| Date | Topic | Readings | Notes |
|---|---|---|---|
|
Background |
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| 8/25 Thu | Course policies (ppt), Overview of Bioinformatics (ppt ) | ||
| 8/30 Tue | Essential CS & Statistics (ppt) | 2.1-2.10 | |
| 9/1 Thu | Essential Molecular Biology (ppt, Animations)) | 3.1-3.11, Hunter's Book Chapter | |
| 9/6 Tue | Overview of Biological Databases (ppt) | Public DB Survey GenBank NCBI Science Primer | Assign #1 out |
|
Genome Sequencing |
|||
| 9/8 Thu | DNA Sequencing (ppt) | 8.6-8.8 | |
| 9/13 Tue | Whole Genome Sequencing (ppt) | Batzoglou's review, Kim's review | Assign #1 due Assign #2 out |
|
Gene Identification |
|||
| 9/15 Thu | Gene Prediction: Similarity-based Approaches (ppt) | 6.11-6.14 | |
| 9/20 Tue | Gene Prediction: Statistical Approaches (ppt) | 6.11-6.14 | Assign #2 due |
|
Sequence Alignment |
|||
| 9/22 Thu | Pairwise sequence alignment (I) (ppt) | 6.4-6.9 | Assign #3 out |
| 9/27 Tue | Pairwise sequence alignment (II) (ppt) | 6.4-6.9 | |
| 9/29 Thu | Pairwise sequence alignment (III)(ppt) | 6.10, BLOSUM note | Assign #3 Due |
| 10/4 Tue | Multiple sequence alignment (I) (ppt) | 6.10 | Assign #4 out |
| 10/6 Thu | Multiple sequence alignment (II) (ppt) | 6.10 | |
| 10/11 Tue | Midterm | Topics to be covered | Assign #4 due |
|
Gene Function Analysis |
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| 10/13 Thu | Microarray data analysis (I) (ppt) | 10.1-10.4 | |
| 10/18 Tue | Microarray data analysis (II) (ppt) | 10.1-10.4 | |
| 10/20 Thu | Regulatory motif finding (I) (ppt) | 4.4-4.9 | |
| 10/25 Tue | Regulatory motif finding (II) (ppt) | 4.4-4.9 | |
|
Hidden Markov Models |
|||
| 10/27 Thu | General Introduction to HMMs (I) (ppt) | 11.1-11.5, HMM note(pdf) | Assign #5 out |
| 11/1 Tue | General Introduction to HMMs (II) (ppt) | 11.1-11.5, HMM note(pdf) | |
| 11/3 Thu | General Introduction to HMMs (III) (ppt) | 11.1-11.5, HMM note(pdf) | |
| 11/8 Tue | HMM Applications (ppt) | 11.1-11.5 | |
| 11/10 Thu | Profile HMMs (ppt) | Assign #5 due; Assign #6 out | |
|
Protein sequencing |
|||
| 11/15 Tue | Protein sequencing (I) (ppt) | 8.10-8.15, [Aebersold1 & Mann 2003] | |
| 11/17 Thu | Protein sequencing (II) (ppt) | 8.10-8.15 , [Aebersold1 & Mann 2003] | |
| 11/22 Tue | Thanksgiving (No class) | ||
| 11/24 Thu | Thanksgiving (No class) | ||
|
Comparative genomics and evolutionary analysis |
|||
| 11/29 Tue | Phylogenetic tree construction (I) (ppt) | 10.5 -10.11 | Assign #6 due |
| 12/1 Thu | Phylogenetic tree construction (II) (ppt) | 10.5 -10.11 | Assign #7 out |
| 12/6 Tue | Genome rearrangements (ppt) | 5.1-5.5 | |
| 12/8 Thu | Review for final (ppt) | Topics to be covered in final | Assign #7 due |
| 12/10 Sat | Reading Day | ||
| 12/13, Tue | Final Exam at 7-10pm, in SC 1302 | ||
| 12/17, Sat | Project report due | For students registered for 4 credit hours only | Email the report to the instructor czhai AT cs.uiuc.edu |