Genome Informatics 1998

December 10-11, 1998
Yebisu Garden Place, Tokyo, Japan

Published as: Miyano, S. and Takagi, T. (eds.); "Genome Informatics 1998" Universal Academy Press, Tokyo, 1998.

Preface by Toshihisa Takagi

Program Committee


Full Talk Papers

[GIW98F01] Katsutoshi Fujita, Tomoya Baba, Katsumi Isono; "Genomic Analysis of the Genes Encoding Ribosomal Proteins in Eight Eubacterial Species and Saccharomyces cerevisiae" [pdf]

[GIW98F02] Hiroaki Kasai, Kanako Watanabe, Elizabeth Gasteiger, Amos Bairoch, Katsumi Isono, Satoshi Yamamoto, Shigeaki Harayama; "Construction of the gyrB Database for the Identification and Classification of Bacteria" [pdf]

[GIW98F03] David Sankoff, Mathieu Blanchette; "Phylogenetic Invariants for Metazoan Mitochondrial Genome Evolution" [pdf]

[GIW98F04] Hidemasa Bono, Susumu Goto, Wataru Fujibuchi, Hiroyuki Ogata, Minoru Kanehisa; "Systematic Prediction of Orthologous Units of Genes in the Complete Genomes" [pdf]

[GIW98F05] Yoshimi Toda, Rintaro Saito, Masaru Tomita; "Comprehensive Sequence Analyses of 5' Flanking Regions of Primate Alu Elements" [pdf]

[GIW98F06] Wayne Dawson, Kenji Yamamoto; "Evidence of Limited Structural Organization in Globin Intron Sequences of Messenger RNA " [pdf]

[GIW98F07] Takeshi Sekimizu, Hyun S. Park, Jun'ichi Tsujii; "Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts" [pdf]

[GIW98F08] Denys Proux, François Rechenmann, Laurent Julliard, Violaine Pillet, Bernard Jacq; "Detecting Gene Symbols and Names in Biological Texts : A First Step toward Pertinent Information Extraction" [pdf]

[GIW98F09] Teruyoshi Hishiki, Nigel Collier, Chikashi Nobata, Tomoko Okazaki-Ohta, Norihiro Ogata, Takeshi Sekimizu, Roland Steiner, Hyun S. Park, Jun'ichi Tsujii; "Developing NLP Tools for Genome Informatics: An Information Extraction Perspective" [pdf]

[GIW98F10] Shin-ichi Usuzaka, Kim Lan Sim, Miyako Tanaka, Hiroshi Matsuno, Satoru Miyano; "A Machine Learning Approach to Reducing the Work of Experts in Article Selection from Database: A Case Study for Regulatory Relations of S. cerevisiae Genes in MEDLINE" [pdf]

[GIW98F11] Jing Chen, Daphna Strauss, Limsoon Wong; "Using Kleisli to Bring Out Features in BLASTP Results" [pdf]

[GIW98F12] Laxmi Parida, Aris Floratos, Isidore Rigoutsos; "MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences" [pdf]

[GIW98F13] Hirotada Kobayashi, Hiroshi Imai; "Improvement of the A* Algorithm for Multiple Sequence Alignment" [pdf]

[GIW98F14] Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi, Makoto Ando; "Parallel Protein Information Analysis (PAPIA) System Running on a 64-Node PC Cluster" [pdf]

[GIW98F15] Kiyoshi Noda, Ayumi Shinohara, Masayuki Takeda, Satoshi Matsumoto, Satoru Miyano, Satoru Kuhara; "Finding Genetic Network from Experiments by Weighted Network Model" [pdf]

[GIW98F16] Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano; "A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions" [pdf]

[GIW98F17] Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe, Akihiko Konagaya; "Fully-Automated Spot Recognition and Matching Algorithms for 2-D Gel Electrophoretogram of Genomic DNA" [pdf]

[GIW98F18] Kui Lin, Anthony E. Ting, Jiren Wang, Limsoon Wong; "Hunting TPR Domains Using Kleisli" [pdf]

[GIW98F19] Marcella A. McClure, Julianna Hudak, John Kowalski; "Low Identity, Low Similarity Protein Sequences: Independent Modeling of the Ordered-Series-of-Motifs and Motif-Intervening-Regions" [pdf]

[GIW98F20] Qian Xie, Gregory E. Arnold, Pedro Romero, Zoran Obradovic, Ethan Garner, A. Keith Dunker; "The Sequence Attribute Method for Determining Relationships Between Sequence and Protein Disorder" [pdf]

[GIW98F21] Ethan Garner, Paul Cannon, Pedro Romero, Zoran Obradovic, A. Keith Dunker; "Predicting Disordered Regions from Amino Acid Sequence: Common Themes Despite Differing Structural Characterization" [pdf]

Software Demonstration Abstracts

[GIW98D01] Yasuhiko Wada, Hirohisa Kishino, Nobuhisa Kashiwagi, Hiroshi Yasue; "Mobile Agent System for Animal Genome Database" [pdf]

[GIW98D02] Katsumi Sakata, Kazunori Waki, Takuji Sasaki, Michihiko Shimomura, Masaki Kise; "A Sample Tracking Tool for Rice Genome Sequencing" [pdf]

[GIW98D03] Tadasu Shin-i, Yuji Kohara; "NEXTDB: The Expression Pattern Map Database for C. elegans" [pdf]

[GIW98D04] Susumu Goto, Kotaro Shiraishi, Kayo Okamoto, Hiroko Ishida, Sanae Asanuma, Hidemasa Bono, Hiroyuki Ogata, Wataru Fujibuchi, Minoru Kanehisa; "Constructing and Annotating GENES Database in KEGG" [pdf]

