Syllabus of Lectures - 2006

Date Topic   Lecturer
T, Jan. 17 Course introduction and overview of genomics & proteomics
Required Reading: B & W Chapter 1
ppt 1 & 2
pdf 1 & 2
SA(1) + GTM(2)
F, Jan. 20 Conformational properties of proteins
Required Reading: B & W Chapter 2
ppt
pdf
GTM
T, Jan. 24 Tools of bioinformatics: Sequence Alignment
Required Reading: Dynamic Programming Algorithm (pdf)
ppt
pdf
GTM
F, Jan. 27 Tools of bioinformatics: Blast, PsiBlast, DNA sequence databases
Required Reading: Bioinformatics References, Gapped Blast
ppt
pdf
GTM
T, Jan. 31 New strategies and technologies for DNA sequencing
Required Reading:Massively parallel sequencing, Genome sequencing in microfabricated high-density picolitre reactors
pdf SA
F, Feb. 3 Analytical protein chemistry
Required Reading: Protein Purification Handbook, pp. 9-27 & pp. 61-71
pdf SA
T, Feb. 7 Preparative protein chemistry
Required Reading: Protein Purification
pdf SA
F, Feb. 10 Exam I    
T, Feb. 14 Protein domains and folds: SCOP, CATH, DALI
Required Reading: B & W Chapters 9, 12 & 13; Dali
ppt
pdf
GTM
F, Feb. 17 Biophysics of amide HD exchange
Required Reading:none
ppt
pdf
GTM
T, Feb. 21 Protein mass spectrometry
Required Reading: Bakhtiar & Tse - pp. 415 - 419; Mann et al - pp. 438 - 447
pdf SA
F, Feb. 24 Protein folding in vitro
Required Reading: Creighton, pp. 286-295; Fersht & Daggett
pdf SA
T, Feb. 28 Protein NMR spectroscopy
Required Reading: B & W Chapter 5
ppt
pdf
GTM
F, Mar. 3 Protein X-ray crystallography
ppt
pdf
GTM
T, Mar. 7 Protein folding in vivo
Required Reading: Dobson 2003, Goldberg 2003
Optional Reading: Schueler-Furman et al 2005
pdf SA
F, Mar. 10 Exam II
T, Mar. 14 Spring Break
   
F, Mar. 17
Spring Break    
T, Mar. 21 Enzyme kinetics ppt
pdf
GTM
F, Mar. 24 Predicting function from structure: GRASP, CONSURF GTM
T, Mar. 28 Protein-protein interactions I
Required Reading:
Interactions with other molecules
,
Additivity-based prediction of equilibrium constants for some protein-protein associations
,
Binding in the growth hormone receptor complex
pdf SA
F, Mar. 31 Protein-protein interactions II
Required Reading: Sidhu et al (2003)
pdf SA
T, Apr. 4 RNA interference
Reference: http://www.nature.com/focus/rnai/animations/rnai_revised_500x280.mov
Required Reading: Dykxhoorn et al (2003)
pdf SA
F, Apr. 7 DNA microarrays
Required Reading: Hoheisel_2006
pdf SA
T, Apr. 11 Structural Genomics
Required Reading: B & W Chapter 29
ppt
pdf
GTM
F, Apr. 14 Exam III
   
T, Apr. 18 Student Presentations:
Lanka, Himabindu; paper 1
Giunta, Michael; paper 7
Radvansky, Brian; paper 10
  GTM+SA
F, Apr. 21 Student Presentations
Chen, Chien-Jou; paper 6
Dinc, Murat; paper 8
Dukleska, Svetlana; paper 9
  GTM+SA
T, Apr. 25
Student Presentations
Chan, Florence; paper 2
Chen, Christopher; paper 5
Agarwal, Sharad; paper 11
  GTM+SA
F, Apr. 28
Student Presentations
Sliwowska, Anna; paper 4
Hamilton, Keith; paper 12
Metry, Sawsan; paper 14
  GTM+SA

Select a paper from the list to present:

Sample Presentations from 2004:

  • Kate Drahos, HTP Protein-Protein Interaction Analysis [HTML] [PPT]
  • Dan Kulp, Macromolecular Complexes [HTML] [PPT]
The Student Presentations and Exams I - III will each count for 25% of your grade. There will be no final exam.