Biocomputing '98

The Table of Contents for the book is as follows:

• Preface
• GENE EXPRESSION AND GENETIC NETWORKS
  • Session Introduction
  • Automated Assay of Gene Expression at Cellular Resolution
  • REVEAL, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures
  • A Gene Network Approach to Modeling Early Neurogenesis in Drosophila
  • Cluster Analysis and Data Visualization of Large-Scale Gene Expression Data
  • Rules for the Evolution of Gene Circuitry
  • Modeling the Normal and Neoplastic Cell Cycle With “Realistic Boolean Genetic Networks”: Their Application for Understanding Carcinogenesis and Assessing Therapeutic Strategies
  • Qualitative Analysis of Gene Networks
  • Genomic Regulation Modeled as a Network with Basins of Attraction
• MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY
  • Session Introduction
  • DINAMO: A Coupled Sequence Alignment Editor/Molecular Graphics Tool for Interactive Homology Modeling of Proteins
  • A Prototype Molecular Interactive Collaborative Environment (MICE)
  • Reusable Graphical Interface to Genome Information Resources
  • Visualization Based on the Enzyme Commission Nomenclature
  • Wavelet-Assisted Volume Ray Casting
  • Visualizing Nerve Cells with VolVis
  • A Virtual Laboratory Notebook for Simulation Models
  • MAVIS: An Interactive Visualization Tool for Computational Chemistry Calculations in a Distributed Networked Environment
  • A High-throughput Graphics Library Designed for a Portable Molecular Structure Viewer
• GENE STRUCTURE IDENTIFICATION IN LARGE-SCALE GENOMIC SEQUENCE
  • Session Introduction
  • An Editing Environment for DNA Sequence Analysis and Annotation
  • Recognition of Human Genes by Stochastic Parsing
  • A Discrimination Study of Human Core-Promoters
  • Automatic Extraction of Position Specific Cooccurrence of Transcription Factor Bindings on Promoters
  • A Computational “Genome Walk” Technique To Identify Regulatory Interactions in Gene Networks
  • Deriving Ribosomal Binding Site (RBS) Statistical Models from Unannotated DNA Sequences and the Use of an RBS Model for N-terminal Prediction
  • The GAIA Software Framework for Genome Annotation
• MOLECULAR MODELING IN DRUG DESIGN AND BIOTECHNOLOGY
  • Session Introduction
  • Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries
  • Surface Solid Angle-Based Site Points for Molecular Docking
  • Molecular Modeling Information Transfer with VRML: From Small Molecules to Large Systems in Bioscience
  • Empirical Free Energy Calculations on Phage 434 Repressor- and cro-DNA Complexes Support the ‘Indirect Readout’ Hypothesis of Specificity
  • The Object Technology Framework: An Object-Oriented Interface to Molecular Data and its Application to Collagen
  • Molecular Anchors with Large Stability Gaps Ensure Linear Binding Free Energy Relationships for Hydrophobic Substituents
• PROTEIN STRUCTURE PREDICTION
  • Session Introduction
  • Combined Multiple Sequence Reduced Protein Model Approach to Predict the Tertiary Structure of Small Proteins
  • Using Constraint Programming for Lattice Protein Folding
  • Are Binding Residues Conserved?
  • Linear Programming Based Approach to the Derivation of a Contact Potential for Protein Threading
  • A Protein Conformational Search Space Defined by Secondary Structure Contacts
  • Thousands of Proteins Likely to Have Long Disordered Regions
  • Protein Model Determination from Crystallographic Data
• THE RELATIONSHIP BETWEEN PROTEIN STRUCTURE AND FUNCTION, OR HOW HAVE PROTEINS OVER TIME DIVERGED IN FUNCTION?
  • Session Introduction
  • Statistical Significance of Ungapped Sequence Alignments
  • Protein Disorder and the Evolution of Molecular Recognition: Theory, Predictions, and Observations
  • Function Driven Protein Evolution. A Possible Proto-protein for the RNA-binding Proteins
  • Recognizing Protein Binding Sites Using Statistical Descriptions of their 3D Environments
  • Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins
• COMPUTING WITH BIOMOLECULES
  • Session Introduction
  • Color Recognition with Bacteriorhodopsin
  • Bidirectional Sticker Systems
  • Finite H-Systems with 3 Test Tubes are not Predictable
• COMPLEXITY AND INFORMATION-THEORETIC APPROACHES TO BIOLOGY
  • Session Introduction
  • An Information Theoretic View of Gapped and Other Alignments
  • Application of a Novel and Fast Information-Theoretic Method to the Discovery of Higher-Order Correlations in Protein Databases
  • An MML Classification of Protein Structure that Knows about Angles and Sequence
  • Discovering Simple DNA Sequences by Compression
  • Self-Assembling Automata: A Model of Conformational Self-Assembly
  • On the Application of Information Theory to Neural Spike Trains
  • Coding of Time-Varying Hormonal Signals in Intracellular Calcium Spike Trains
  • Coarse-Grained Entropy Rates Quantify Fast CA²⁺ Dynamics Modulated by Pharmacological Stimulation
  • Is the Hippocampus a Kalman Filter?
  • Maximum A Posteriori Classification of DNA Structure from Sequence Information
• DISTRIBUTED AND INTELLIGENT DATABASES
  • Session Introduction
  • DBGET/LinkDB: an Integrated Database Retrieval System
  • Ontologies for Molecular Biology
  • Toward Information Extraction: Identifying Protein Names from Biological Papers
  • ProClass Protein Family Database: New Version with Motif Alignments
• BUILDING BIOINFORMATION INFRASTRUCTURE IN THE PACIFIC RIM
  • Session Introduction
  • Development of Software Tools at Bioinformatics Centre (BIC) at the National University of Singapore (NUS)
  • From Sequence to Structure to Literature: The Protocol Approach to Bioinformation
  • Towards the Asia-Pacific Bioinformatics Network