CS 43/143 | Intro to Bioinformatics

Date	Topics	References	Out	Due
Mar 25	Intro to course, alignment, and python	Hunter, Introduction to molecular biology for the computer scientist CLRS, Introduction to Algorithms, Ch. 15 Python docs	HW 0
Mar 27	Pairwise sequence alignment	General tutorial by Pearson BLAST \| tutorial Literature: Needleman & Wunsch and Gotoh; Smith & Waterman; Pearson & Lipman (FASTA); Altschul et al. and Altschul et al. (BLAST)
Apr 1	Hidden Markov models	Eddy, "Profile hidden Markov models" Krogh, "An introduction to hidden Markov models for biological sequences" Tutorial by Cline, Barrett, and Karplus Rabiner, "A tutorial on hidden Markov models and selected applications in speech recognition"	HW 1	HW 0
Apr 3	Structure alignment	Protein structure: PDB (see education, molecule of month); chapter from MBOC Literature: Holm & Sander (DALI); Shindyalov & Bourne (CE); Ye & Godzik (FATCAT) Sites: CATH; SCOP; DALI; CE; FATCAT
Apr 8	Structure prediction	Literature: Sali & Blundell (MODELLER); Lathrop & Smith (threading); Simons et al. (Rosetta); Bystroff & Baker (I-Sites); Bystroff, Thorsson, & Baker (HMMSTR) Sites: CASP; MODELLER and ModBase; fold prediction metaserver; Robetta and Rosetta @ home	HW 2	HW 1
Apr 10	DNA Microarrays	Microarrays (flash animation) Literature: Eisen et al. (hierarchical); Tamayo et al. (SOM); Cheng & Church (bicluster); Alter et al. (SVD)
Apr 15	No class	Protein Structure Initiative "Bottlenecks"
Apr 17	Phenotype classification	Literature: Golub et al. (microarray, voting); Brown et al. (microarray, SVM); Lilien, Farid, & Donald (proteomics, PCA/FLD) Surveys: Ressom et al. (phenotype classification); Burges (SVM); Mann et al. (proteomics)	HW 3	HW 2
Apr 22	Sequence motifs	Literature: Rigoutsos & Floratos (Teiresias), Bailey & Elkan (MEME); Dempster et al. (EM) Sites: PROSITE; MEME
Apr 24	Phylogeny and multiple sequence alignment	Surveys: Kim & Warnow (phylogeny); Holder & Lewis (phylogeny); Edgar & Batzoglou (MSA) Literature: Thompson et al. (ClustalW) Sites: Tree of Life, ClustalW, Phylip		HW 3
Apr 29	Structure-based protein design	Dahiyat & Mayo (DEE-based); Kuhlman et al. (Rosetta-based); Pierce et al. (DEE extension); Voigt et al. (comparison)
May 1	Docking	Literature: Sousa et al. (survey); Gabb et al. (FTDock); Norel et al. (geom hashing) Sites: DOCK; AutoDock; FT Dock; ZDock; CAPRI
May 6	Midterm
May 8	Protein interaction networks	Signaling: chapter from MBOC Literature: Barabasi & Oltvai (network analysis review); Tong et al. (SH3 analysis); Kelley et al. (PathBlast); Flannick et al. (Graemlin) Sites: DIP	Project
May 13	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.		Project proposal
May 15	Systems biology (paper discussion)	Ideker et al. More at the Institute for Systems Biology	HW 4
May 20	Genome assembly (paper discussion)	Pevzner, Tang, & Waterman Background: Genome sequence assembly primer; human genome project; The Race for the $1000 genome		Project update
May 22	Protein-protein interactions (paper discussion)	Wang et al.; be sure to get the additional files
May 27	Project presentations	Anuj & Sahil Jarman & Riley Jeff & Rob Paopao, Stephanie, & Tom		HW 4
May 29	Project presentations, 110 Moore	Bornika & Himanshu Clea & Jon Evan, Jeff, & Taylor Jeremy & Tiger

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