(Note: check here for the assignments and labs)
| Week | Topics (lectures) | Notes |
| 1 |
Mon 8/27: Brief overview of the course Wed 8/29: Math primer & database primer |
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| 2 |
Primers for pairwise alignment (basics of algorithms and big O annotation) Paper reading: selected from Bioinformatics Journal |
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| 3 |
Mon 9/10: Edit distance & alignment Wed 9/12: Introduction of Entropy Paper reading: What is a gene, post-ENCODE? |
Notes for entropy |
| 4 |
SW alignment algorithm (metric distance, scoring matrix, log odd) Paper reading: A reality check for alignments and trees |
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| 5 |
Mon 9/24: RNA folding 1 Wed 9/27: RNA folding 2 Paper reading: The Consensus Coding Sequences of Human Breast and Colorectal Cancers and the rebutal papers |
RNA folding lecture 1 RNA folding lecture 2 |
| 6 |
BLAST (5 programs, E-value calculation) Paper reading: A Study of Accessible Motifs and RNA Folding Complexity |
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| 7 |
Paper reading 1: A Human Protein-Protein Interaction Network Paper reading 2: Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia |
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| 8 |
Mon 10/15: Probability calculation (Z-score, P-value) Wed 10/17: Multiple sequence alignment (MSA) Paper reading: Functional Representation of Enzymes by Specific Peptides |
MSA lecture T-coffee paper |
| 9 | Mon 10/22: Sequence database searching |
Database search lecture |
| 10 |
Mon 10/29: Phylogeny 1 Wed 10/31: Phylogeny 2 |
Phylogeny lecture 1 Phylogeny lecture 2 NJ paper 1 NJ paper 2 |
| 11 |
Mon 11/5: Gene prediction Wed 11/7: Daphnia genome annotation (invited speaker: John Colbourne) Thur 11/8: Take-home midterm exam posted |
Gene prediction Mount Chapter 9 |
| 12 |
Mon 11/12: Answering midterm questions Wed 11/14: Introduction of Markov process Paper reading: The Genome of the Sea Urchin Strongylocentrotus purpuratus (NO writeup assigned) |
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| 13 |
Mon 11/19: Basics of protein bioinformatics and structural bioinformatics Wed 11/21: No class because of Thanksgiving Paper reading: High-resolution structure prediction and the crystallographic phase problem (it's a very recent research article on protein structure prediction; by David Baker) (NO writeup assigned) |
Lecture slides Mount Chapter 10 |
| 14 |
Mon 11/26: Protein function annotation Wed 11/28: |
Function annotation lecture slides |
| 15 |
Mon 12/3: Microarray data analysis Wed 12/5: |
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