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CENG 465 - Introduction to Bioinformatics (Fall 2013-2014) OVERVIEW SCHEDULE ASSIGNMENTS RESOURCES |
| Date | Lecture Topics | Reading | Assignments | |
|---|---|---|---|---|
| Week #1 |
Sep 26, Thur Sep 27, Fri |
Introduction to molecular biology and genetics, biological databases, and high-throughput data sources. Overview of bioinformatics problems. Lecture Slides |
Class Web Page Bioinformatics - An Introduction for Computer Scientists Introduction to Molecular Biology More reading on cells and genomes: Cells and Genomes How cells read the genome |
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| Week #2 |
Oct 3, Thur Oct 4, Fri |
Pairwise sequence alignment algorithms: Dynamic programming Lecture Slides |
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| Week #3 |
Oct 10, Thur Oct 11, Fri |
Pairwise sequence alignment algorithms: Dynamic programming Lecture Slides |
Pairwise Sequence Alignment |
Assignment #1 DUE DATE: October 27, 23:55 via COW |
| Week #4 |
Oct 24, Thur Oct 25, Fri |
Statistical significance of alignments - Part I Statistical significance of alignments - Part II Lecture Slides |
Statistical Significance of Alignments Statistical Significance of Alignments (Reading 2) |
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| Week #5 |
Oct 31, Thur Nov 1, Fri |
Suffix Trees, Suffix Arrays Lecture Slides |
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| Week #6 |
Nov 7, Thur Nov 8, Fri |
Patterns, Profiles, and Multiple Alignments Hidden Markov Models Lecture Slides |
Chapter 6 from the textbook |
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| Week #7 |
Nov 14, Thur Nov 15, Fri |
Multiple Sequence Alignment Algorithms Week 5 Lecture Slides Continued |
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Assignment #2 DUE DATE: November 29, 23:55 via COW or hardcopy |
| Week #8 |
Nov 21, Thur Nov 22, Fri |
Phylogenetic trees Lecture Slides |
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| Week #9 |
Nov 28, Thur Nov 29, Fri |
Introduction to protein structures Lecture Slides Midterm Exam (at 9:40) in BMB-4 and BMB-5 Last year's midterm |
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| Week #10 |
Dec 5, Thur Dec 6, Fri |
Protein Structure Prediction Lecture Slides (continued) |
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| Week #11 |
Dec 12, Thur Dec 13, Fri |
Structural Alignment of Proteins (lecture notes continued) |
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Assignment #3 DUE DATE: December 29, 23:55 via COW |
| Week #12 |
Dec 19, Thur Dec 20, Fri |
Microarray data analysis Clustering techniques Lecture Slides K-means Empty Cluster Example K-means Demo Self Organizing Maps Demo |
Microarrays Intro Paper - 1 Microarrays Intro Paper - 2 Microarrays Intro Paper - 3 |
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| Week #13 |
Dec 26, Thur Dec 27, Fri |
Introduction to Systems Biology Gene regulatory networks Lecture Slides |
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| Week #14 |
Jan 2, Thur Jan 3, Fri |
Analysis of biological networks Lecture Slides |
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Assignment #4 DUE DATE: January 19, 23:55 via COW |
| Week #15 |
Jan 9, Thur Jam 10, Fri |
Theoretical computational models for systems biology Reading: Algorithmic Systems Biology |
A systems view of protein-protein interactions A systems view of metabolism A systems view of regulatory mechanisms |
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