Genomics, Proteomics, and Systems Biology
Reading Schedule: Spring 2014
Discovering
Genomics, Proteomics and Bioinformatics 2nd edition - by A.
Malcolm Campbell and Laurie
J. Heyer. (ISBN
0-8053-4722-4;
published by Cold Spring Harbor Laboratory Press and Benjamin
Cummings: 28 February, 2006)
| Dates | Day | Chapter | Read Before Class | Discovery Questions |
| Jan 13 | M | Intro.; entrance exam; email your thoughts | none | none |
| Jan 15 | W | 1.1: & 1.2 Stop at "How can they have..." | ix - xiii & 1 - 14 |
8, 10, 13, (MM 1 & 2), 17 |
| Jan 17 | F | 1.2: What's wrong with my child? | 14 - 29 | 26, 27, 29, 36, 38, 39, 45 |
| Jan 20 | M | MLK Celebration | none | none |
| Jan 22 | W | 2.1: How are genomes sequenced? | 34 - 48 (stop at What shapes...) JASPAR
|
5, 9, (MM2.1: 1, 2, 5), (MM2.2: 1, 2), 12, 15a &15b (MM2.3: 2, 3) |
| Jan 24 | F | 2.1: finsih section Epigenetics paper |
48 - 59 |
22, 28, 30, 33, 38 summarize paper |
| first draft |
M |
Choose an Area | Due Monday Jan 27, 10:30 am | |
| Jan 27 | M | 2.2: What have we learned from unicelluar genomes?
NextGen Sequencing Methods |
59 - 74 454 and pyrosequenicng, Illumina, SOLiD, Ion Torrent, single molecule, Nanopore |
51, 58
focus on basic elements & typical read lengths |
| Jan 29 | W | 2.3: What have we learned from multicelluar genomes? | 90 - 109 | 88, (MM2.5: 2), 94 |
| Jan 31 | F | 3.1: Comparative Genomics (stop at What can we...) Bacterial Evolution |
114 - 123 |
2, 8 summarize paper |
final version |
M
|
First Web Page | Present Your Area | Due Mon Feb 3, 10:30 am |
| Feb 3 | M | 3.2 Human Evolution human biome |
138 - 145 |
38, 39, 41 summarize paper |
| Feb 5 | W | 3.3: Genomic Identifications | 145 - 161 | 47, 50, 58, 61, 67 |
| Feb 7 | F | Family of four | Read Paper | discusss figures and conclusions |
| Feb 7 | F |
1st Exam |
DUE Wed Feb 12, 10:30
am |
|
| Feb 10 | M | 4.1: What drives population diversity? | 178 - 186 | No DQ's |
| Feb 12 | W | EXAM RECOVERY DAY |
Turn In Exam |
DUE Wed Feb 12, 10:30
am |
| Feb 14 | F | 4.2: What are SNPs?
