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 |
---|---|---|---|---|
Jan 5 | Introduction |
| HW 0 | |
Pairwise sequence alignment |
| |||
Jan 10 | Sequence search |
| HW 1 | HW 0 |
Multiple sequence alignment |
| |||
Jan 12 | Structure alignment |
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Jan 17 | Structure prediction |
| HW 2 | HW 1 |
Jan 19 | Microarray clustering |
| ||
Jan 24 | Microarray classification |
| ||
Hidden Markov models | HW 3 | HW 2 | ||
Jan 26 | Sequence motifs |
| ||
Jan 31 | Protein design |
| HW 4 | HW 3 |
Protein folding |
| |||
Feb 2 | Docking |
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Feb 7 | Protein interaction networks |
| Project | HW 4 |
Feb 9 | Gene regulatory networks |
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Feb 14 | Systems biology | Discussing Ideker et al., "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network", Science 2001 and di Bernardo et al., "Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks", Nature Biotechnology 23, 377 - 383 (2005). | ||
Feb 16 | 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 | Proposal | |
Feb 21 | Phosphorlyation networks | Discussing Tan et al., "Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases", Science Signaling 2009 | ||
Feb 23 | Nucleic Acid Design | Discussing Venkatraman et al., "Selective cell death mediated by small conditional RNAs", PNAS, 2010 and Dirks et al., "Paradigms for computational nucleic acid design", Nucleic Acids Res, 2004. | ||
Feb 28 | No class | |||
Mar 1 | Project presentations | [Jennifer, Emily, Kevin], [Milka], [Evert], [Rob] | ||
Mar 6 | Project presentations | [Jon Connell], [Jon Guerrette], [Qinxin, Yuting], [Xiaoming] | ||
Mar 8 | Project presentations | [David], [Sandeep] |