Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Edited by Thomas Lengauer, Reinhard Schneider, Peer Bork, Douglas Brutlad, Janice Glasgow, Hans-Werner Mewes, and Ralf Zimmer
August 6–10, 1999, Heidelberg, Germany. Published by The AAAI Press, Menlo Park, California. This proceedings is available in book format.
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Contents
ISMB Organization / vi
ISMB Sponsors / viii
Preface / ix
Thomas Lengauer, Reinhard Schneider, Peer Bork, Douglas Brutlag, Janice Glasgow, Hans -Werner Mewes, Ralf Zimmer
Invited Talks / xi
Amos Bairoch, Manfred Eigen, Richard M. Karp, Anthony R. Kerlavage, Eugene V. Koonin, Robert J. Lipshutz, Matthias Mann, Michael J. E. Sternberg, Paul A. Bates, Lawrence A. Kelley, Robert M. MacCallum, Arne Müller, Stephen Muggleton, Marcel Turcotte
Crystallographic Threading / 2
A. Ableson and J. I. Glasgow
A Phylogenetic Approach to RNA Structure Prediction / 10
Viatcheslav R. Akmaev, Scott T. Kelley, and Gary D. Stormo
Genomics via Optical Mapping III: Contiging Genomic DNA / 18
Thomas Anantharaman, Bud Mishra, and David Schwartz
Position-Specific Annotation of Protein Function Based on Multiple Homologs / 28
Miguel A. Andrade
Nearest Neighbor Classification in 3D Protein Databases / 34
Mihael Ankerst, Gabi Kastenmüller, Hans-Peter Kriegel, and Thomas Seidl
Reconstructing the Duplication History of a Tandem Repeat / 44
Gary Benson and Lan Dong
Identity by Descent Genome Segmentation Based on Single Nucleotide
Polymorphism Distributions / 54
Thomas W. Blackwell, Eric Rouchka, and David J. States
Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions
/ 60
Christian Blaschke, Miguel A. Andrade, Christos Ouzounis, and Alfonso
Valencia
A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion / 68
Rita Casadio, Mario Compiani, Piero Fariselli, and Pier Luigi
Martelli
Constructing Biological Knowledge Bases by Extracting Information from Text Sources / 77
Mark Craven and Johan Kumlien
INTERACT: An Object Oriented Protein-Protein Interaction Database / 87
Karen Eilbeck, Andy Brass, Norman Paton, and Charlie Hodgman
Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints
/ 95
Jan Gorodkin, Ole Lund, Claus A. Andersen, and Søren Brunak
Protein Fold Class Prediction: New Methods of Statistical Classification / 106
Janet Grassmann, Martin Reczko, Sandor Suhai, and Lutz Edler
Fidelity Probes for DNA Arrays / 113
Earl Hubbell and Pavel A. Pevzner
Solving Large Scale Phylogenetic Problems using DCM2 / 118
Daniel H. Huson, Lisa Vawter, and Tandy J. Warnow
TEXTAL: A Pattern Recognition System for Interpreting Electron Density Maps / 130
Thomas R. Ioerger, Thomas Holton, Jon A. Christopher, and James C. Sacchettini
ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences / 138
Christian Iseli, C. Victor Jongeneel, and Philipp Bucher
Using the Fisher Kernel Method to Detect Remote Protein Homologies / 149
Tommi Jaakkola, Mark Diekhans, and David Haussler
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping / 159
R. M. Karp, I. Pe'er, and R. Shamir
Multiple Structural Alignment and Core Detection by Geometric Hashing / 169
Nathaniel Leibowitz, Zipora Y. Fligelman, Ruth Nussinov, and Haim J. Wolfson
Metrics and Similarity Measures for Hidden Markov Models / 178
Rune B. Lyngsø, Christian N. S. Pedersen, and Henrik Nielsen
Quantitative, Scalable Discrete-Event Simulation of Metabolic Pathways / 187
Peter A. Meric and Michael J. Wise
Spatio-Temporal Registration of the Expression Patterns of Drosophila Segmentation Genes / 195
Ekaterina M. Myasnikova, David Kosman, John Reinitz, and Maria G.
Samsonova
A Dataset Generator for Whole Genome Shotgun Sequencing / 202
Gene Myers
Rapid Assessment of Extremal Statistics for Gapped Local Alignment / 211
Rolf Olsen, Ralf Bundschuh, and Terence Hwa
Building Dictionaries of 1D and 3D Motifs by Mining the Unaligned1D Sequences of 17 Archaeal and Bacterial Genomes / 223
Isidore Rigoutsos, Yuan Gao, Aris Floratos, and Laxmi Parida
A Linear Time Algorithm for Finding All Maximal Scoring Subsequences / 234
Walter L. Ruzzo and Martin Tompa
Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity / 242
Volker Schnecke and Leslie A. Kuhn
A Motion Planning Approach to Flexible Ligand Binding / 252
Amit P. Singh, Jean-Claude Latombe, and Douglas L. Brutlag
An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem / 262
Martin Tompa
Seamless Integration of Biological Applications within a Database Framework / 272
Thodoros Topaloglou, Anthony Kosky, and Victor Markowitz
Pharmaceutical Target Discovery Using Guilt-by-Association: Schizophrenia and Parkinson’s Disease Genes / 282
Michael G. Walker, Wayne Volkmuth, and Tod M. Klingler
Analysis of Ribosomal RNA Sequences by Combinatorial Clustering / 287
Poe Xing, Casimir Kulikowski, Ilya Muchnik, Inna Dubchak, Denise M. Wolf, Sylvia Spengler, and Manfred Zorn
Database Search Based on Bayesian Alignment / 297
Jun Zhu, Roland Lüthy, and Charles E. Lawrence