The Pacific Symposium on Biocomputing brings together key researchers from the international biocomputing community. PSB is designed to be maximally responsive to the need for critical mass in subdisciplines within biocomputing. These proceedings contain peer-reviewed articles in computational biology.
Preface v GENE EXPRESSION AND GENETIC NETWORKS Session Introduction 3(3) B. Bryant A. Milosavljevic R. Somogyi Automated Assay of Gene Expression at Cellular Resolution 6(12) D. Kosman J. Reinitz D. H. Sharp REVEAL, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures 18(12) S. Liang S. Fuhrman R. Somogyi A Gene Network Approach to Modeling Early Neurogenesis in Drosophila 30(12) G. Marnellos E. Mjolsness Cluster Analysis and Data Visualization of Large-Scale Gene Expression Data 42(12) G. S. Michaels D. B. Carr M. Askenazi S. Fuhrman X. Wen R. Somogyi Rules for the Evolution of Gene Circuitry 54(12) M. A. Savageau Modeling the Normal and Neoplastic Cell Cycle With ``Realistic Boolean Genetic Networks: Their Application for Understanding Carcinogenesis and Assessing Therapeutic Strategies 66(11) Z. Szallasi S. Liang Qualitative Analysis of Gene Networks 77(12) D. Thieffry R. Thomas Genomic Regulation Modeled as a Network with Basins of Attraction 89(14) A. Wuensche MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY Session Introduction 103(3) T. E. Ferrin E. T. Kraemer DINAMO: A Coupled Sequence Alignment Editor/Molecular Graphics Tool for Interactive Homology Modeling of Proteins 106(12) M. Hansen J. Bentz A. Baucom L. Gregoret A Prototype Molecular Interactive Collaborative Environment (MICE) 118(12) P. Bourne M. Gribskov G. Johnson J. Moreland S. Wavra H. Weissig Reusable Graphical Interface to Genome Information Resources 130(12) A. Grigoriev Visualization Based on the Enzyme Commission Nomenclature 142(11) I. Shah L. Hunter Wavelet-Assisted Volume Ray Casting 153(12) T. He Visualizing Nerve Cells with VolVis 165(12) A. Kaufman A Virtual Laboratory Notebook for Simulation Models 177(12) A. J. Winfield MAVIS: An Interactive Visualization Tool for Computational Chemistry Calculations in a Distributed Networked Environment 189(12) C. I. Parkinson M. D. Cooper W. T. Hewitt I. H. Hillier A High-throughput Graphics Library Designed for a Portable Molecular Structure Viewer 201(12) Y. Ueno K. Asai GENE STRUCTURE IDENTIFICATION IN LARGE-SCALE GENOMIC SEQUENCE Session Introduction 213(4) E. C. Uberbacher Y. Xu An Editing Environment for DNA Sequence Analysis and Annotation 217(11) E. C. Uberbacher Y. Xu M. B. Shah V. Olman M. Parang R. J. Mural Recognition of Human Genes by Stochastic Parsing 228(12) K. Asai K. Itou Y. Ueno T. Yada Discrimination Study of Human Core-Promoters 240(12) M. Q. Zhang Automatic Extraction of Position Specific Cooccurrence of Transcription Factor Bindings on Promoters 252(12) T. Tsunoda T. Takagi A. Computational ``Genome Walk Technique To Identify Regulatory Interactions in Gene Networks 264(15) A. Wagner Deriving Ribosomal Binding Site (RBS) Statistical Models from Unannotated DNA Sequences and the Use of an RBS Model for N-terminal Prediction 279(12) W. S. Hayes M. Borodovsky The GAIA Software Framework for Genome Annotation 291(12) G. C. Overton C. Bailey J. Crabtree M. Gibson S. Fischer J. Schug MOLECULAR MODELING IN DRUG DESIGN AND BIOTECHNOLOGY Session Introduction 303(2) J. Bajorath T. E. Klein T. P. Lybrand Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries 305(12) S. J. Cho W. Zheng A. Tropsha Surface Solid Angle-Based Site Points for Molecular Docking 317(10) D. K. Hendrix I. D. Kuntz Molecular Modeling Information Transfer with VRML: From Small Molecules to Large Systems in Bioscience 327(12) G. Moeckel M. Keil T. Exner J. Brickmann Empirical Free Energy Calculations on Phage 434 Repressor- and cro-DNA Complexes Support the `Indirect Readout Hypothesis of Specificity 339(10) L. M. Brown R. E. Bruccoleri J. Novotny The Object Technology Framework: An Object-Oriented Interface to Molecular Data and its Application to Collagen 349(13) C. C. Huang G. S. Couch E. F. Pettersen T. E. Ferrin A. E. Howard T. E. Klein Molecular Anchors with Large Stability Gaps Ensure Linear Binding Free Energy Relationships for Hydrophobic Substituents 362(12) P. A. Rejto G. M. Verkhivker PROTEIN STRUCTURE PREDICTION Session Introduction 374(3) R. H. Lathrop Combined Multiple Sequence Reduced Protein Model Approach to Predict the Tertiary Structure of Small Proteins 377(12) A. R. Ortiz A. Kolinski J. Skolnick Using Constraint Programming for Lattice Protein Folding 389(12) R. Backofen Are Binding Residues Conserved? 