Syllabus of Lectures - 2008 |
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| Date | Topic | Lecture | Lecturer |
| T, 22 Jan 2008 | Course introduction and overview of genomics & proteomics Required Reading: - DNA sequencing: bench to bedside and beyond |
GTM- |
GTM+SA |
| SA- |
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| F, 25 Jan 2008 | Principles of thermodynamics and kinetics Required Reading: Lehninger, Principles of Biochemistry, pp 47-58 |
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GTM |
| T, 29 Jan 2008 | Conformational properties of proteins Required Reading: - B&H, Chapters 1 and 2, Intro to Structural Bioinformatics |
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GTM |
| F, 1 Feb 2008 | Tools of bioinformatics: Blast, PsiBlast, DNA sequence databases Required Reading: -A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins |
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GTM |
| T, 5 Feb 2008 | Protein sequence and structure databases Required Reading: - Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs |
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GTM |
| F, 8 Feb 2008 | Protein domains and folds: SCOP, CATH, DALI Required Reading: - A global representation of the protein fold space - Hiddden Markov Models |
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GTM |
| T, 12 Feb 2008 | New strategies and technologies for DNA sequencing Required Reading: - The Race to Read Genomes on a Shoestring, Relatively Speaking - Whole-genomere-sequencing - Genome sequencing in micro fabricated high-density picolitre reactors - Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing - Massively parallel sequencing |
Part Ia Part Ib Part II |
SA |
| F, 15 Feb 2008 | Analytical protein chemistry Required Reading: none |
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SA |
| T, 19 Feb 2008 | Preparative protein chemistry Required Reading: - Protein Purification - Protein Purification Handbook, pages 9-27 and 61-71. |
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SA |
| F, 22 Feb 2008 | SNOW DAY | SA | |
| T, 26 Feb 2008 | 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 - The biological impact of mass-spectrometry-based proteomics Take-home Exam I handed out |
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SA |
| F, 29 Feb 2008 | 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 |
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SA |
| T, 4 Mar 2008 | 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 |
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SA |
| F, 7 Mar 2008 | Protein X-ray crystallography Take-home Exam I due Required Reading: - Protein Crystallography for non-crystallographers |
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GTM/RG |
| T, 11 Mar 2008 | 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 |
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SA |
| F, 14 Mar 2008 | NMR Principles Required Reading: - Structural Bioinformatics Chapter 5: Macromolecular Structure Determination by NMR Spectroscopy |
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GTM |
| T, 18 Mar 2008 | Spring Break |
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| F, 21 Mar 2008 |
Spring Break | ||
| T, 25 Mar 2008 | Protein NMR Structure Analysis Suggested Reading: - Protein NMR Spectroscopy Chapter 10: Sequential Assignment, Structure Determination |
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GTM |
| F, 28 Mar 2008 | Protein-protein interactions II Required Reading: - Reaching for high-hanging fruit in drug discovery at protein–protein interfaces |
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SA |
| T, 1 Apr 2008 | DNA microarrays Required Reading: - The Affymetrix GeneChip® Platform: An Overview - Microarray technology: beyond transcript profiling and genotype analysis Take-home Exam II handed out Papers for student presentations chosen. Select a paper from the Research Paper Presentations list to present. |
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SA |
| F, 4 Apr 2008 | Reading: - Biochemistry, Chapter 4: Enzymes: Biological Catalysts |
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| T, 8 Apr 2008 | RNA interference Required Reading: - RNA Silencing Poster - RNA Interference: Big Applause for Silencing in Stockholm - DNA Study Forces Rethink of What It Means to Be a Gene - Encyclopaedia of humble DNA - Genome project turns up evolutionary surprises |
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SA |
| F, 11 Apr 2008 | Predicting function from structure, disorder prediction, GRASP, CONSURF Required Reading: - Structural genomics: keystone for a Human Proteome Project - Protein Structure Initiative: Phase 3 or Phase Out Take-home Exam II due |
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GTM/JH |
| T, 15 Apr 2008 | LABORATORY TOURS |
GTM | |
| F, 18 Apr 2008 | Student Presentations: Rachel Belote, Paper 1 Irina Fridman, Paper 10 |
GTM+SA | |
| T, 22 Apr 2008 | Student Presentations: Petrit Mavraj, Paper 20 Kaitlyn Turo, Paper 19 Paul Harvilla, Paper 7 |
GTM+SA | |
| F, 25 Apr 2008 |
Student Presentations: Daya Patel, Paper 9 Mai Mahmoud, Paper 8 Michael Merolla, Paper 2 |
GTM+SA | |
| T, 29 Apr 2008 |
Student Presentations: Joanne Ahn, Paper 13 Ria John, Paper 16 Rabab Haider, Paper 12 |
GTM+SA | |
| F, 2 May 2008 | Student Presentations: Seema Sahdev, Paper 23 Zach Perlman, Paper 15 William Buchwald, Paper 5 Take-home Exam III handed out |
GTM+SA | |
| MONDAY, MAY 12 | Take Home Exam III Due | GTM+SA | |
Sample Presentations from 2004:
The Student Presentations + Exam III will count for 40% of your grade. There will be no final exam. |
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Prof. Montelione’s email address: guy@cabm.rutgers.edu |
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