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CENG 465 - Introduction to Bioinformatics (Fall 2016-2017) OVERVIEW SCHEDULE ASSIGNMENTS RESOURCES |
| Date | Lecture Topics | Reading | Assignments | |
|---|---|---|---|---|
| Week #1 |
Oct 4, Tue Oct 7, Fri |
No classes in the first week. Away for the ACM-BCB conference in Seattle. |
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| Week #2 |
Oct 11, Tue Oct 14, 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 #3 |
Oct 18, Tue Oct 21, Fri |
Pairwise sequence alignment algorithms: Dynamic programming Lecture Slides Sequence alignment C code Sample input for alignment |
Pairwise Sequence Alignment |
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| Week #4 |
Oct 25, Tue Oct 28, Fri |
Statistical significance of alignments Lecture Slides Suffix Trees, Suffix Arrays Lecture Slides |
Statistical Significance of Alignments Statistical Significance of Alignments (Reading 2) |
Assignment #1 DUE DATE: November 6, 23:55 via ODTU-Class |
| Week #5 |
Nov 1, Tue Nov 4, Fri |
Patterns, Profiles, and Multiple Alignments Hidden Markov Models Lecture Slides |
Chapter 6 from the textbook |
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| Week #6 |
Nov 8, Tue Nov 11, Fri |
Hidden Markov Models continued |
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| Week #7 |
Nov 15, Tue Nov 18, Fri |
Multiple Sequence Alignment Algorithms Week 5 Lecture Slides Continued |
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Assignment #2 DUE DATE: November 29, 23:55 via ODTU-Class |
| Week #8 |
Nov 22, Tue Nov 25, Fri |
Phylogenetic trees Lecture Slides |
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| Week #9 |
Nov 29, Tue Dec 2, Fri |
Midterm review on Tuesday Midterm Exam (at 17:40 on Thursday) Sample midterm |
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| Week #10 |
Dec 6, Tue Dec 9, Fri |
Introduction to protein structures Lecture Slides |
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| Week #11 |
Dec 13, Tue Dec 16, Fri |
Protein Structure Prediction Structural Alignment of Proteins Lecture Slides (continued) |
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Assignment #3 DUE DATE: December 25, 23:55 via ODTU-Class |
| Week #12 |
Dec 20, Tue Dec 23, 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 27, Tue Dec 30, Fri |
Introduction to Systems Biology Lecture Slides |
Reading: Algorithmic Systems Biology A systems view of protein-protein interactions A systems view of metabolism A systems view of regulatory mechanisms |
Assignment #4 DUE DATE: January 22, 23:55 via ODTU-Class |
| Week #14 |
Jan 3, Tue Jan 6, Fri |
Analysis of biological networks Lecture Slides |
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