes? | 59 - 74 | 40, 51, 52, 58 |
| Jan 30 | W | 2.3: What have we learned from multicelluar genomes? | 90 - 109 | 88, (MM2.5:2), 94 |
| Feb 1 | F | 3.1: Comparative Genomics human biome |
114 - 123 |
4, 5, 6, 8, 14 (DQ#5 GC Skew link) summarize paper |
revised page |
M
|
First Web Page | Trait and Gene | Due Mon Feb 4, 10:30 am |
| Feb 4 | M | 3.2 Human Evolution | 138 - 145 and Queen Bee Paper |
38, 39, 41 - summarize paper |
| Feb 6 | W | 3.3: Genomic Identifications | 145 - 155 | 47, 50, 53 |
| Feb 8 | F | Family of four | Read Paper | discusss figures and conclusions |
| Feb 8 | F |
1st Exam |
DUE Wed Feb 13, 10:30
am |
|
| Feb 11 | M | 4.1: What drives environmental diversity? | 178 - 186 | No DQ's |
| Feb 13 | W | EXAM RECOVERY DAY |
Turn In Exam |
DUE Wed Feb 13, 10:30
am |
| Feb 15 | F | 4.2: What are SNPs? Cancer genomics |
186 - 198 |
17, 28, 32, 37, 39
|
| Feb 18 | M | 4.4: What are the ethical implications? | 203 - 214 | 48, 52, (MM4.4:1, 2), 57, 63, 69 ACMG CF testing Patent Search |
| Feb 20 | W | Copy Number Variation (News & Paper) | News & Paper | discusss figures and conclusions |
| Feb 22 | F |
Copy Number Variation (continued) | Paper | discusss figures and conclusions |
Review Paper #1 |
Choose paper A or paper B | Summarize Paper & Every Figure | Web Page Due Friday Mar 1, 2 pm | |
| Feb 25 | M | 5: Why can't I lose weight? Gut bacteria |
219 - 231 |
2, 9, 14, 20, 22, 27 summarize information |
| Feb 27 | W | 6.1: What are DNA microarrays? Log transform data |
234 - 250 Short animation(Full Animation optional) |
4, 6, 9, 11, 12, 17, 20, 25 |
| Mar 1 | F | Choose paper A or B | Summarize Paper & Every Figure | Web Page Due Friday Mar 1, 2 pm |
| Mar 1 | F | 6.2: Any alternative uses of chips? | 250 - 261 | 31, 36, 51 (compare UniGene EST profile vs GEO Explorer) |
| Mar 4 | M | Spring Break |
ZZZZZZZ |
No Class |
| Mar 6 | W | Spring Break |
flip |
No Class |
| Mar 8 | F | Spring Break |
ZZZZZZZ |
No Class |
| Mar 11 | M | 7.1: Can microarrays diagnose cancer? | 264 - 269 NY Times breast cancer |
2, 6, 12, 19, 26 Cancer Staging |
| Mar 13 | W | Salmon Microarray Paper | Paper | discusss figures and conclusions |
| Mar 15 | F | Sins of our Fathers (News and Paper) | News & Paper | discusss figures and conclusions |
| Mar18 | M | Fun day to watch, listen, learn and discuss | Wed Lecture (16m) |
no need to watch in advance |
| Mar 20 | W | 8.1: What do all these
proteins do? 8.2: Does a protein's shape reveal its function? |
286 - 299 |
No DQs |
| Mar 22 | F | SNP Proteomics (News and Paper) | News & PaperFACS method | discusss figures and conclusions |
| Mar 22 | F |
2nd Exam |
DUE Wed March 27, 10:30
am |
|
| Mar 25 | M | Finish Paper | Paper & Correction | discusss figures and conclusions |
| Mar 27 | W | EXAM RECOVERY DAY |
Turn In Exam |
DUE Wed March 27, 10:30
am |
| Mar 29 | F | 8.3: Which proteins interact with each other? | 299 - 307 | 33, 40, 44 |
| Apr 1 | M | Easter Break |
rest | exercise and have fun |
| Apr 3 | W | 8.4: How do we measure and ID proteins? |
307-19 | 48, 51, 52, 54, 55, 56 |
| Apr 5 | F | 10.1: Are genes hardwired? |
342 - 355 | 3, 5, 9, 10 |
| Apr 8 | M | 10.1: What controls amount, location and timing? | 355 - 366 | 15, 16, (MM10.1:1, 3) |
| Apr 10 | W |
11.1: How do genes regulate each other? | 370 - 378 | 1, 2, 7, 8 |
| Apr 12 | F | 11.1: How are memories formed? |
378 - 391 |
9, 13, 14, 19, 21, 25, 26, 27 |
| Apr 15 | M | 11.1: How are memories formed? continued Departmental Survey |
continued |
9, 13, 14, 19, 21, 25, 26, 27 |
| Apr 17 | W | 11.1: Can we learn about cancer through circuits? 11.2: Synthetic Biology |
391 - 400 |
30, 31, 33, 35, 39, 41, 43, 44 Seminar 4:30 Wednesday: genomic medicine |
| Apr 19 | F | Guest Speaker, Dr. Raye Alford, Ph.D. (Baylor) Lunch with seminar speaker after class? |
career advice from alumna |
Q & A |
| Apr 22 | M | 11.2: Synthetic cont. | 400 - 407 | 44, 52, 53, 57, 58b&c |
| Review Paper #2
|
Summarize Paper & Every Figure | Web page Due Friday, April 26, 2 pm | ||
| Apr 24 | W | RNA Regulators of Cells (News and Paper) |
||
| Apr 26 | F | Summarize Paper & Every Figure | Web page Due Friday, April 26, 2 pm | |
| Apr 26 | F | RNA Regulators of Cells (News and Paper) |
continued |
none |
| Apr 29 | M |
12: Can systems biology reveal new properties? Simple lessons from complexity. |
410 - 419 | 1, 4, 5, 9 |
| May 1 | W | Fly Systems Biology (News and Paper) |
News & Paper |
discusss figures and conclusions |
| May 3 | F | Fly Systems Biology | Paper | discusss figures and conclusions |
| May 6 |
M | Fly Systems Biology |
Paper | discusss figures and conclusions |
| May 8 | W | Last class & distribute final exam | Course Evaluation Fellowships Teacher Training |
Course Evaluations! |
| May 8 - 13 | F - M |