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<HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=windows-1252"> <META NAME="Generator" CONTENT="Microsoft Word 97"> <TITLE>PSB 98 On-Line Proceedings</TITLE> <META NAME="Template" CONTENT="C:\Program Files\Microsoft Office\OFFICE\html.dot"> </HEAD> <BODY LINK="#0000ff" VLINK="#800080"> <H2 ALIGN="CENTER"><a href="http://www.cgl.ucsf.edu/psb/psb98/">PSB 98 On-Line Proceedings</a></H2> NOTE: This site is currently under construction. Approx. 75% of these links are operational, leading to Adobe .pdf files of the papers. Free .pdf readers may be obtained <A HREF="http://www.adobe.com/prodindex/acrobat/readstep.html">here</A>. <a href="/psb-online/"> PSB Proceedings For All Years</a> <hr> CONTENTS <HR> <A HREF="preface.pdf">Preface</A> GENE EXPRESSION AND GENETIC NETWORKS <A HREF="bryant.pdf">Session Introduction</A> B. Bryant, A. Milosavljevic and R. Somogyi; Pacific Symposium on Biocomputing 3:3-5 (1998). <A HREF="kosman.pdf">Automated Assay of Gene Expression at Cellular Resolution</A> D. Kosman, J. Reinitz and D.H. Sharp; Pacific Symposium on Biocomputing 3:6-17 (1998). <A HREF="liang.pdf">REVEAL, A General Reverse Engineering Algorithm for Inference of GeneticNetwork Architectures</A> S. Liang, S. Fuhrman and R. Somogyi; Pacific Symposium on Biocomputing 3:18-29 (1998). <A HREF="marnellos.pdf">A Gene Network Approach to Modeling Early Neurogenesis in Drosophila</A> G. Marnellos and E. Mjolsness; Pacific Symposium on Biocomputing 3:30-41 (1998). <A HREF="michaels.pdf">Cluster Analysis and Data Visualization of Large-Scale Gene Expression Data</A> G.S. Michaels, D.B. Carr, M. Askenazi, S. Fuhrman, X. Wen and R. Somogyi; Pacific Symposium on Biocomputing 3:42-53 (1998). <A HREF="savageau.pdf">Rules for the Evolution of Gene Circuitry</A> M.A. Savageau; Pacific Symposium on Biocomputing 3:54-65 (1998). <A HREF="szallasi.pdf">Modeling the Normal and Neoplastic Cell Cycle With "Realistic BooleanGenetic Networks": Their Application for Understanding Carcinogenesisand Assessing Therapeutic Strategies</A> Z. Szallasi and S. Liang; Pacific Symposium on Biocomputing 3:66-76 (1998). <A HREF="thieffry.pdf">Qualitative Analysis of Gene Networks</A> D. Thieffry and R. Thomas; Pacific Symposium on Biocomputing 3:77-88 (1998). <A HREF="wuensche.pdf">Genomic Regulation Modeled as a Network with Basins of Attraction</A> A. Wuensche; Pacific Symposium on Biocomputing 3:89-102 (1998). MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION <A HREF="ferrin.pdf">Session Introduction </A> T. E. Ferrin and E. T. Kraemer; Pacific Symposium on Biocomputing 3:103-105 (1998). <A HREF="hansen.pdf">DINAMO: A Coupled Sequence Alignment Editor/Molecular Graphics Toolfor Interactive Homology Modeling of Proteins</A> M. Hansen, J. Bentz, A. Baucom and L. Gregoret; Pacific Symposium on Biocomputing 3:106-117 (1998). <A HREF="bourne.pdf">A Prototype Molecular Interactive Collaborative Environment (MICE)</A> P. Bourne, M. Gribskov, G. Johnson, J. Moreland, S. Wavra and H. Weissig; Pacific Symposium on Biocomputing 3:118-129 (1998). <A HREF="grigoriev.pdf">Reusable Graphical Interface to Genome Information Resources</A> A. Grigoriev; Pacific Symposium on Biocomputing 3:130-141 (1998). <A HREF="shah.pdf">Visualization Based on the Enzyme Commission