401(12) C. Ouzounis C. Perez-Irratxeta C. Sander A. Valencia Linear Programming Based Approach to the Derivation of a Contact Potential for Protein Threading 413(12) T. Akutsu H. Tashimo A Protein Conformational Search Space Defined by Secondary Structure Contacts 425(12) M. Parisien F. Major M. Peitsch Thousands of Proteins Likely to Have Long Disordered Regions 437(12) P. Romero Z. Obradovic C. R. Kissinger J. E. Villafranca E. Garner S. Guilliot A. K. Dunker Protein Model Determination from Crystallographic Data 449(12) K. Edgecombe A. Ableson K. Baxter A. Chiverton J. Glasgow S. Fortier THE RELATIONSHIP BETWEEN PROTEIN STRUCTURE AND FUNCTION, OR HOW HAVE PROTEINS OVER TIME DIVERGED IN FUNCTION? Session Introduction 461(2) P. C. Babbitt Statistical Significance of Ungapped Sequence Alignments 463(10) N. N. Alexandrov V. V. Solovyev Protein Disorder and the Evoluation of Molecular Recognition: Theory, Predictions, and Observations 473(12) A. K. Dunker E. Garner S. Guilliot P. Romero K. Albrecht J. Hart Z. Obradovic C. Kissinger J. E. Villafranca Function Driven Protein Evolution. A Possible Proto-protein for the RNA-binding Proteins 485(12) J. S. Fetrow A. Godzik Recognizing Protein Binding Sites Using Statistical Descriptions of their 3D Environments 497(12) L. Wei R. B. Altman Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins 509(12) T. D. Wu S. C. Schmidler T. Hastie D. L. Brutlag COMPUTING WITH BIOMOLECULES Session Introduction 521(2) P. Clote M. Hagiya T. Head Color Recognition with Bacteriorhodopsin 523(12) M. Frydrych P. Silfsten S. Parkkinen J. Parkkinen T. Jaaskelainen Bidirectional Sticker Systems 535(12) R. Freund G. Paun G. Rozenberg A. Salomaa Finite H-Systems with 3 Test Tubes are not Predictable 547(12) L. Priese Y. Rogojine M. Margenstern COMPLEXITY AND INFORMATION-THEORETIC APPROACHES TO BIOLOGY Session Introduction 559(2) D. L. Dowe K. Prank An Information Theoretic View of Gapped and Other Alignments 561(12) J. P. Schmidt Application of a Novel and Fast Information-Theoretic Method to the Discovery of Higher-Order Correlations in Protein Databases 573(12) E. W. Steeg H. Pham An MML Classification of Protein Structure that Knows about Angles and Sequence 585(12) T. Edgoose L. Allison D. L. Dowe Discovering Simple DNA Sequences by Compression 597(12) D. R. Powell D. L. Dowe L. Allison T. I. Dix Self-Assembling Automata: A Model of Conformational Self-Assembly 609(12) K. Saitou On the Application of Information Theory to Neural Spike Trains 621(12) S. P. Strong R. R. de Ruyter van Steveninck W. Bialek R. Koberle Coding of Time-Varying Hormonal Signals in Intracellular Calcium Spike Trains 633(12) K. Prank C. Schofl L. Laer M. Wagner A. von Zur Muhlen G. Brabant F. Gabbiani Coarse-Grained Entropy Rates Quantify Fast CA2+ Dynamics Modulated by Pharmacological Stimulation 645(12) M. Palus C. Schofl A. von Zur Muhlen G. Brabant K. Prank Is the Hippocampus a Kalman Filter? 657(12) O. Bousquet K. Balakrishnan V. Honavar Maximum A Posteriori Classification of DNA Structure from Sequence Information 669(12) D. M. Loewenstern H. M. Berman H. Hirsh DISTRIBUTED AND INTELLIGENT DATABASES Session Introduction 681(2) D. Frishman DBGET/LinkDB: an Integrated Database Retrieval System 683(12) W. Fujibuchi S. Goto H. Migimatsu I. Uchiyama A. Ogiwara Y. Akiyama M. Kanehisa Ontologies for Molecular Biology 695(12) S. Schulze-Kremer Toward Information Extraction: Identifying Protein Names from Biological Papers 707(12) K. Fukuda A. Tamura T. Tsunoda T. Takagi ProClass Protein Family Database: New Version with Motif Alignments 719(14) C. H. Wu S. Shivakumar BUILDING BIOINFORMATION INFRASTRUCTURE IN THE PACIFIC RIM Session Introduction 733(2) T. W. Tan S. Subbiah Development of Software Tools at Bioinformatics Centre (BIC) at the National University of Singapore (NUS) 735(12) P. R. Kolatkar M. K. Sakharkar C. R. Tse B. K. Kiong L. Wong T. W. Tan S. Subbiah From Sequence to Structure to Literature: The Protocol Approach to Bioinformation 747(12) O. P. Wu K. T. Seow L. Wong S. Y. Chung S. Subbiah Towards the Asia-Pacific Bioinformatics Network 759 H. Sugawara S. Miyazaki
Daugiau apie elektronines knygas