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Home / Proceedings / Proceedings of the Twentieth International Conference on Machine Learning, 2000 /

Book One

Contents

  • CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis

    Roded Sharan and Ron Shamir, Tel Aviv University

    PDF
  • A Statistical Method for Finding Transcription Factor Binding Sites

    Saurabh Sinha and Martin Tompa, University of Washington

    PDF
  • Towards a Complete Map of the Protein Space Based on a Unified Sequence and Structure Analysis of All Known Proteins

    Golan Yona and Michael Levitt, Stanford University

    PDF
  • Biclustering of Expression Data

    Yizong Cheng and George M. Church, Harvard Medical Schoo

    PDF
  • The Conserved Exon Method for Gene Finding

    Vineet Bafna and Daniel H. Huson, Celera Genomics Corporation

    PDF
  • Protein Family Classification Using Sparse Markov Transducers

    Eleazar Eskin and William Noble Grundy, Columbia University; and Yoram Singer, Hebrew University

    PDF
  • Spectrum Alignment: Efficient Resequencing by Hybridization

    I. Pe'er and R. Shamir, Tel Aviv University

    PDF
  • A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy

    Yukako Tohsato, Hideo Matsuda, and Akihiro Hashimoto, Osaka University

    PDF
  • Integrative Analysis of Protein Interaction Data

    M. Fellenberg, K. Albermann, and A. Zollner, Biomax Informatics GmbH; H. W. Mewes, Max-Planck-Institute for Biochemistry; and J. Hani, Biomax Informatics GmbH

    PDF
  • Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks

    Pierre Baldi and Gianluca Pollastri, University of California, Irvine; Claus A. F. Andersen and Søren Brunak, The Technical University of Denmark

    PDF
  • An Evaluation of Ontology Exchange Languages for Bioinformatics

    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

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  • A Probabilistic Learning Approach to Whole-Genome Operon Prediction

    Mark Craven, David Page, Jude Shavlik, Joseph Bockhorst, and Jeremy Glasner, University of Wisconsin, Madison

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  • Index

    David Hamilton

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  • Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold

    Iddo Friedberg, Tommy Kaplan, and Hanah Margalit, The Hebrew University

    PDF
  • An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species

    Mathieu Blanchette, Benno Schwikowski, and Martin Tompa, University of Washington

    PDF
  • Analysis of Yeast’s ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods

    Steven Hampson, Pierre Baldi, Dennis Kibler, and Suzanne B. Sandmeyer, University of California, Irvine

    PDF
  • Efficient Attractor Analysis Based on Self-Dependent Subsets of Elements–An Application to Signal Transduction Studies

    Maura Cárdenas-García and Jaime Lagúnez-Otero, UNAM Ciudad Universitaria; and Nikolai Korneev, Instituto Nacional de Astrofisica Optica y Electrónica

    PDF
  • Alignment of Flexible Protein Structures

    Maxim Shatsky, Zipora Y. Fligelman, Ruth Nussinov, and Haim J. Wolfson, Tel Aviv University

    PDF
  • Analysis of Gene Expression Microarrays for Phenotype Classification

    Andrea Califano, Gustavo Stolovitzky, and Yuhai Tu, IBM T. J. Watson Research Center

    PDF
  • Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis

    Hagit Shatkay, Stephen Edwards, W. John Wilbur, and Mark Boguski, National Center for Biotechnology Information

    PDF
  • Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data

    Jaak Vilo and Alvis Brazma, European Bioinformatics Institute; Inge Jonassen, University of Bergen; Alan Robinson, European Bioinformatics Institute; Esko Ukkonen, University of Helsinki

    PDF
  • Analysis of Gene Expression Data with Pathway Scores

    Alexander Zien, Robert Küffner, Ralf Zimmer, and Thomas Lengauer, GMD-German National Research Center for Information Technology

    PDF
  • A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data

    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

    PDF
  • Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images

    Robert F. Murphy, Michael V. Boland, and Meel Velliste, Carnegie Mellon University

    PDF
  • Robust Parametric and Semi-Parametric Spot Fitting for Spot Array Images

    Norbert Brändle, Horng-Yang Chen, and Horst Bischof, Vienna University of Technology; and Hilmar Lapp, Novartis Research Institute Vienna

    PDF
  • Accelerating Protein Classification Using Suffix Trees

    Bogdan Dorohonceanu and C. G. Nevill-Manning, Rutgers University

    PDF
  • Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization

    Vanathi Gopalakrishnan, Bruce G. Buchanan, and John M. Rosenberg, University of Pittsburgh

    PDF
  • Linear Modeling of Genetic Networks from Experimental Data

    E. P. van Someren, L. F. A. Wessels, and M. J. T. Reinders, Delft University of Technology

    PDF
  • Genomic Fold Assignment and Rational Modeling of Proteins of Biological Interest

    J. Michael Sauder and Roland L. Dunbrack, Jr., Fox Chase Cancer Center

    PDF
  • UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences

    Zhengyan Kan, Warren Gish, Eric Rouchka, Jarret Glasscock, and David States, Washington University

    PDF
  • A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations

    Dan Gusfield, University of California, Davis

    PDF
  • Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars

    Michael P. S. Brown, HNC

    PDF
  • Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling

    Chris Bailey-Kellogg, John J. Kelley, III, Cliff Stein, and Bruce Randall Donald, Dartmouth College

    PDF
  • Prediction of the Number of Residue Contacts in Proteins

    Piero Fariselli and Rita Casadio, University of Bologna

    PDF
  • Search for a New Description of Protein Topology and Local Structure

    Lukasz Jaroszewski and Adam Godzik, The Burnham Institute

    PDF
  • Combinatorial Approaches to Finding Subtle Signals in DNA Sequences

    Pavel A. Pevzner and Sing-Hoi Sze, University of Southern California

    PDF
  • Preface

    Philip E. Bourne and Michael Gribskov

    PDF
  • Computation and Visualization of Degenerate Repeats in Complete Genomes

    Stefan Kurtz, Enno Ohlebusch, and Chris Schleiermacher, University of Bielefeld; Jens Stoye, German Cancer Reserch Center; and Robert Giegerich, University of Bielefeld

    PDF
  • A Pragmatic Information Extraction Strategy for Gathering Data on Genetic Interactions

    Denys Proux, Xerox Research Centre Europe; François Rechenmann, INRIA Rhône-Alpes; and Laurent Julliard, Xerox Research Centre Europe

    PDF
  • Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium tuberculosis Strains

    Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, and Russ B. Altman, Stanford University

    PDF
  • Sequence Database Search Using Jumping Alignments

    Rainer Spang, Duke University; Marc Rehmsmeier and Jens Stoye, German Cancer Research Center

    PDF
  • Regulatory Element Detection Using a Probabilistic Segmentation Model

    Harmen J. Bussemaker, University of Amsterdam; Hao Li, University of California, Irvine,; and Eric D. Siggia, The Rockefeller University

    PDF
  • Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data

    Ian Holmes, University of California, Berkeley; and William J. Bruno, Los Alamos National Laboratory

    PDF

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