Syllabus of Lectures - 2005

Date Topic   Lecturer
T, Jan. 18th

Course introduction and overview of genomics & proteomics
Reading: Proteomics to study genes and genomes
Reading: Proteomics

HTML
PowerPoint
GTM + SA
F, Jan. 21st Genomics and proteomics (con’d) HTML
PowerPoint
SA
T, Jan. 25th Introduction to Bioinformatics HTML
PowerPoint
GTM
F, Jan. 28th

Sequence-based Bioinformatics I – Dynamic Programming, Blast

HTML
PowerPoint
GTM
T, Feb. 1st

Analytical and preparative protein chemistry I
Reading (optional): Solvation and hydration of proteins and nucleic acids
Reading: APB manual, pages 9-27 and 61-71

HTML
PowerPoint
SA
F, Feb. 4th Analytical and preparative protein chemistry II HTML
PowerPoint
SA
T, Feb. 8th Sequence bioinformatics II, Gapped Blast, MSA, PsiBlast, HMM
Reading: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Reading: Hidden Markov models
HTML
PowerPoint
GTM
F, Feb. 11th
Structural Bioinformatics, SCOP, CATH, Dali
Reading: Protein sStructure comparison by alignment of distance matrices
HTML
PowerPoint
GTM
T, Feb. 15th EXAM I    
F, Feb. 18th Protein folding
Reading: Proteins: structures and molecular principles
Reading: Protein folding and misfolding
Reading: Protein folding and unfolding at atomic resolution
HTML
PowerPoint
SA
T, Feb. 22nd

Protein-protein interactions
Reading: Interactions with other molecules
Reading: Additivity-based prediction of equilibrium constants for some protein-protein associations
Reading: Binding in the growth hormone receptor complex

HTML
PowerPoint
SA
F, Feb. 25th

Protein Mass Spectrometry
Reading: Biological mass spectrometry: a primer (438 - 447 only)
Reading: Analysis of proteins and proteomes by mass spectrometry (pp. 415 - 419)

HTML
PowerPoint
SA
T, Mar. 1st Conformational Properties of Proteins I
Required Reading: Bourne & Weisig, Chapter 2
HTML
PowerPoint
GTM
F, Mar. 4th Conformational Properties of Proteins II
Required Reading: A global representation of the protein fold space
HTML
PowerPoint
GTM
T, Mar. 8th Biophysics of Amide Hydrogen Exchange HTML
PowerPoint
GTM
F, Mar. 11th Protein NMR Spectroscopy, Part I
Required Reading: Bourne & Weisig, Chapter 5
HTML
PowerPoint
GTM
T, Mar. 15th Spring Break
   
F, Mar. 18th
Spring Break    
T, Mar. 22nd Exam II (covers material through "Biophysics of Amide Hydrogen Exchange")
F, Mar. 25th Protein NMR Spectroscopy, Part II HTML
PowerPoint
GTM
T, Mar. 29th Enzyme Kinetics I
Required Reading: Kinetics reading
HTML
PowerPoint
SA
F, Apr. 1st Enzyme Kinetics II
Required Reading:Dissecting the catalytic triad of a serine protease
HTML
PowerPoint
SA
T, Apr. 5th DNA Microarrays
Required Reading: Expressing what’s on your mind: DNA arrays and the brain
HTML
PowerPoint
SA
F, Apr. 8th RNA Interference
Required Reading: Killing the messenger: Short RNAs that silence gene expression
HTML
PowerPoint
SA
T, Apr. 12th X-ray Crystallography HTML
PowerPoint
GTM
F, Apr. 15th Structural Genomics I & II
HTML
PowerPoint
GTM
T, Apr. 19th Exam III

   
F, Apr. 22nd Student Presentations: Biological Networks    
T, Apr. 26th
Student Presentations: Biological Networks
   
F, Apr. 29th
Student Presentations: Biological Networks    

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.

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