PSB 98 On-Line Proceedings

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CONTENTS


Preface

GENE EXPRESSION AND GENETIC NETWORKS

Session Introduction
B. Bryant, A. Milosavljevic and R. Somogyi; Pacific Symposium on Biocomputing 3:3-5 (1998).

Automated Assay of Gene Expression at Cellular Resolution
D. Kosman, J. Reinitz and D.H. Sharp; Pacific Symposium on Biocomputing 3:6-17 (1998).

REVEAL, A General Reverse Engineering Algorithm for Inference of GeneticNetwork Architectures
S. Liang, S. Fuhrman and R. Somogyi; Pacific Symposium on Biocomputing 3:18-29 (1998).

A Gene Network Approach to Modeling Early Neurogenesis in Drosophila
G. Marnellos and E. Mjolsness; Pacific Symposium on Biocomputing 3:30-41 (1998).

Cluster Analysis and Data Visualization of Large-Scale Gene Expression Data
G.S. Michaels, D.B. Carr, M. Askenazi, S. Fuhrman, X. Wen and R. Somogyi; Pacific Symposium on Biocomputing 3:42-53 (1998).

Rules for the Evolution of Gene Circuitry
M.A. Savageau; Pacific Symposium on Biocomputing 3:54-65 (1998).

Modeling the Normal and Neoplastic Cell Cycle With "Realistic BooleanGenetic Networks": Their Application for Understanding Carcinogenesisand Assessing Therapeutic Strategies
Z. Szallasi and S. Liang; Pacific Symposium on Biocomputing 3:66-76 (1998).

Qualitative Analysis of Gene Networks
D. Thieffry and R. Thomas; Pacific Symposium on Biocomputing 3:77-88 (1998).

Genomic Regulation Modeled as a Network with Basins of Attraction
A. Wuensche; Pacific Symposium on Biocomputing 3:89-102 (1998).

MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION

Session Introduction
T. E. Ferrin and E. T. Kraemer; Pacific Symposium on Biocomputing 3:103-105 (1998).

DINAMO: A Coupled Sequence Alignment Editor/Molecular Graphics Toolfor Interactive Homology Modeling of Proteins
M. Hansen, J. Bentz, A. Baucom and L. Gregoret; Pacific Symposium on Biocomputing 3:106-117 (1998).

A Prototype Molecular Interactive Collaborative Environment (MICE)
P. Bourne, M. Gribskov, G. Johnson, J. Moreland, S. Wavra and H. Weissig; Pacific Symposium on Biocomputing 3:118-129 (1998).

Reusable Graphical Interface to Genome Information Resources
A. Grigoriev; Pacific Symposium on Biocomputing 3:130-141 (1998).

Visualization Based on the Enzyme Commission Nomenclature
I. Shah and L. Hunter; Pacific Symposium on Biocomputing 3:142-152 (1998).

Wavelet-Assisted Volume Ray Casting
T. He; Pacific Symposium on Biocomputing 3:153-164 (1998).

Visualizing Nerve Cells with VolVis
A. Kaufman; Pacific Symposium on Biocomputing 3:165-176 (1998).

A Virtual Laboratory Notebook for Simulation Models
A.J. Winfield; Pacific Symposium on Biocomputing 3:177-188 (1998).

MAVIS: An Interactive Visualization Tool for Computational ChemistryCalculations in a Distributed Networked Environment
C.I. Parkinson, M.D. Cooper, W.T. Hewitt and I.H. Hillier; Pacific Symposium on Biocomputing 3:189-200 (1998).

A High-throughput Graphics Library Designed for a Portable Molecular Structure Viewer
Y. Ueno and K. Asai; Pacific Symposium on Biocomputing 3:201-212 (1998).

GENE STRUCTURE IDENTIFICATION IN LARGE-SCALE GENOMIC SEQUENCE

Session Introduction
E.C. Uberbacher and Y. Xu; Pacific Symposium on Biocomputing 3:213-216 (1998).

An Editing Environment for DNA Sequence Analysis and Annotation
E.C. Uberbacher, Y. Xu, M.B. Shah, V. Olman, M. Parang and R.J. Mural; Pacific Symposium on Biocomputing 3:217-227 (1998).

Recognition of Human Genes by Stochastic Parsing
K. Asai, K. Itou, Y. Ueno and T. Yada; Pacific Symposium on Biocomputing 3:228-239 (1998).

A Discrimination Study of Human Core-Promoters
M.Q. Zhang; Pacific Symposium on Biocomputing 3:240-251 (1998).

Automatic Extraction of Position Specific Cooccurrence of TranscriptionFactor Bindings on Promoters
T. Tsunoda and T. Takagi; Pacific Symposium on Biocomputing 3:252-263 (1998).

A Computational "Genome Walk" Technique To Identify RegulatoryInteractions in Gene Networks
A. Wagner; Pacific Symposium on Biocomputing 3:264-278 (1998).

Deriving Ribosomal Binding Site (RBS) Statistical Models from UnannotatedDNA Sequences and the Use of an RBS Model for N-terminal Prediction
W.S. Hayes and M. Borodovsky; Pacific Symposium on Biocomputing 3:279-290 (1998).

