Genomics, Proteomics, and Systems Biology
Reading Schedule: Spring 2014

Book for This Course:


Tentative Schedule

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

Queen Bee Paper

22, 28, 30, 33, 38

summarize paper

first draft
M

Pilot Web Page

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

Read Paper

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

Read Paper

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
TAKE HOME
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

 

Read Review

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

News story

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

Read Summary

31, 36, 51
(compare UniGene EST profile vs GEO Explorer)

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

Salmon spawning movie

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?
8.2: Does a protein's shape reveal its function?

286 - 299 12, 20, 25, 27, 29, 32
Mar 21
F
2nd Exam
TAKE HOME
DUE Wed March 26, 10:30 am
Mar 24 M 8.3: Which proteins interact with each other? 299 - 307

33, 40, 44

RPC19 Gene - interactions

Visual Thesaurus

Mar 26 W
EXAM RECOVERY DAY
Turn In Exam
DUE Wed March 26, 10:30 am
Mar 28 F SNP Proteomics (News and Paper)

trp attenuation

News & Paper
FACS method

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
UniProt
Fat 2D gel

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
 

Choose paper A OR B OR C OR D

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
cell cycle PDF
Endo16 extended
p53 extended

definition

30, 31, 33, 35, 39, 41, 43

Apr 18 F

11.2: Synthetic cont.

Logic Gates

400 - 407

Read Paper

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)

News & Paper

NFkB
Wnt

What is synthetic biology?

Apr 25 F

Submit review of paper A OR B OR C OR D

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

RNAi animation

histone modifications
NippedB protein
RNA structure
Network Motifs

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 - 13 W - S Final Exam
Due May. 11, 9 am
   

Genomics Overview

Genomics Reading Syllabus

Biology Home Page


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