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CENG 465 - Introduction to Bioinformatics (Fall 2017-2018) OVERVIEW SCHEDULE ASSIGNMENTS RESOURCES |
| Date | Lecture Topics | Reading | Assignments | |
|---|---|---|---|---|
| Week #1 |
Oct 2, Mon Oct 3, Tue |
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 9, Mon Oct 10, Tue |
Pairwise sequence alignment algorithms: Dynamic programming Lecture Slides Sequence alignment C code Sample input for alignment |
Pairwise Sequence Alignment |
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| Week #3 |
Oct 16, Mon Oct 17, Tue |
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. Submit via ODTU-Class. |
| Week #4 |
Oct 23, Mon Oct 24, Tue |
Patterns, Profiles, and Multiple Alignments Hidden Markov Models Lecture Slides |
Chapter 6 from the textbook |
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| Week #5 |
Oct 30, Mon Oct 31, Tue |
Hidden Markov Models continued |
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| Week #6 |
Nov 6, Mon Nov 7, Tue |
Multiple Sequence Alignment Algorithms Week 5 Lecture Slides Continued |
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Assignment #2 Due date: November 22, 23:55. Submit via ODTU-Class. |
| Week #7 |
Nov 13, Mon Nov 14, Tue |
Phylogenetic trees Lecture Slides |
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| Week #8 |
Nov 20, Mon Nov 21, Tue |
Phylogenetic trees continued. Midterm review on Tuesday Midterm Exam (at 17:40 on Thursday) Sample midterm |
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| Week #9 |
Nov 27, Mon Nov 28, Tue |
Introduction to protein structures Lecture Slides |
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| Week #10 |
Dec 4, Mon Dec 5, Tue |
Protein Structure Prediction Structural Alignment of Proteins Lecture Slides (continued) |
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Assignment #3 Due date: December 19, 23:55. Submit via ODTU-Class. |
| Week #11 |
Dec 11, Mon Dec 12, Tue |
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 #12 |
Dec 18, Mon Dec 19, Tue |
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 21, 23:55. Submit via ODTU-Class. |
| Week #13 |
Dec 25, Mon Dec 26, Tue |
Analysis of biological networks Lecture Slides |
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| Week #14 |
Jan 1, Mon Jan 2, Tue |
No class on Monday. New Year's first day. Final review on Tuesday. |
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