The GAIA Software Framework for Genome Annotation
G.C. Overton, C. Bailey, J. Crabtree, M. Gibson, S. Fischer and J. Schug; Pacific Symposium on Biocomputing 3:291-302 (1998).

MOLECULAR MODELING IN DRUG DESIGN AND BIOTECHNOLOGY

Session Introduction
J. Bajorath, T.E. Klein and T.P. Lybrand; Pacific Symposium on Biocomputing 3:303-304 (1998).

Focus-2D: A New Approach to the Design of Targeted CombinatorialChemical Libraries
S.J. Cho, W. Zheng and A. Tropsha; Pacific Symposium on Biocomputing 3:305-316 (1998).

Surface Solid Angle-Based Site Points for Molecular Docking
D.K. Hendrix and I.D. Kuntz; Pacific Symposium on Biocomputing 3:317-326 (1998).

Molecular Modeling Information Transfer with VRML: From SmallMolecules to Large Systems in Bioscience
G. Moeckel, M. Keil, T. Exner and J. Brickmann; Pacific Symposium on Biocomputing 3:327-338 (1998).

Empirical Free Energy Calculations on Phage 434 Repressor- and cro-DNAComplexes Support the 'Indirect Readout' Hypothesis of Specificity
L.M. Brown, R.E. Bruccoleri and J. Novotny; Pacific Symposium on Biocomputing 3:339-348(1998).

The Object Technology Framework: An Object-Oriented Interface to Molecular Data and its Application to Collagen
C.C. Huang, G.S. Couch, E.F. Pettersen, T.E. Ferrin, A.E. Howard and T.E. Klein; Pacific Symposium on Biocomputing 3:349-359 (1998).

Molecular Anchors with Large Stability Gaps Ensure Linear Binding FreeEnergy Relationships for Hydrophobic Substituents
P.A. Rejto and G.M. Verkhivker; Pacific Symposium on Biocomputing 3:360-371 (1998).

PROTEIN STRUCTURE PREDICTION

Session Introduction
R.H. Lathrop; Pacific Symposium on Biocomputing 3:372-374 (1998).

Combined Multiple Sequence Reduced Protein Model Approach to Predictthe Tertiary Structure of Small Proteins
A.R. Ortiz, A. Kolinski and J. Skolnick; Pacific Symposium on Biocomputing 3:375-386 (1998).

Using Constraint Programming for Lattice Protein Folding
R. Backofen; Pacific Symposium on Biocomputing 3:387-398 (1998).

Are Binding Residues Conserved?
C. Ouzounis, C. Pérez-Irratxeta, C. Sander and A. Valencia; Pacific Symposium on Biocomputing 3:399-410 (1998).

Linear Programming Based Approach to the Derivation of a Contact Potential for Protein Threading
T. Akutsu and H. Tashimo; Pacific Symposium on Biocomputing 3:411-422 (1998).

A Protein Conformational Search Space Defined by Secondary StructureContacts
M. Parisien, F. Major and M. Peitsch; Pacific Symposium on Biocomputing 3:423-434 (1998).

Thousands of Proteins Likely to Have Long Disordered Regions
P. Romero, Z. Obradovic, C.R. Kissinger, J.E. Villafranca, E. Garner, S. Guilliot and A.K. Dunker; Pacific Symposium on Biocomputing 3:435-446 (1998).

Protein Model Determination from Crystallographic Data
K. Edgecombe, A. Ableson, K. Baxter, A. Chiverton, J. Glasgow and S. Fortier; Pacific Symposium on Biocomputing 3:447-458 (1998).

THE RELATIONSHIP BETWEEN PROTEIN STRUCTURE AND FUNCTION, OR HOW HAVE PROTEINS OVER TIMEDIVERGED IN FUNCTION?

Session Introduction
P.C. Babbitt; Pacific Symposium on Biocomputing 3:459-460 (1998).

Statistical Significance of Ungapped Sequence Alignments
N.N. Alexandrov and V.V. Solovyev; Pacific Symposium on Biocomputing 3:461-470 (1998).

Protein Disorder and the Evolution of Molecular Recognition: Theory, Predictions, and Observations
A.K. Dunker, E. Garner, S. Guilliot, P. Romero, K. Albrecht, J. Hart, Z. Obradovic, C. Kissinger and E. Villafranca; Pacific Symposium on Biocomputing 3:471-482 (1998).

Function Driven Protein Evolution. A Possible Proto-protein for the RNA-binding Proteins
J.S. Fetrow and A. Godzik; Pacific Symposium on Biocomputing 3:483-494 (1998).

Recognizing Protein Binding Sites Using Statistical Descriptions of their 3D Environments
L. Wei and R.B. Altman; Pacific Symposium on Biocomputing 3:495-506 (1998).

Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins
T.D. Wu, S.C. Schmidler, T. Hastie and D.L. Brutlag; Pacific Symposium on Biocomputing 3:507-518 (1998).

