CS 88/188 (Bioinformatics), Fall 2005: Schedule
 
This page will be updated daily to weekly regarding current/upcoming topics. The details are subject to change and are provided without warranty. I typically provide pointers to much more material than is needed; read what you find useful in following up on the lectures. I welcome additional pointers -- please email me or post directly on the class message board.
 
DateLabTopicReading
Sept.220 Course overview and introduction AI and Molecular Biology, Ch. 1
CLRS, Ch. 15
Python documentation
Michael Fromberger's Python intro
27 Pairwise sequence alignment Pearson's ISMB-00 tutorial
Tompa's lecture notes
PSC tutorial
Classic papers: Smith and Waterman; Needleman and Wunsch; Gotoh
BLAST: Altshcul et al., JMB, 1990 (classic papers archive); Altschul et al., NAR, 1997 (paper)
FASTA: Pearson and Lipman, PNAS, 1988 (paper)
29 No class; Sara will be in the lab
Sequence
Oct.41 Hidden Markov models Cline, Barrett, Karplus, ISMB-99 tutorial
Krogh, "An introduction to hidden Markov models for biological sequences" (paper)
Eddy, "Profile hidden Markov models", Bioinformatics, 1998 (paper)
Rabiner, "A tutorial on hidden Markov models and selected applications in speech recognition", Proc. IEEE, 1989 (paper)
Software (and more papers): SAM and HMMER
6 Multiple sequence alignment and phylogeny Tree of Life
Phylip software and links to many more
ClustalW: Thompson, Higgins, Gibson, "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment...", NAR, 1994 (paper)
112 Sequence motifs Lawrence et al., "Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment", Science, 1993 (paper)
Lawrence, Overview of the Gibbs Motif Sampler
Bailey and Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proc. ISMB, 1994 (paper) and other papers
Dempster, Laird, Rubin, "Maximum likelihood from incomplete data via the EM algorithm", J. Royal Statistical Society B, 1977 (paper)
Farid, "Fundamentals of Image Processing", description of and Matlab example for EM
MEME software
PROSITE database
13 Genome analysis GLIMMER: Salzberg et al., "Microbial gene identification using interpolated Markov models," NAR, 1998 (paper)
GenScan: Burge and Karlin, "Prediction of complete gene structures in human genomic DNA," J. Mol. Biol., 1997 (paper)
MUMmer: Delcher et al., "Alignment of whole genomes", NAR, 1999 (paper)
Some suffix tree stuff: intro and demo; overview; links; Gusfield's software
18 Lab presentations (1-2)
Structure
203 Structure comparison Various protein structure tutorials by EXPASY, Birkbeck
PDB: molecule of the month; education
Holm and Sander, "Mapping the protein universe", Science, 1996 (paper)
Shindyalov and Bourne, "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path", Protein Engineering, 1998 (paper)
Murzin et al., "SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 1995 (paper)
Web sites: DALI/FSSP, CE, SCOP
CVonline has a section on pose estimation (e.g. 3D-3D); so does the Kwon3D Motion Analaysis Web (rotation matrices)
25 Docking Ewing and Kuntz, "Critical evaluation of search algorithms for automated molecular docking and database screening", J. Comp. Chem., 1997 (paper)
Ewing, Makino, Skillman, and Kuntz, "DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases," J. CAMD, 2001 (paper)
Gabb, Jackson, and Sternberg, "Modelling protein docking using shape complementarity, electrostatics and biochemical information", JMB, 1997 (paper)
Chen and Weng, "A novel shape complementarity scoring function for protein-protein docking", Proteins, 2003 (paper)
Halperin, Ma, Wolfson, Nussinov, "Principles of docking: An overview of search algorithms and a guide to scoring functions", Proteins, 2002 (paper)
Some geometric hashing papers: Proteins, 1999, Wolfson's archive (e.g. Salzberg book chapter and IEEE CiSE)
Example software: DOCK, AutoDock, FT Dock, ZDock
CAPRI prediction website
274 Structure prediction Viewpoint: Baker and Sali, "Protein structure prediction and structural genomics", Science, 2001 (paper)
Survey: Marti-Renom et al., "Comparative protein structure modeling of genes and genomes", Annu. Rev., 2000 (paper)
Sali and Blundell, "Comparative protein modelling by satisfaction of spatial restraints", JMB, 1993 (paper)
Lathrop and Smith, "Global optimum protein threading with gapped alignment and empirical pair score functions", JMB, 1996 (paper)
Simons, Kooperberg, Huang, and Baker, "Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions", JMB, 1997 (paper)
Bystroff and Baker, "Prediction of local structure in proteins using a library of sequence-structure motifs", JMB, 1998 (paper)
Bystroff, Thorsson, and Baker, "HMMSTR: a hidden markov model for local sequence-structure correlations in proteins", JMB, 2000 (paper)
