CS 43/143 | 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
Sept 23	Introduction	Hunter, Intro to molecular biology for the computer scientist Python docs (including tutorial) Cormen et al., Intro to Algorithms, Ch. 15	HW 0
Sept 25	Pairwise sequence alignment	Site: EMBOSS tool Tutorials: Pearson; Reiners Literature: Needleman & Wunsch and Gotoh; Smith & Waterman
Sept 28	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
Sept 30	Multiple sequence alignment	Site: ClustalW Survey: Edgar & Batzoglou Literature: Thompson et al. (ClustalW)
Oct 2	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)
Oct 5	Continued		HW 2	HW 1
Oct 7	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)
Oct 9	Microarray clustering	Microarray (flash animation) Sites: Stanford microarray db, EPCLUST Literature: Eisen et al. (hierarchical); Tamayo et al. (SOM); Alter et al. (SVD)
Oct 12	Continued
Oct 14	Microarray classification	Literature: Golub et al. (voting); Brown et al. (SVM) Surveys: Ressom et al. (phenotype classification); Burges (SVM)	HW 3	HW 2
Oct 16	Hidden Markov models	HMMs: Rabiner Profile HMMs: Eddy; Krogh; Cline et al. Sites: HMMER; SAM
Oct 19	Continued
Oct 21	Sequence motifs	Literature: Bailey & Elkan, ML (MEME); Bailey & Elkan, ISMB (MEME); Dempster et al. (EM) Sites: PROSITE; MEME	HW 4	HW 3
Oct 23	Protein design	Dahiyat & Mayo (DEE-based); Pierce et al. (DEE extension); Kuhlman et al. (Rosetta-based)
Oct 26	No class
Oct 28	Docking	Literature: Sousa et al. (survey); Gabb et al. (FTDock); Norel et al. (geom hashing) Sites: DOCK; AutoDock; FT Dock; ZDock; CAPRI	Project	HW 4
Oct 30	Continued
Nov 2	Protein interaction networks	Signaling: chapter from MBOC Literature: Barabasi & Oltvai (network analysis review); Tong et al. (SH3 analysis); Kelley et al. (PathBlast) Sites: DIP
Nov 4	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.		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