Nomenclature</A> I. Shah and L. Hunter; Pacific Symposium on Biocomputing 3:142-152 (1998). <A HREF="he.pdf">Wavelet-Assisted Volume Ray Casting</a> T. He; Pacific Symposium on Biocomputing 3:153-164 (1998). <A HREF="kaufman.pdf">Visualizing Nerve Cells with VolVis</a> A. Kaufman; Pacific Symposium on Biocomputing 3:165-176 (1998). <A HREF="winfield.pdf">A Virtual Laboratory Notebook for Simulation Models</A> A.J. Winfield; Pacific Symposium on Biocomputing 3:177-188 (1998). <A HREF="parkinson.pdf">MAVIS: An Interactive Visualization Tool for Computational ChemistryCalculations in a Distributed Networked Environment</A> C.I. Parkinson, M.D. Cooper, W.T. Hewitt and I.H. Hillier; Pacific Symposium on Biocomputing 3:189-200 (1998). <A HREF="ueno.pdf">A High-throughput Graphics Library Designed for a Portable Molecular Structure Viewer</A> 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). <A HREF="uberbacher2.pdf">An Editing Environment for DNA Sequence Analysis and Annotation</A> E.C. Uberbacher, Y. Xu, M.B. Shah, V. Olman, M. Parang and R.J. Mural; Pacific Symposium on Biocomputing 3:217-227 (1998). <A HREF="asai.pdf">Recognition of Human Genes by Stochastic Parsing</a> K. Asai, K. Itou, Y. Ueno and T. Yada; Pacific Symposium on Biocomputing 3:228-239 (1998). <A HREF="zhang.pdf">A Discrimination Study of Human Core-Promoters</A> M.Q. Zhang; Pacific Symposium on Biocomputing 3:240-251 (1998). <A HREF="tsunoda.pdf">Automatic Extraction of Position Specific Cooccurrence of TranscriptionFactor Bindings on Promoters</a> T. Tsunoda and T. Takagi; Pacific Symposium on Biocomputing 3:252-263 (1998). <A HREF="wagner.pdf">A Computational "Genome Walk" Technique To Identify RegulatoryInteractions in Gene Networks</a> A. Wagner; Pacific Symposium on Biocomputing 3:264-278 (1998). <A HREF="hayes.pdf">Deriving Ribosomal Binding Site (RBS) Statistical Models from UnannotatedDNA Sequences and the Use of an RBS Model for N-terminal Prediction</A> W.S. Hayes and M. Borodovsky; Pacific Symposium on Biocomputing 3:279-290 (1998). <A HREF="overton.pdf">The GAIA Software Framework for Genome Annotation</A> 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 <A HREF="bajorath.pdf">Session Introduction</A> J. Bajorath, T.E. Klein and T.P. Lybrand; Pacific Symposium on Biocomputing 3:303-304 (1998). <A HREF="cho.pdf">Focus-2D: A New Approach to the Design of Targeted CombinatorialChemical Libraries</A> S.J. Cho, W. Zheng and A. Tropsha; Pacific Symposium on Biocomputing 3:305-316 (1998). <A HREF="hendrix.pdf">Surface Solid Angle-Based Site Points for Molecular Docking</A> D.K. Hendrix and I.D. Kuntz; Pacific Symposium on Biocomputing 3:317-326 (1998). <A HREF="moeckel.pdf">Molecular Modeling Information Transfer with VRML: From SmallMolecules to Large Systems in Bioscience</A> G. Moeckel, M. Keil, T. Exner and J. Brickmann; Pacific Symposium on Biocomputing 3:327-338 (1998). <A HREF="brown.pdf">Empirical Free Energy Calculations on Phage 434 Repressor- and cro-DNAComplexes Support the 'Indirect Readout' Hypothesis of Specificity</a> L.M. Brown, R.E. Bruccoleri and J. Novotny; Pacific Symposium on Biocomputing 3:339-348(1998). <a href="couch.pdf">The Object Technology Framework: An Object-Oriented Interface to Molecular Data and its Application to Collagen</a> 