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.

Jan 5Introduction HW 0
Pairwise sequence alignment
Jan 10Sequence search HW 1HW 0
Multiple sequence alignment
Jan 12Structure alignment
Jan 17Structure prediction HW 2HW 1
Jan 19Microarray clustering
Jan 24Microarray classification
Hidden Markov models HW 3HW 2
Jan 26Sequence motifs
Jan 31Protein design HW 4HW 3
Protein folding
Feb 2Docking
Feb 7Protein interaction networks ProjectHW 4
Feb 9Gene regulatory networks
Feb 14Systems biologyDiscussing 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 16Enzyme designDiscussing 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 2006Proposal
Feb 21Phosphorlyation networksDiscussing Tan et al., "Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases", Science Signaling 2009
Feb 23Nucleic Acid DesignDiscussing 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 28No class
Mar 1Project presentations[Jennifer, Emily, Kevin], [Milka], [Evert], [Rob]
Mar 6Project presentations[Jon Connell], [Jon Guerrette], [Qinxin, Yuting], [Xiaoming]
Mar 8Project presentations[David], [Sandeep]