Syllabus of Lectures - 2007

Date Topic Lecture Lecturer
T, Jan. 16th Course introduction and overview of genomics & proteomics
Required Reading: B&W Chapter 1
F, Jan. 19th Conformational properties of proteins
Required Reading: B&W Chapter 2
T, Jan. 23rd Tools of bioinformatics: Blast, PsiBlast, DNA sequence databases
Required Reading: none
F, Jan. 26th Protein sequence and structure databases
Required Reading:
- A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
- Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs
- Hidden Markov models
T, Jan. 30th Protein domains and folds: SCOP, CATH, DALI
Required Reading:
- B&W Ch 12; Protein Structure Evolution and the SCOP Database
- B&W Ch 13; The CATH Domain Structure Database
- Protein Structure Comparison by Alignment of Distance Matrices
F, Feb. 2nd New strategies and technologies for DNA sequencing
Supplemental Slides:
Required Reading:
- GENE SEQUENCING: The Race for the $1000 Genome
- Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing
Massively parallel sequencing
Genome sequencing in microfabricated high-density picolitre reactors
T, Feb. 6th Analytical protein chemistry SA
F, Feb. 9th Preparative protein chemistry
Required Reading:
- Protein Purification
- APB Protein Purification Handbook, pages 9-27 and 61-71
T, Feb. 13th Protein mass spectrometry
Required Reading:
- Biological Mass Spectrometry: A Primer; pp. 415-419
- Analysis of Proteins and Proteomes by Mass Spectrometry; pp. 438-447
- Mass Spectrometry and Protein Analysis
F, Feb. 16th Biophysics of amide HD exchange
Take-home Exam I handed out
T, Feb. 20th Protein folding in vitro
Required Reading:
- PROTEINS: Structures and Molecular Principles
- Protein Folding and Unfolding at Atomic Resolution
Suggested Reading:
- Progress in Modeling of Protein Structures and Interactions
F, Feb. 23rd Protein folding in vivo
Required Reading:
- Protein folding and misfolding
- Protein degradation and protection against misfolded or damaged proteins
Take-home Exam I due
T, Feb. 27th Protein NMR spectroscopy GTM
F, Mar. 2nd Protein X-ray crystallography
T, Mar. 6th Enzyme kinetics I GTM
F, Mar. 9th Enzyme kinetics II GTM
T, Mar. 13th Spring Break
F, Mar. 16th
Spring Break    
T, Mar. 20th Genomic programming and epigenetic states
Required Reading: CSHL "Epigenetic" Textbook
V. Pirrotta
F, Mar. 23rd Protein-protein interactions I
Required Reading:
- Interactions with Other Molecules
- Binding in the growth hormone receptor complex
- Additivity-based predictions of equilibrium constants for some protein-protein associations
T, Mar. 27th Protein-protein interactions II
Required Reading:
- Analysing protein-protein interactions with the yeast two-hybrid system
F, Mar. 30th DNA microarrays
Take-home Exam II handed out
Required Reading:
- The Affymetrix GeneChip Platform: An Overview
- Microarray technology: beyond transcript profiling and genotype analysis
T, Apr. 3rd RNA interference
Required Reading:
- Poster: RNA Silencing
- RNA Interference: Big Applause for Silencing in Stockholm
- Killing the Messenger: Short RNAs that Silence Gene Expression
F, Apr. 6th Shortened class due to MBB Poster Session
Papers for student presentations chosen. Select a paper from the Research Paper Presentations list to present.
T, Apr. 10th Predicting function from structure:
Structural Genomics, GRASP, & CONSURF
Take-home Exam II due
F, Apr. 13th Student Presentations
Sara Khalil, paper 3
T, Apr. 17th Student Presentations
Weather Emergency - Rutgers Closed
F, Apr. 20th
Student Presentations
Alex Greenfield, paper 12
Jason Merkin, paper 19
Matt Zegarek, paper 1
T, Apr. 24th
Student Presentations
Betty Kong, paper 9
Jaspinder Singh, paper 6
James Wang, paper 8
F, Apr. 27th Student Presentations
Jeffrey Hyun, paper 5
Sid Pattanam, paper 4
Eden Seitomer, paper 14
Official Exam Date Students can pick up Exam III from Laura Venner in CABM 019 after 1pm on Monday, April 30th. Exam III is due by 4pm on Monday, May 7th.    

Each take-home exam will count for 30% of your grade.

The Student Presentations + Exam III will count for 40% of your grade.

There will be no final exam.

GTM away: Week of Jan 4 – 13; Feb 19; Mar 19 – 20; Apr 23 - 27; May 4.
SA away: Mar 19 - 20.

Prof. Montelione’s email address:
Prof. Anderson’s email address: