CS 75/175 | Intro to Bioinformatics

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	Hunter, Intro to molecular biology for the computer scientist Python docs (including tutorial) Cormen et al., Intro to Algorithms, Ch. 15	HW 0
	Pairwise sequence alignment	Site: EMBOSS tool Tutorials: Pearson; Reiners Literature: Needleman & Wunsch and Gotoh; Smith & Waterman
Jan 10	Sequence search	Sites: BLAST; FASTA Tutorials: Pearson (more); BLAST Literature: Pearson & Lipman (FASTA); Altschul et al. and Altschul et al. (BLAST)	HW 1	HW 0
	Multiple sequence alignment	Site: ClustalW Survey: Edgar & Batzoglou Literature: Thompson et al. (ClustalW)
Jan 12	Structure alignment	Protein structure: PDB (see education, molecule of month); chapter from MBOC Sites: CATH; SCOP; DALI; CE Literature: Holm & Sander (DALI); Shindyalov & Bourne (CE)

Jan 17	Structure prediction	Sites: CASP; MODELLER and ModBase; fold prediction metaserver; Robetta and Rosetta @ home Literature: Sali & Blundell (MODELLER); Lathrop & Smith (threading); Simons et al. (Rosetta)	HW 2	HW 1
Jan 19	Microarray clustering	Microarray (flash animation) Sites: Stanford microarray db, EPCLUST Literature: Eisen et al. (hierarchical); Tamayo et al. (SOM); Alter et al. (SVD)
Jan 24	Microarray classification	Literature: Golub et al. (voting); Brown et al. (SVM) Surveys: Ressom et al. (phenotype classification); Burges (SVM)
	Hidden Markov models	HMMs: Rabiner Profile HMMs: Eddy; Krogh; Cline et al. Sites: HMMER; SAM	HW 3	HW 2
Jan 26	Sequence motifs	Literature: Bailey & Elkan, ML (MEME); Bailey & Elkan, ISMB (MEME); Dempster et al. (EM) Sites: PROSITE; MEME
Jan 31	Protein design	Dahiyat & Mayo (DEE-based); Pierce et al. (DEE extension); Kuhlman et al. (Rosetta-based)	HW 4	HW 3
	Protein folding	Lindroff-Larsen et al. (DESHAW); Voelz et al. (Folding@HOME); Bowman et al. (Pande, folding review)
Feb 2	Docking	Literature: Sousa et al. (survey); Gabb et al. (FTDock); Norel et al. (geom hashing) Sites: DOCK; AutoDock; FT Dock; ZDock; CAPRI
Feb 7	Protein interaction networks	Signaling: chapter from MBOC Literature: Barabasi & Oltvai (network analysis review); Tong et al. (SH3 analysis); Kelley et al. (PathBlast) Sites: DIP	Project	HW 4
Feb 9	Gene regulatory networks	Regulation: chapter from MBOC Bayes nets: Heckerman; Koller et al.; Murphy Literature: Tavazoie et al.; Segal et al. and Segal et al.
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]