Cancer genomics |
186 - 198
|
17, 28, 32, 37, 39
|
| Feb 17 | M | NO CLASS |
Work on your Paper | Presenting seminar at Rhodes College |
Review Paper #1 |
Choose paper A or paper B or paper C | Summarize Paper & Every Figure | Web Page Due Friday Feb 28, 2 pm | |
| Feb 19 | W | 4.4: What are the ethical implications of variation? |
203 - 214 | 48, 52, (MM4.4: 1, 2), 57, 69 ACMG CF testing Patent Search |
| Feb 21 | F |
Copy Number Variation (News & Paper) | News & Paper | discusss figures and conclusions |
| Feb 24 | M | Copy Number Variation (continued) | Paper | discusss figures and conclusions |
| Feb 26 | W | 5: Why can't I lose weight? Gut bacteria |
219 - 231 |
2, 9*, 14, 20, 22, 27 summarize information |
| Feb 28 | F | Submit paper A or B or C | Summarize Paper & Every Figure | Web Page Due Friday Feb. 28, 2 pm |
| Feb 28 | F | 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 3 | M | Spring Break |
ZZZZZZZ |
No Class |
| Mar 5 | W | Spring Break |
flip |
No Class |
| Mar 7 | F | Spring Break |
ZZZZZZZ |
No Class |
| Mar 10 | M | 6.2: Any alternative uses of chips? mRNA vs. protein levels in primates |
250 - 261 |
31, 36, 51 What is the major lesson? |
| Mar 12 | W | 7.1: Can microarrays diagnose cancer? | 264 - 269 NY Times breast cancer |
2, 6, 12, 19, 26 Cancer Staging |
| Mar 14 | F | Salmon Microarray Paper |
discusss figures and conclusions | |
| Mar17 | M | Sins of our Fathers (News and Paper) | News & Paper | discusss figures and conclusions |
| Mar 19 | W | Guest Speaker, Dr. Rick Peek '84, M.D. (Vanderbilt) Lunch with seminar speaker after class? |
Cancer Applications of Genomics | Seminar at 4:30 pm, Dana 146 |
| Mar 21 | F | 8.1: What do all these
proteins do? |
286 - 299 | 12, 20, 25, 27, 29, 32 |
| Mar 21 | F |
2nd Exam |
DUE Wed March 26, 10:30
am |
|
| Mar 24 | M | 8.3: Which proteins interact with each other? | 299 - 307 | 33, 40, 44 |
| Mar 26 | W | EXAM RECOVERY DAY |
Turn In Exam |
DUE Wed March 26, 10:30
am |
| Mar 28 | F | SNP Proteomics (News and Paper) | discusss figures and conclusions | |
| Mar 31 | M | Finish Paper | Paper & Correction | discusss figures and conclusions |
| Apr 2 | W | 8.4: How do we measure and ID proteins? | 307-19 (stop at Is the Last...) | 48, 51, 52, 54, 55, 56 |
| Apr 4 | F | 10.1: Are genes hardwired? |
342 - 355 | 3, 5, 9, 10 |
| Apr 7 | M | 10.1: What controls amount, location and timing? | 355 - 366 | 15, 16, (MM10.1: 1, 3) |
| Apr 9 | W |
11.1: How do genes regulate each other? | 370 - 378 | 1, 2, 7, 8 |
| Apr 11 | F | 11.1: How are memories formed? |
378 - 391 |
9, 13, 14, 19, 21, 25, 26, 27 |
| Apr 14 | M | 11.1: How are memories formed? continued Departmental Survey |
continued |
9, 13, 14, 19, 21, 25, 26, 27 |
Review Paper #2
|
Summarize Paper & Every Figure | Web page Due Friday, April 25, 2 pm | ||
| Apr 16 | W | 11.1: Can we learn about cancer through circuits? 11.2: Synthetic Biology (Stop at Can Syntehtic...) |
391 - 400 |
30, 31, 33, 35, 39, 41, 43 |
| Apr 18 | F | 11.2: Synthetic cont. Logic Gates |
400 - 407 |
44, 52, 53, 57, 58b&c Summarize Results |
| Apr 21 | M | EASTER |
Work on your Paper | catch up on sleep |
| Apr 23 | W | RNA Regulators of Cells (News and Paper) |
||
| Apr 25 | F | Summarize Paper & Every Figure | Web page Due Friday, April 25, 2 pm | |
| Apr 25 | F | RNA Regulators of Cells (News and Paper) |
continued |
none |
| Apr 28 | M |
12: Can systems biology reveal new properties? Simple lessons from complexity. |
410 - 419 | 1, 4, 5, 9 |
| Apr 30 | W | Fly Systems Biology (News and Paper) |
News & Paper |
discusss figures and conclusions |
| May 2 | F | Fly Systems Biology | Paper | discusss figures and conclusions |
| May 5 |
M | Fly Systems Biology |
Paper | discusss figures and conclusions |
| May 7 | W | Last class & distribute final exam | Course Evaluation Fellowships Teacher Training |
Course Evaluations! |
| May 7 - 11 | W - S |