| Week | Date | Topics | Slides | Readings |
| Week 1 |
Aug 31 (M) | Overview of I519 & Introduction to Bioinformatics |
slides (handout) |
Chapter 1 Molecular biology primer |
| Sep 2 (W) | Introduction to programming with python |
slides (handout) |
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| Sep 4 (F) | Lab 1: Linux and Genbank | link | ||
| Week 2 |
Sep 7 (M) | Algorithm basics |
slides (handout) coin change problem |
Chapter 2 Machine learning in bioinformatics (optional) What is Bayesian statistics? (optional) |
| Sep 9 (W) | Introduction to statistics using R |
slides (handout) |
||
| Sep 11 (F) | Lab 2: SwissProt, IPI, and R | link | ||
| Week 3 |
Sep 14 (M) | Sequence comparison (and edit distance) |
slides (handout) word ladder |
Chapter 3 What is dynamic programming |
| Sep 16 (W) | Pairwise sequence alignment (and SW algorithm) |
slides (handout) |
||
| Sep 18 (F) | Lab 3: regular expression, urllib, etc | link | ||
| Week 4 |
Sep 21 (M) | Pairwise sequence alignment (Cont.) | ||
| Sep 23 (W) | Sequence database searching |
slides (handout) |
Chapter 6 | |
| Sep 25 (F) | Lab 4: Sequence database searching tools - BLAST, etc. | link | ||
| Week 5 |
Sep 28 (M) | Multiple sequence alignment |
slides (handout) |
Chapter 5 ClustalW paper T-Coffee paper |
| Sep 30 (W) | Motif & HMM |
slides (handout) |
||
| Oct 2 (F) | Lab 5: Multiple sequences alignment tools (ClustalW, T-coffee, MUSCLE) | link | ||
| Week 6 |
Oct 5 (M) | Phylogeny |
slides (handout) |
Chapter 7 |
| Oct 7 (W) | Phylogeny (Cont.) | |||
| Oct 9 (F) | Lab 6: Inference of phylogeny (PHYLIP, etc.) | link | ||
| Week 7 |
Oct 12 (M) | Genome sequencing & assembly |
slides (handout) |
Chapter 11 Next-generation sequencing transforms today's biology |
| Oct 14 (W) | Genome sequencing & assembly (Cont.) | |||
| Oct 16 (F) | Lab 7: DNA sequencing and assembly related tools (Phred, Phrap, Velvet, etc.) | link | ||
| Week 8 |
Oct 19 (M) | Gene finding |
slides (handout) |
Chapter 9 |
| Oct 21 (W) | Midterm | |||
| Oct 23 (F) | NO lab | |||
| Week 9 |
Oct 26 (M) | Genome comparison (suffix tree & suffix array) |
slides (handout) |
Chapter 11 |
| Oct 28 (W) | Genome variation and SNP |
slides (handout) |
||
| Oct 30 (F) | Lab 8: Gene predictors & tools for whole genome comparison | link | ||
| Week 10 |
Nov 2 (M) | RNA folding |
slides (handout) |
Chapter 8 |
| Nov 4 (W) | non-coding RNA finding | |||
| Nov 6(F) | Lab 9: RNA folding and RNA gene finding | link | ||
| Week 11 |
Nov 9 (M) | Protein bioinformatics & structural bioinformatics |
slides (handout) |
Chapter 10 A review on protein structure prediction |
| Nov 11 (W) | Protein bioinformatics & structural bioinformatics (Cont. ) | |||
| Nov 13(F) | Lab 10: PDB viewer & Modeller | link | ||
| Week 12 |
Nov 16 (M) | Function annotation |
slides (handout) |
Review 1: Protein function annotation by homology-based inference Review 2: Semantic similarity in biomedical ontologies |
| Nov 18 (W) | Function annotation (Cont.) | |||
| Nov 20(F) | Lab 11: Gene ontology & graphviz | link | ||
| Week 13 |
Nov 23 (M) | Biological pathways & networks (e.g., PPI network) |
slides (handout) |
|
| Nov 25 (W) | Thanksgiving--No class | |||
| Week 14 |
Nov 30 (M) | Transcriptomics and microarray (&a very brief introduction of R) | ||
| Dec 2 (W) | RNA-Seq (& Chip-Seq) | |||
| Week 15 |
Dec 7 (M) | Mass spectrometry in proteomics | ||
| Dec 9 (W) | Biological database & MySQL | |||
| Week 16 |
Dec 16 (W) | Final |