Syllabus of Lectures - 2006 |
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| 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 |
GTM |
| T, Jan. 24 | Tools of bioinformatics: Sequence Alignment Required Reading: Dynamic Programming Algorithm (pdf) |
ppt |
GTM |
| F, Jan. 27 | Tools of bioinformatics: Blast, PsiBlast, DNA sequence databases Required Reading: Bioinformatics References, Gapped Blast |
ppt |
GTM |
| T, Jan. 31 | New strategies and technologies for DNA sequencing Required Reading:Massively parallel sequencing, Genome sequencing in microfabricated high-density picolitre reactors |
SA | |
| F, Feb. 3 | Analytical protein chemistry Required Reading: Protein Purification Handbook, pp. 9-27 & pp. 61-71 |
SA | |
| T, Feb. 7 | Preparative protein chemistry Required Reading: Protein Purification |
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 |
GTM |
| F, Feb. 17 | Biophysics of amide HD exchange Required Reading:none |
ppt |
GTM |
| T, Feb. 21 | Protein mass spectrometry Required Reading: Bakhtiar & Tse - pp. 415 - 419; Mann et al - pp. 438 - 447 |
SA | |
| F, Feb. 24 | Protein folding in vitro Required Reading: Creighton, pp. 286-295; Fersht & Daggett |
SA | |
| T, Feb. 28 | Protein NMR spectroscopy Required Reading: B & W Chapter 5 |
ppt |
GTM |
| F, Mar. 3 | Protein X-ray crystallography |
ppt |
GTM |
| T, Mar. 7 | Protein folding in vivo Required Reading: Dobson 2003, Goldberg 2003 Optional Reading: Schueler-Furman et al 2005 |
SA | |
| F, Mar. 10 | Exam II | ||
| T, Mar. 14 | Spring Break |
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| F, Mar. 17 |
Spring Break | ||
| T, Mar. 21 | Enzyme kinetics | ppt |
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 |
SA | |
| F, Mar. 31 | Protein-protein interactions II Required Reading: Sidhu et al (2003) |
SA | |
| T, Apr. 4 | RNA interference Reference: http://www.nature.com/focus/rnai/animations/rnai_revised_500x280.mov Required Reading: Dykxhoorn et al (2003) |
SA | |
| F, Apr. 7 | DNA microarrays Required Reading: Hoheisel_2006 |
SA | |
| T, Apr. 11 | Structural Genomics Required Reading: B & W Chapter 29 |
ppt |
GTM |
| F, Apr. 14 | Exam III |
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| 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: |
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The Student Presentations and Exams I - III will each count for 25% of your grade. There will be no final exam.
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