Syllabus of Lectures - 2007 |
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| Date | Topic | Lecture | Lecturer |
| T, Jan. 16th | Course introduction and overview of genomics & proteomics Required Reading: B&W Chapter 1 |
GTM- |
GTM+SA |
| SA- |
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| F, Jan. 19th | Conformational properties of proteins Required Reading: B&W Chapter 2 |
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GTM |
| T, Jan. 23rd | Tools of bioinformatics: Blast, PsiBlast, DNA sequence databases Required Reading: none |
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GTM |
| 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 |
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GTM |
| 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 |
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GTM |
| 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 |
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SA |
| 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 |
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SA |
| 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 |
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SA |
| F, Feb. 16th | Biophysics of amide HD exchange Take-home Exam I handed out |
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GTM |
| 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 |
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SA |
| 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 |
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SA |
| T, Feb. 27th | Protein NMR spectroscopy | |
GTM |
| F, Mar. 2nd | Protein X-ray crystallography |
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GTM |
| T, Mar. 6th | Enzyme kinetics I | |
GTM |
| F, Mar. 9th | Enzyme kinetics II | |
GTM |
| T, Mar. 13th | Spring Break |
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| F, Mar. 16th |
Spring Break | ||
| T, Mar. 20th | Genomic programming and epigenetic states Required Reading: CSHL "Epigenetic" Textbook |
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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 |
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SA |
| T, Mar. 27th | Protein-protein interactions II Required Reading: - Analysing protein-protein interactions with the yeast two-hybrid system |
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SA |
| 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 |
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SA |
| 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 |
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SA |
| 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. |
SA | |
| T, Apr. 10th | Predicting function from structure: Structural Genomics, GRASP, & CONSURF Take-home Exam II due |
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GTM |
| F, Apr. 13th | Student Presentations Sara Khalil, paper 3 |
GTM+SA | |
| T, Apr. 17th | Student Presentations Weather Emergency - Rutgers Closed |
GTM+SA | |
| F, Apr. 20th |
Student Presentations Alex Greenfield, paper 12 Jason Merkin, paper 19 Matt Zegarek, paper 1 |
GTM+SA | |
| T, Apr. 24th |
Student Presentations Betty Kong, paper 9 Jaspinder Singh, paper 6 James Wang, paper 8 |
GTM+SA | |
| F, Apr. 27th | Student Presentations Jeffrey Hyun, paper 5 Sid Pattanam, paper 4 Eden Seitomer, paper 14 |
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| 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. |
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GTM away: Week of Jan 4 – 13; Feb 19; Mar 19 – 20; Apr 23 - 27; May 4. Prof. Montelione’s email address: guy@cabm.rutgers.edu |
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