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). <A HREF="rejto.pdf">Molecular Anchors with Large Stability Gaps Ensure Linear Binding FreeEnergy Relationships for Hydrophobic Substituents</A> P.A. Rejto and G.M. Verkhivker; Pacific Symposium on Biocomputing 3:360-371 (1998). PROTEIN STRUCTURE PREDICTION <A HREF="lathrop.pdf">Session Introduction </A> R.H. Lathrop; Pacific Symposium on Biocomputing 3:372-374 (1998). <A HREF="ortiz.pdf">Combined Multiple Sequence Reduced Protein Model Approach to Predictthe Tertiary Structure of Small Proteins</A> A.R. Ortiz, A. Kolinski and J. Skolnick; Pacific Symposium on Biocomputing 3:375-386 (1998). <A HREF="backofen.pdf">Using Constraint Programming for Lattice Protein Folding</A> R. Backofen; Pacific Symposium on Biocomputing 3:387-398 (1998). <A HREF="ouzounis.pdf">Are Binding Residues Conserved?</a> C. Ouzounis, C. Pérez-Irratxeta, C. Sander and A. Valencia; Pacific Symposium on Biocomputing 3:399-410 (1998). <A HREF="akutsu.pdf">Linear Programming Based Approach to the Derivation of a Contact Potential for Protein Threading</A> T. Akutsu and H. Tashimo; Pacific Symposium on Biocomputing 3:411-422 (1998). <A HREF="parisien.pdf">A Protein Conformational Search Space Defined by Secondary StructureContacts</A> M. Parisien, F. Major and M. Peitsch; Pacific Symposium on Biocomputing 3:423-434 (1998). <A HREF="romero.pdf">Thousands of Proteins Likely to Have Long Disordered Regions </A> 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). <A HREF="edgecombe.pdf">Protein Model Determination from Crystallographic Data </A> 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? <A HREF="babbitt.pdf">Session Introduction </A> P.C. Babbitt; Pacific Symposium on Biocomputing 3:459-460 (1998). <A HREF="alexandrov.pdf">Statistical Significance of Ungapped Sequence Alignments</a> N.N. Alexandrov and V.V. Solovyev; Pacific Symposium on Biocomputing 3:461-470 (1998). <A HREF="dunker.pdf">Protein Disorder and the Evolution of Molecular Recognition: Theory, Predictions, and Observations</a> 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). <A HREF="fetrow.pdf">Function Driven Protein Evolution. A Possible Proto-protein for the RNA-binding Proteins</A> J.S. Fetrow and A. Godzik; Pacific Symposium on Biocomputing 3:483-494 (1998). <A HREF="wei.pdf">Recognizing Protein Binding Sites Using Statistical Descriptions of their 3D Environments</A> L. Wei and R.B. Altman; Pacific Symposium on Biocomputing 3:495-506 (1998). <A HREF="wutd.pdf">Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins</A> 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). <A HREF="frydrych.pdf">Color Recognition with Bacteriorhodopsin </A> M. Frydrych, P. Silfsten, S. Parkkinen, J. Parkkinen and T. Jaaskelainen; Pacific Symposium on Biocomputing 3:521-532 (1998). <A HREF="freund.pdf">Bidirectional Sticker Systems </A> R. Freund, G. Paun, G. Rozenberg and A. Salomaa; Pacific Symposium on Biocomputing 3:533-544 (1998). <A HREF="priese.pdf">Finite H-Systems with 3 Test Tubes are not Predictable </A> L. Priese, Y. Rogojine and M. Margenstern; Pacific Symposium on Biocomputing 3:545-556 (1998). COMPLEXITY AND INFORMATION THEORETIC APPROCHES TO BIOLOGY <A HREF="dowe.pdf">Session Introduction </A> D.L. Dowe and K. Prank; Pacific Symposium on Biocomputing 3:557-558 (1998). <A