COMPUTING WITH BIOMOLECULES

Session Introduction
P. Clote, M. Hagiya and T. Head; Pacific Symposium on Biocomputing 3:519-520 (1998).

Color Recognition with Bacteriorhodopsin
M. Frydrych, P. Silfsten, S. Parkkinen, J. Parkkinen and T. Jaaskelainen; Pacific Symposium on Biocomputing 3:521-532 (1998).

Bidirectional Sticker Systems
R. Freund, G. Paun, G. Rozenberg and A. Salomaa; Pacific Symposium on Biocomputing 3:533-544 (1998).

Finite H-Systems with 3 Test Tubes are not Predictable
L. Priese, Y. Rogojine and M. Margenstern; Pacific Symposium on Biocomputing 3:545-556 (1998).

COMPLEXITY AND INFORMATION THEORETIC APPROCHES TO BIOLOGY

Session Introduction
D.L. Dowe and K. Prank; Pacific Symposium on Biocomputing 3:557-558 (1998).

An Information Theoretic View of Gapped and Other Alignments
J.P. Schmidt; Pacific Symposium on Biocomputing 3:559-570 (1998).

Application of a Novel and Fast Information-Theoretic Method to the Discovery of Higher-Order Correlations in Protein Databases
E.W. Steeg and H. Pham; Pacific Symposium on Biocomputing 3:571-582 (1998).

An MML Classification of Protein Structure that Knows about Angles and Sequence
T. Edgoose, L. Allison and D.L. Dowe; Pacific Symposium on Biocomputing 3:583-594 (1998).

Discovering Simple DNA Sequences by Compression
D.R. Powell, D.L. Dowe, L. Allison and T.I. Dix; Pacific Symposium on Biocomputing 3:595-606 (1998).

Self-Assembling Automata: A Model of Conformational Self-Assembly
K. Saitou; Pacific Symposium on Biocomputing 3:607-618 (1998).

On the Application of Information Theory to Neural Spike Trains
S.P. Strong, R. R. de Ruyter van Steveninck, E. Bialek and R. Koberle; Pacific Symposium on Biocomputing 3:619-630 (1998).

Coding of Time-Varying Hormonal Signals in Intracellular Calcium Spike Trains
K. Prank, C. Schöfl, L. Läer, M. Wagner, A. von Zur Mühlen, G. Brabant and F. Gabbiani; Pacific Symposium on Biocomputing 3:631-642 (1998).

Coarse-Grained Entropy Rates Quantify Fast CA2+ Dynamics Modulated by Pharmacological Stimulation
M. Palus, C. Schöfl, A. von Zur Mühlen, G. Brabant and K. Prank; Pacific Symposium on Biocomputing 3:643-654 (1998).

Is the Hippocampus a Kalman Filter?
O. Bousquet, K. Balakrishnan and V. Honavar; Pacific Symposium on Biocomputing 3:655-666 (1998).

Maximum A Posteriori Classification of DNA Structure from Sequence Information
D.M. Loewenstern, H.M. Berman and H. Hirsh; Pacific Symposium on Biocomputing 3:667-678 (1998).

DISTRIBUTED AND INTELLIGENT DATABASES

Session Introduction
D. Frishman; Pacific Symposium on Biocomputing 3:679-680 (1998).

DBGET/LinkDB: an Integrated Database Retrieval System
W. Fujibuchi, S. Goto, H. Migimatsu, I. Uchiyama, A. Ogiwara, Y. Akiyama and M. Kanehisa; Pacific Symposium on Biocomputing 3:681-692 (1998).

Ontologies for Molecular Biology
S. Schulze-Kremer; Pacific Symposium on Biocomputing 3:693-704 (1998).

Toward Information Extraction: Identifying Protein Names from Biological Papers (REVISED VERSION)
K. Fukuda, T. Tsunoda, A. Tamura and T. Takagi; Pacific Symposium on Biocomputing 3:705-716 (1998).

ProClass Protein Family Database: New Version with Motif Alignments
C.H. Wu and S. Shivakumar; Pacific Symposium on Biocomputing 3:717-728 (1998).

BUILDING BIOINFORMATION INFRASTRUCTURE IN THE PACIFIC RIM

Session Introduction
T.W. Tan and S. Subbiah; Pacific Symposium on Biocomputing 3:731-732 (1998).

Development of Software Tools at Bioinformatics Centre (BIC) at the National University of Singapore (NUS)
P.R. Kolatkar, M.K. Sakharkar, C.R. Tse, B.K. Kiong, L. Wong, T.W. Tan and S. Subbiah; Pacific Symposium on Biocomputing 3:733-744 (1998).

From Sequence to Structure to Literature: The Protocol Approach to Bioinformation
O.P. Wu, K.T. Seow, L. Wong, S.Y. Chung and S. Subbiah; Pacific Symposium on Biocomputing 3:745-756 (1998).

Towards the Asia-Pacific Bioinformatics Network
H. Sugawara and S. Miyazaki; Pacific Symposium on Biocomputing 3:757-762 (1998).