Syllabus of Lectures - 2009

Date Topic Lecture Lecturer
T, Jan. 20 Lecture: Introduction and overview of genomics & proteomics
Required Reading: DNA sequencing: bench to bedside and beyond
pdf document
GTM + SA
F, Jan. 23 Lecture: Principles of thermodynamics pdf document GTM
T, Jan. 27 Lecture: New strategies and technologies for DNA sequencing

Required Reading:
-
Real-Time DNA Sequencing from Single Polymerase Molecules
- The Race to Read Genomes on a Shoestring, Relatively Speaking
- Whole-genomere-sequencing
- Massively parallel sequencing

Suggested Reading:

- Genome sequencing in microfabricated high-density picolitre reactors
pdf document SA
F, Jan. 30 Lecture: Conformational properties of proteins pdf document GTM
T, Feb. 3 Lecture: Tools of bioinformatics: Blast, PsiBlast, DNA sequence databases
pdf document GTM
F, Feb. 6 Lecture: Protein sequence and structure databases
Required Reading:
-
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
  GTM
T, Feb. 10 Lecture: Sequence Bioinformatics
Required Reading:
- Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs
- Hidden Markov Models
pdf document GTM
F, Feb. 13 Lecture:
Part A - New Strategies & Technologies for DNA Sequencing
Part B - Analytical Protein ChemistrySome Biophysical Properties of Proteins
Required Reading:
- Genome sequencing in microfabricated high-density picolitre reactors
- Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing
A: pdf document
B: pdf document
SA
T, Feb. 17 Lecture: Analytical and preparative protein chemistry
Required Reading:
- Protein Purification
- Protein Purification Handbook, pages 9-27 and 61-71
pdf document SA
F, Feb. 20 Lecture: Protein mass spectrometry
Required Reading:
- Biological Mass Spectrometry: A Primer, pp. 415 - 419 only
- Analysis of Proteins and Proteomes by Mass Spectrometry, pp. 438 - 447 only

Suggested Reading:
- The biological impact of mass-spectrometry-based proteomics
pdf document SA
T, Feb. 24 Lecture: Structural Bioinformatics
Required Reading:

- A global representation of the protein fold space

Take-home Exam I handed out

pdf document GTM
F, Feb. 27 Lecture: NMR - Basic Principals
pdf document GTM
T, Mar. 3 NO CLASS
   
F, Mar. 6 Lecture: X-ray Crystallography
Required Reading:
- Protein Crystallography for non-crystallographers
Take-home Exam I due by 1:40 PM class
pdf document RG
T, Mar. 10 Lecture: Protein NMR Methods
Required Reading:
- Protein NMR Spectroscopy Chapter 10: Sequential Assignment, Structure Determination
pdf document GTM
F, Mar. 13 Lecture: Enzyme Kinetics
pdf document GTM
T, Mar. 17 Spring Break
   
F, Mar. 20
Spring Break    
T, Mar. 24 Lecture: Protein folding in vitro
Required Reading:
- Folding and binding: implementing the game plan
- The protein folding problem: when will it be solved?
- Protein Folding and Unfolding at Atomic Resolution
- Proteins: Structures and Molacular Principles
Suggested Reading:
- Progress in Modeling of Protein Structures and Interactions
pdf document SA
F, Mar. 27 Lecture: Protein folding in vivo
Required Reading:
- Experimental investigation of protein folding and misfolding
- Protein degradation and protection against misfolded or damaged proteins
Suggested Reading:
- Pathways of chaperone-mediated protein folding in the cytosol
pdf document
SA
T, Mar. 31 Lecture: Protein-protein interactions I
Required Reading:
- Interactions with Other Molecules
-
Binding in the growth hormone receptor complex
- The molecular architecture of protein–protein binding sites
Suggested Reading:
- Additivity-based prediction of equilibrium constants for some protein-protein associations
pdf document SA
F, Apr. 3 Lecture: Protein-protein interactions II
Required Reading:
- Reaching for high-hanging fruit in drug discovery at protein–protein interfaces
Take-home Exam II handed out

Papers for student presentations chosen. Select a paper from the
Research Paper Presentations list to present.
pdf document SA
T, Apr. 7 Lecture: DNA microarrays and RNA interference
Required Reading:
- A three-dimensional view of the molecular machinery of RNA interference
pdf document SA
F, Apr. 10 Lecture: Structural Proteomics and Function Prediction
Required Reading:
- Structural genomics: keystone for a Human Proteome Project
- Protein Structure Initiative: Phase 3 or Phase Out
Take-home Exam II due
pdf document GM
T, Apr. 14 Student Presentations:
- Sha, Daniel, Paper 6
- Nocetti, Nicolas, Paper 31
- Huang, Bridget, Paper 27
  GTM+SA
F, Apr. 17 Student Presentations:
- Hakhverdyan, Zhanna, Paper 5
- Lee, Jung Ah (Grace), Paper 10
- Skalenko, Kyle, Paper 30
  GTM+SA
T, Apr. 21 Student Presentations:
- Changela, Neha, Paper 26
- Dong, Kimberly, Paper 8
- Jakubowski, Chris, Paper 15
- Martinez, Ana, Paper 25
  GTM+SA
F, Apr. 24 Student Presentations:
- Sung, Hee Chang (Paul), Paper 13
- Sung, Linda, Paper 28
- Venkateswaran, Suresh, Paper 12
  GTM+SA
T, Apr. 28 Student Presentations:
- Corbiere, Jason, Paper 16
- Fan, William, Paper 1
- Lopez, Deonnae, Paper 21
- Schauder, Curtis, Paper 13
  GTM+SA
F, May 1 Student Presentations:
- Heck, Bryan, Paper 20, (PowerPoint 2007 to show design features)
- Vibulbhan, Suban, Paper 3, Video
- Yuk, Louis, Paper 23

Take-home Exam III handed out
Required Reading:
- Structural genomics: keystone for a Human Proteome Project
- Protein Structure Initiative: Phase 3 or Phase Out
  GTM+SA
M, May 11 Take-home Exam III due    
Sample Presentations from 2004:
  • Kate Drahos, HTP Protein-Protein Interaction Analysis pdf document
  • Dan Kulp, Macromolecular Complexes pdf document
Take-home Exams I & II will each count for 30% of your grade.
The Student Presentations + Take-home Exam III will count for 40% of your grade.
There will be no final exam.
Prof. Montelione’s email address: guy@cabm.rutgers.edu
Prof. Anderson’s email address: anderson@cabm.rutgers.edu