Homology modelers: MODELLER, Swiss-model
Fold prediction meta-server, with links to other fold recognition servers
I-Sites/HMMSTR/Rosetta server
CASP web page
Nov.1 Protein design Lovell et al., "The Penultimate Rotamer Library", Proteins, 2000: paper, web page
Dahiyat and Mayo, "De novo protein design: fully automated sequence selection," Science, 1997 (paper)
Pierce, Spriet, Desmet, and Mayo. "Conformational splitting: a more powerful criterion for dead-end elimination," J. Comp. Chem., 2000 (paper)
Voigt, Gordon, and Mayo, "Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design," JMB, 2000 (paper)
Koehl and Delarue, "Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy," JMB, 1994 (paper)
Looger, Dwyer, Smith, and Hellinga, "Computational design of receptor and sensor proteins with novel functions", Nature, 2003 (paper)
Lilien, Stevens, Anderson, and Donald, "A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase A phenylalanine adenylation enzyme", J. Comp. Biol., 2005 (paper)
3 Lab presentations (3-4)
Function
85 Microarray data analysis Eisen et al., "Cluster analysis and display of genome-wide expression patterns", PNAS, 1998 (paper)
Tamayo et al., "Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoetic differentiation", PNAS, 1999 (paper)
Valafar, "Pattern recognition techniques in microarray data analysis: a survey", Annals of NYAS, 2002 (paper)
Tavazoie et al., "Systematic determination of genetic network architecture", Nature Genetics, 1999 (paper)
Segal et al., "Genome-wide discovery of transcriptional modules from DNA sequence and gene expression", Bioinformatics, 2003 (paper)
Segal et al., "Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data", Nature Genetics, 2003 (paper)
Bayes net tutorials: Heckerman, Murphy, Moore, selections from Jordan's book
SOM toolbox for Matlab
Example software (and data): Eisen, ExpressionProfiler, Stanford microarray database
Flash animation of DNA microarray technology
10 Microarrays, part 2 Golub et al., "Molecular classification of cancer: class discovery and class prediction by gene expression monitoring", Science, 1999 (paper; website)
Brown et al., "Knowledge-based analysis of microarray gene expression data by using support vector machines", PNAS, 2000 (paper; website)
Burges, "A tutorial on support vector machines for pattern recognition", Data Mining and Knowledge Discovery, 1998 (paper). Other tutorials available at kernel-machines.org
Alter, Brown, and Botstein, "Singular value decomposition for genome-wide expression data processing and modeling", PNAS, 2000 (paper)
156 Interaction networks Tong et al., "A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules", Science, 2002 (paper)
Interaction data papers: Ho et al. (mass spec): Nature 2002; Ito et al. (two hybrid) PNAS 2001; Uetz et al. (two hybrid): Nature 2000
Databases: BIND, DIP, etc.
Jeong et al., "Lethality and centrality in protein networks", Nature, 2001 (paper)
Goldberg and Roth, "Assessing experimentally derived interactions in a small world", PNAS, 2003 (paper)
Watts and Strogatz, "Collective dynamics of 'small-world' networks", Nature, 1998 (paper)
Newman, "The structure and function of complex networks", SIAM Review, 2003 (paper)
Sharan et al., "Conserved patterns of protein interaction in multiple species", PNAS, 2005 (paper)
Kelley et al., "Conserved pathways within bacteria and yeast as revealed by global protein network alignment", PNAS, 2003 (paper)
Scott et al., "Efficient algorithms for detecting signaling pathways in protein interaction networks", Proc. RECOMB 2005 (paper)
17 Proteomics and systems biology Aebersold, Mann, "Mass spectrometry-based proteomics", Nature, 2003 (paper)
Mann, Hendrickson, Pandey, "Analysis of proteins and proteomes by mass spectrometry", Annual Reviews, 2001 (paper)
Some MS tutorials: Scripps, Leeds, Davidson
Example MS software: Protein Prospector, PeptideMass, PROWL
Potluri et al., "Geometric analysis of cross-linkability for protein fold discrimination", Proc. Pacific Symposium on Biocomputing (PSB), 2004 (paper)
Ye et al., "Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure", Protein Sci., 2004 (paper)
Lilien, Farid, Donald, "Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum", J. Comp. Biol., 2003 (paper)
Ideker et al., "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network," Science, 2001 (paper)
Ideker, Galitski, and Hood, "A new approach to decoding life: systems biology", Annu. Rev. Genomics Hum. Genet., 2001 (paper)
The Institute for Systems Biology
22 Lab time
29 Lab presentations (5-6)
Bonus
Dec.1 Research in bioinformatics Short presentations by Shobha, Xiaoduan, John, Fei, Michal
 
CS 88/188 CS 88/188
Chris Bailey-Kellogg
Last modified: Wed Nov 16 11:20:57 EST 2005