Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Edited by Russ Altman, Timothy L. Bailey, Philip Bourne, Michael Gribskov, Thomas Lengauer, Ilya N. Shindyalov, Lynn F. Ten Eyck, and Helge Weissig
August 16–23, 2000, La Jolla, California. Published by The AAAI Press, Menlo Park, California. This proceedings is available in book format.
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Contents
ISMB Organization / vii
ISMB Sponsors / ix
ISMB Invited Talks / ix
Preface / x
Philip E. Bourne and Michael Gribskov
Invited Talks / xi
Gerald M. Edelman, Leroy Hood, Minoru Kanehisa, J. Andrew McCammon, Gene Myers, David B. Searls, Harold A. Scheraga
The Conserved Exon Method for Gene Finding / 3
Vineet Bafna and Daniel H. Huson, Celera Genomics Corporation
Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling / 13
Chris Bailey-Kellogg, John J. Kelley, III, Cliff Stein, and Bruce Randall Donald, Dartmouth College
Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks / 25
Pierre Baldi and Gianluca Pollastri, University of California, Irvine; Claus A. F. Andersen and Søren Brunak, The Technical University of Denmark
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species / 37
Mathieu Blanchette, Benno Schwikowski, and Martin Tompa, University of Washington
Robust Parametric and Semi-Parametric Spot Fitting for Spot Array Images / 46
Norbert Brändle, Horng-Yang Chen, and Horst Bischof, Vienna University of Technology; and Hilmar Lapp, Novartis Research Institute Vienna
Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars / 57
Michael P. S. Brown, HNC
Regulatory Element Detection Using a Probabilistic Segmentation Model / 67
Harmen J. Bussemaker, University of Amsterdam; Hao Li, University of California, Irvine,; and Eric D. Siggia, The Rockefeller University
Analysis of Gene Expression Microarrays for Phenotype Classification / 75
Andrea Califano, Gustavo Stolovitzky, and Yuhai Tu, IBM T. J. Watson Research Center
Efficient Attractor Analysis Based on Self-Dependent Subsets of Elements--An Application to Signal Transduction Studies / 86
Maura Cárdenas-García and Jaime Lagúnez-Otero, UNAM Ciudad Universitaria; and Nikolai Korneev, Instituto Nacional de Astrofisica Optica y Electrónica
Biclustering of Expression Data / 93
Yizong Cheng and George M. Church, Harvard Medical School
A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data / 104
Mary E. Cosner, The Ohio State University; Robert K. Jansen, University of Texas, Austin; Bernard M. E. Moret, University of New Mexico; Linda A. Raubeson, Central Washington University; Li-San Wang, Tandy Warnow, and Stacia Wyman, University of Texas, Austin
A Probabilistic Learning Approach to Whole-Genome Operon Prediction / 116
Mark Craven, David Page, Jude Shavlik, Joseph Bockhorst, and Jeremy Glasner, University of Wisconsin, Madison
Accelerating Protein Classification Using Suffix Trees / 128
Bogdan Dorohonceanu and C. G. Nevill-Manning, Rutgers University
Protein Family Classification Using Sparse Markov Transducers / 134
Eleazar Eskin and William Noble Grundy, Columbia University; and Yoram Singer, Hebrew University
Prediction of the Number of Residue Contacts in Proteins / 146
Piero Fariselli and Rita Casadio, University of Bologna
Integrative Analysis of Protein Interaction Data / 152
M. Fellenberg, K. Albermann, and A. Zollner, Biomax Informatics GmbH; H. W. Mewes, Max-Planck-Institute for Biochemistry; and J. Hani, Biomax Informatics GmbH
Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold / 162
Iddo Friedberg, Tommy Kaplan, and Hanah Margalit, The Hebrew University
Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization / 172
Vanathi Gopalakrishnan, Bruce G. Buchanan, and John M. Rosenberg, University of Pittsburgh
A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations / 183
Dan Gusfield, University of California, Davis
Analysis of Yeast’s ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods / 190
Steven Hampson, Pierre Baldi, Dennis Kibler, and Suzanne B. Sandmeyer, University of California, Irvine
Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data / 202
Ian Holmes, University of California, Berkeley; and William J. Bruno, Los Alamos National Laboratory
Search for a New Description of Protein Topology and Local Structure / 211
Lukasz Jaroszewski and Adam Godzik, The Burnham Institute
UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences / 218
Zhengyan Kan, Warren Gish, Eric Rouchka, Jarret Glasscock, and David States, Washington University
Computation and Visualization of Degenerate Repeats in Complete Genomes / 228
Stefan Kurtz, Enno Ohlebusch, and Chris Schleiermacher, University of Bielefeld; Jens Stoye, German Cancer Reserch Center; and Robert Giegerich, University of Bielefeld
An Evaluation of Ontology Exchange Languages for Bioinformatics / 239
Robin McEntire, SmithKline Beecham Pharmaceuticals; Peter Karp, SRI International; Neil Abernethy, InGenuity; David Benton, SmithKline Beecham Pharmaceuticals; Gregg Helt, University of California, Berkeley; Matt DeJongh, NetGenics; Robert Kent, Ontologos; Anthony Kosky, GeneLogic; Suzanna Lewis, University of California, Berkeley; Dan Hodnett, NetGenics; Eric Neumann, 3rd Millenium; Frank Olken, Lawrence Berkeley Livermore Laboratory; Dhiraj Pathak, SmithKline Beecham Pharmaceuticals; Peter Tarczy-Hornoch, University of Washington; Luca Toldo, Merck KgaA; and Thodoros Topaloglou, GeneLogic
Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images / 251
Robert F. Murphy, Michael V. Boland, and Meel Velliste, Carnegie Mellon University
Spectrum Alignment: Efficient Resequencing by Hybridization / 260
I. Pe'er and R. Shamir, Tel Aviv University
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences / 269
Pavel A. Pevzner and Sing-Hoi Sze, University of Southern California
A Pragmatic Information Extraction Strategy for Gathering Data on Genetic Interactions / 279
Denys Proux, Xerox Research Centre Europe; François Rechenmann, INRIA Rhône-Alpes; and Laurent Julliard, Xerox Research Centre Europe
Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium tuberculosis Strains / 286
Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, and Russ B. Altman, Stanford University
Genomic Fold Assignment and Rational Modeling of Proteins of Biological Interest / 296
J. Michael Sauder and Roland L. Dunbrack, Jr., Fox Chase Cancer Center
CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis / 307
Roded Sharan and Ron Shamir, Tel Aviv University
Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis / 317
Hagit Shatkay, Stephen Edwards, W. John Wilbur, and Mark Boguski, National Center for Biotechnology Information
Alignment of Flexible Protein Structures / 329
Maxim Shatsky, Zipora Y. Fligelman, Ruth Nussinov, and Haim J. Wolfson, Tel Aviv University
A Statistical Method for Finding Transcription Factor Binding Sites / 344
Saurabh Sinha and Martin Tompa, University of Washington
Linear Modeling of Genetic Networks from Experimental Data / 355
E. P. van Someren, L. F. A. Wessels, and M. J. T. Reinders, Delft University of Technology
Sequence Database Search Using Jumping Alignments / 367
Rainer Spang, Duke University; Marc Rehmsmeier and Jens Stoye, German Cancer Research Center
A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy / 376
Yukako Tohsato, Hideo Matsuda, and Akihiro Hashimoto, Osaka University
Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data / 384
Jaak Vilo and Alvis Brazma, European Bioinformatics Institute; Inge Jonassen, University of Bergen; Alan Robinson, European Bioinformatics Institute; Esko Ukkonen, University of Helsinki
Towards a Complete Map of the Protein Space Based on a Unified Sequence and Structure Analysis of All Known Proteins / 395
Golan Yona and Michael Levitt, Stanford University
Analysis of Gene Expression Data with Pathway Scores / 407
Alexander Zien, Robert Küffner, Ralf Zimmer, and Thomas Lengauer, GMD-German National Research Center for Information Technology
Index / 418
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