Book One

Contents

• GeneExpress: A Computer System for Description, Analysis, and Recognition of Regulatory Sequences in Eukaryotic Genome

  Nikolay Kolchanov, Mikhail Ponomarenko, Alexander Kel, Yury Kondrakhin, Anatoly Frolov, Fedor Kolpakov, Tatyana Goryachkovsky, Olga Kel, Elena Ananko, Elena Ignatieva, Olga Podkolodnaya, Vladimir. Babenko, Irina Stepanenko, Ada Romashchenko, Tatyana Merkulova, Denis Vorobiev, Sergey Lavryushev, Yulia Ponomarenko, Alexay Kochetov, Gregory Kolesov, Victor Solovyev, Luciano Milanesi, Nikolay Podkolodny, Edgar Wingender, and Thomas Heinemeyer

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• Advanced Query Mechanisms for Biological Databases

  M Markowitz Chen, I-Min A.; Kosky, Anthony; Szeto, Ernest; Topaloglou, Thodoros

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• The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection

  Pankaj Agarwal and Vineet Bafna

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• Identification of Divergent Functions in Homologous Proteins by Induction over Conserved Modules

  Imran Shah and Lawrence Hunter

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• Segment-Based Scores for Pairwise and Multiple Sequence Alignments

  Burkhard Morgenstern, William R. Atchley, Klaus Hahn, and Andreas Dress

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• Hierarchical Minimization with Distance and Angle Constraints

  John R. Gunn

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• Genetic Algorithms for Protein Threading

  Jacqueline Yadgari, Amihood Amir and Ron Unger

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• Modeling Protein Homopolymeric Repeats: Possible Polyglutamine Structural Motifs For Huntington’s Disease

  Richard H. Lathrop, Malcolm Casale, Douglas J. Tobias, J. Lawrence Marsh, and Leslie M. Thompson

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• Computational Applications of DNA Structural Scales

  Pierre Baldi, Søren Brunak, Yves Chauvin, and Anders Gorm Pedersen

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• Preface

  Janice Glasgow, Terry Gaasterland, Richard Lathrop, Tim Littlejohn, François Major, Manuel Peitsch. Christoph Sensen, David Sankoff

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• A Surface Measure for Probabilistic Structural Computations

  Jeanette P. Schmidt, Cheng C. Chen, Jonathan L. Cooper, and Russ B. Altman

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• The LabFlow System for Workflow Management in Large Scale Biology Research Laboratories

  Nathan Goodman, Steve Rozen, Lincoln D. Stein

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• A Computational System for Modeling Flexible Protein-Protein and Protein-DNA Docking

  J. E Sternberg, Patrick Aloy, Henry A. Gabb, Richard M. Jackson, Gidon Moont, Enrique Querol, Francesc X Aviles

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• Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis

  Eric C. Rouchka and David J. States,

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• A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences

  Erik L. L. Sonnhammer, Gunnar von Heijne, and Anders Krogh

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• Calculating the Exact Probability of Language-Like Patterns in Biomolecular Sequences

  Kevin Atteson

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• IMGT/LIGM-DB: A Systematized Approach for ImMunoGeneTics Database Coherence and Data Distribution Improvement

  Véronique Giudicelli, Denys Chaume, and Marie-Paule Lefranc

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• Automated Clustering and Assembly of Large EST Collections

  David P. Yee and Darrell Conklin

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• A Map of the Protein Space – An Automatic Hierarchical Classification of All Protein Sequences

  Golan Yona, Nathan Linial, Naftali Tishby, and Michal Linial

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• A Statistical Theory of Sequence Alignment with Gaps

  Dirk Drasdo, Terence Hwa, and Michael Lässig

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• Compression of Strings with Approximate Repeats

  L. Allison, T. Edgoose and T. I. Dix

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• Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model

  Henrik Nielsen and Anders Krogh

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• Bayesian Protein Family Classifier

  Kunbin Qu, Lee Ann McCue, and Charles E. Lawrence

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• BioSim – A New Qualitative Simulation Environment for Molecular Biology

  Karsten R. Heidtke and Steffen Schulze-Kremer

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• Phylogenetic Inference in Protein Superfamilies: Analysis of SH2 Domains

  Kimmen Sjölander

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