Fall, 2006
Meet every Tuesday and Thurday 9:30am
- 10:45am 419 CMW 419
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Instructor: Hui
Lu |
TA: Nitin Bhardwaj Room W103, 835 S Wolcott. |
Reference Book: Biological Sequence Analysis: Probablisitic models of proteins and nucleis acids by R. Durbin, S. Eddy, A. Krogh and G. Mitchison
Announcement: Seminar titled Final Project: Due Dec 8th, 2006.
The schedule below is a tentative one and is subject to changes.
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Date |
Content |
References |
Homework |
Solution |
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Aug 29 |
Lecture 1: Introduction -- bioinformatics topics and molecular biology. Slides. |
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Aug 31 |
Lecture 2: Introduction to Molecular Biology part 2. Slides. |
Ch 2 and others |
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Sept 5 |
Lecture 3: Programming and databases in bioinformatics. Slides. Slides. |
Ch 3 |
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Sept 7 |
Lecture 4: Pairwise Sequence Alignment. Slides |
Ch 3 |
Homework1 (due on Sept 14 before class) |
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Sept 12 |
Lecture 5:
Scoring Matrix. Slides |
Ch 3 |
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Sept 14 |
Lecture 6: Multiple Sequence Alignment Slides |
Ch 3 |
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Sept 19 |
Lecture 7: Statisticalmethods in sequence analysis Slides |
Ch 3 |
Homework 2 Due on Sept 28th before class |
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Sept 21 |
Lecture 8: Hidden Markov
Models Slides |
Ch 3 |
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Sept 26 |
Lecture 9: Hidden Markov Models on Sequence Analysis Slides
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Sept 28 |
Lecture 9: Hidden Markov Models on Sequence Analysis Slides |
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Oct 3 |
Lecture 10: Statistical methods in
bioinformatics/sequence analysis Slides |
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Oct 5 |
Lecture 10: Statistics in sequence analysis (Lecture cancelled due to the Workshop) |
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Oct 10 |
Lecture 11: Database search Slides |
1.5 lecture |
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Oct 12 |
No class; BMES Chicago |
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Oct 17 |
Review session. |
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Oct 19 |
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Oct 24 |
Lecture 12: Microarray analysis Slides |
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Oct 26 |
Lecture 13: Phylogenetic analysis Slides |
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Oct 31 |
Lecture 14: Phylogenetic analysis 2 Slides |
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Nov 2 |
Lecture 15: Gene Identification Slide |
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Nov 7 |
Lecture 16: Whole Genome Analysis Slide |
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Homework 4 Due Nov 16th |
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Nov 9 |
Lecture 17: Genomic Circuits Slides |
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Nov 14 |
Lecture 18: Protein structure and prediction Slides |
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Nov 16 |
Lecture 19: Protein secondary structure prediction and homology modeling Slides |
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Nov 21 |
Lecture 20: Protein folding and structure prediction Slides |
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Nov 23 |
Lecture 20:Protein folding and structure prediction Slides |
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Dec 7th |
Project Presentation |
Individual presentation for no more than 10 mins. Introduce your protein in 1 or 2 slides followed by results for 7-8 slides. Order of presentation (by last name):Davide Candaro, Adam Carlson, Fabio Cuncure, Andrea Franceschini, Ali Husain, David Jimnez-Morales, Ramkrishna Mehendale, Himanshu Patel, Aishwarya Parmeswaran, Tom Ronan, Gobind Singh. |
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Nov 30 |
Project Presentation: |
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Dec 5 |
Project Presentation: |
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Dec 7 |
TBA |
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