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