HREF="schmidt.pdf">An Information Theoretic View of Gapped and Other Alignments </A> J.P. Schmidt; Pacific Symposium on Biocomputing 3:559-570 (1998). <A HREF="steeg.pdf">Application of a Novel and Fast Information-Theoretic Method to the Discovery of Higher-Order Correlations in Protein Databases</A> E.W. Steeg and H. Pham; Pacific Symposium on Biocomputing 3:571-582 (1998). <A HREF="edgoose.pdf">An MML Classification of Protein Structure that Knows about Angles and Sequence </A> T. Edgoose, L. Allison and D.L. Dowe; Pacific Symposium on Biocomputing 3:583-594 (1998). <A HREF="powell.pdf">Discovering Simple DNA Sequences by Compression </A> D.R. Powell, D.L. Dowe, L. Allison and T.I. Dix; Pacific Symposium on Biocomputing 3:595-606 (1998). <A HREF="saitou.pdf">Self-Assembling Automata: A Model of Conformational Self-Assembly</a> K. Saitou; Pacific Symposium on Biocomputing 3:607-618 (1998). <A HREF="strong.pdf">On the Application of Information Theory to Neural Spike Trains</A> S.P. Strong, R. R. de Ruyter van Steveninck, E. Bialek and R. Koberle; Pacific Symposium on Biocomputing 3:619-630 (1998). <A HREF="prank.pdf">Coding of Time-Varying Hormonal Signals in Intracellular Calcium Spike Trains</A> 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). <A HREF="palus.pdf">Coarse-Grained Entropy Rates Quantify Fast CA2+ Dynamics Modulated by Pharmacological Stimulation</A> M. Palus, C. Schöfl, A. von Zur Mühlen, G. Brabant and K. Prank; Pacific Symposium on Biocomputing 3:643-654 (1998). <A HREF="bousquet.pdf">Is the Hippocampus a Kalman Filter? </A> O. Bousquet, K. Balakrishnan and V. Honavar; Pacific Symposium on Biocomputing 3:655-666 (1998). <A HREF="loewenstern.pdf">Maximum A Posteriori Classification of DNA Structure from Sequence Information</A> D.M. Loewenstern, H.M. Berman and H. Hirsh; Pacific Symposium on Biocomputing 3:667-678 (1998). DISTRIBUTED AND INTELLIGENT DATABASES <A HREF="frishman.pdf">Session Introduction </A> D. Frishman; Pacific Symposium on Biocomputing 3:679-680 (1998). <A HREF="fujibuchi.pdf">DBGET/LinkDB: an Integrated Database Retrieval System</A> W. Fujibuchi, S. Goto, H. Migimatsu, I. Uchiyama, A. Ogiwara, Y. Akiyama and M. Kanehisa; Pacific Symposium on Biocomputing 3:681-692 (1998). <A HREF="schulze-kremer.pdf">Ontologies for Molecular Biology </A> S. Schulze-Kremer; Pacific Symposium on Biocomputing 3:693-704 (1998). <A HREF="fukuda.pdf">Toward Information Extraction: Identifying Protein Names from Biological Papers</A> (REVISED VERSION) K. Fukuda, T. Tsunoda, A. Tamura and T. Takagi; Pacific Symposium on Biocomputing 3:705-716 (1998). <A HREF="wu.pdf">ProClass Protein Family Database: New Version with Motif Alignments</a> 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). <A HREF="kolatkar.pdf">Development of Software Tools at Bioinformatics Centre (BIC) at the National University of Singapore (NUS)</A> 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). <A HREF="wu_o.pdf">From Sequence to Structure to Literature: The Protocol Approach to Bioinformation</a> O.P. Wu, K.T. Seow, L. Wong, S.Y. Chung and S. Subbiah; Pacific Symposium on Biocomputing 3:745-756 (1998). <A HREF="sugawara.pdf">Towards the Asia-Pacific Bioinformatics Network </A> H. Sugawara and S. Miyazaki; Pacific Symposium on Biocomputing 3:757-762 (1998).</BODY> </HTML>