This page will be updated regularly with current/upcoming topics. Notes will be provided for each class, linked from the date. Notes and some materials are password-restricted with your Dartmouth login (DND). Feedback is appreciated—typos and broken links, suggestions for more detailed explanations, pointers to supporting materials on the web, etc.
| Date | Topics | References | Out | Due |
|---|---|---|---|---|
| Sept 23 | Introduction |
| HW 0 | |
| Sept 25 | Pairwise sequence alignment |
| ||
| Sept 28 | Sequence search |
| HW 1 | HW 0 |
| Sept 30 | Multiple sequence alignment |
| ||
| Oct 2 | Structure alignment |
| ||
| Oct 5 | Continued | HW 2 | HW 1 | |
| Oct 7 | Structure prediction |
| ||
| Oct 9 | Microarray clustering |
| ||
| Oct 12 | Continued | |||
| Oct 14 | Microarray classification |
| HW 3 | HW 2 |
| Oct 16 | Hidden Markov models | |||
| Oct 19 | Continued | |||
| Oct 21 | Sequence motifs |
| HW 4 | HW 3 |
| Oct 23 | Protein design |
| ||
| Oct 26 | No class | |||
| Oct 28 | Docking |
| Project | HW 4 |
| Oct 30 | Continued | |||
| Nov 2 | Protein interaction networks |
| ||
| Nov 4 | Gene regulatory networks |
| Proposal | |
| Nov 6 | No class | |||
| Nov 9 | Continued | |||
| Nov 11 | Colloquium | Andy Kern speaking at 4:30 in Steele 006: "The tortoise and the hare: finding the targets of selection in genomes" | ||
| Nov 13 | Systems biology | Discussing Ideker et al., "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network", Science 2001 | ||
| Nov 16 | Next-gen sequencing | Discussing Langmead et al., "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome", Genome Biology 2009 (be sure to read additional file; see also BWT background) | Update | |
| Nov 18 | Enzyme design | Discussing Jiang et al., "De novo computational design of retro-aldol enzymes", Science 2008 and Zanghellini et al., "New algorithms and an in silico benchmark for computational enzyme design", Protein Science 2006 | ||
| Nov 20 | Phosphorlyation networks | Discussing Tan et al., "Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases", Science Signaling 2009 | ||
| Nov 30 | Project presentations | Dan; Hao/Lei/Wenyu; Richard; Rui/Zhifei | ||
| Dec 1 [x] | Project presentations | Dan/Dov/Igor; Jen/John/Morgon; John/Jyo | ||
| Dec 2 | Project presentations | Hannah; Jingzhou/Xiaoyu; Lu/Tuobin; Rouslan; Senate |