[GIW98D05] Hideaki Mizuno, Yoshimasa Tanaka, Yoshihiro Ugawa, Akinori Sarai; "ORI-GENE: A Tool for Gene Classification Based on Evolutional Tree" [pdf]

[GIW98D06] Mitsuteru Nakao, Kazushige Sato, Tomomi Kamiya, Yoshiko Kimura, Minoru Kanehisa; "Genome-Scale Gene Expression Profiles Mapped onto the Pathway and Genome Maps in KEGG" [pdf]

[GIW98D07] Koji Kyoda, Hiroaki Kitano; "Virtual Drosophila Project: Simulation of Drosophila Leg Formation" [pdf]

[GIW98D08] Shinsei Minoshima, Susumu Mitsuyama, Saho Ohno, Takashi Kawamura, Nobuyoshi Shimizu; "KMeyeDB: Keio Mutation Database for Eye Disease Genes Constructed on a Graphical Distributed Database System Mutation View" [pdf]

[GIW98D09] Ken Kurokawa, Kenichi Kawashima, Toshiyuki Okumura, Tatsuya Takagi, Teruo Yasunaga; "GeneWeb II: Sequence Analysis Tools on Web Server Using Java API" [pdf]

[GIW98D10] Hideo Bannai, Toshio Masuda, Masao Nagasaki, Tomohiro Yasuda, Osamu Maruyama, S atoru Miyano; "Parallelized Knowledge Discovery System: An Enhancement to BONSAI" [pdf]

Poster Abstracts

[GIW98P01] Meeta Rani, Pedro Romero, Zoran Obradovic, A. Keith Dunker; "Annotation of PDB with respect to ``Disordered Regions'' in Proteins" [pdf]

[GIW98P02] Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Sakura Tanida, Thomas S. Shimizu; "E-CELL Project Overview: Towards Integrative Simulation of Cellular Processes" [pdf]

[GIW98P03] Kenta Hashimoto, Fumihiko Miyoshi, Thomas S. Shimizu, Takeshi Satoyoshi, Masaru Tomita; "Modeling of Transcription and DNA Replication Using the E-CELL Simulation System" [pdf]

[GIW98P04] Yuri Matsuzaki, Kanako Saito, Tom Shimizu, Masaru Tomita; "Modeling of Signal Transduction for Bacterial Chemotaxis Using the E-CELL Simulation System" [pdf]

[GIW98P05] Riou Matsushima, Akiko Kawase, Naoko Watanabe, Hisako Nakano, Kanako Saito, Masaru Tomita; "Modeling of Human Red Blood Cell Using the E-CELL Simulation System" [pdf]

[GIW98P06] Kouichi Takahashi, Tom Shimizu, Katsuyuki Yugi, Masaru Tomita; "Modeling Theory and Software Architecture of the E-CELL Simulation System" [pdf]

[GIW98P07] Yusuke Saito, Kouichi Takahashi, Masaru Tomita; "Multivariate Time Series Analysis of Metabolic Network Using the E-CELL Simulation System" [pdf]

[GIW98P08] Yoko Fukuda, Takanori Washio, Masaru Tomita; "Evolution of Overlapping Genes: Comparative Genomics of Mycoplasma genitalium and Mycoplasma pneumoniae" [pdf]

[GIW98P09] Masahiko Wada, Yukihiro Kawashima, Masaru Tomita; "On Periodicity of Adenine-Adenine Dinucleotides in Bacterial Genomes" [pdf]

[GIW98P10] Yuko Osada, Rintaro Saito, Masaru Tomita; "Computer Analysis of Base Pairing Free-Energy between Shine-Dalgarno Sequence and 16S rRNA in Various Procaryotes" [pdf]

[GIW98P11] Mami Goto, Takanori Washio, Masaru Tomita; "On Low Frequency of CpG Dinucleotides in Bacterial Genomes" [pdf]

[GIW98P12] Rintaro Saito, Masaru Tomita; "Analysis of Translation Initation Sites in the Complete Genome of Mycoplasma genitalium Suggests That This Bacterium Uses Alternative Signal for Translation Initiation" [pdf]

[GIW98P13] Taku Okada, Masaru Tomita, Kazuhiko Kawasaki, Shinsei Minoshima, Nobuyoshi Shimizu; "Expression Frequency of the Human Immunoglobulin lambda Light Chain Genes and the Roles of Their Recombination Signal and Spacer Sequences" [pdf]

[GIW98P14] Brian Karlak, Winston Hide; "Assessment of Utility of ESTs for Nucleotide Diversity Using Available Assembled Alignments from dbESt, STACK 2.0 and STACK-INDEX" [pdf]

[GIW98P15] Junaid Gamieldien, Winston Hide; "A Genome-Level Search for Bacterial Genes on Which Positive Selection May Operate: A Means for Identifying Possible Virulence Factors?" [pdf]

[GIW98P16] Joseph Oppon, Winston Hide; "A Statistical Model for Prokaryotic Promoter Prediction" [pdf]

[GIW98P17] Shoji Watanabe, Yukihiro Maki, Yukihiro Eguchi, Daisuke Tominaga, Masahiro Okamoto; "Algorithms for Inference of Genetic Networks (AIGNET)" [pdf]

[GIW98P18] Shigehiro Fukase, Masato Wayama; "An Educational Tool for Visualize DNA Structures in vivo" [pdf]

[GIW98P19] Susumu Hiraoka; "Extended Sequence Alignment Method for Protein Secondary Structure Prediction" [pdf]

[GIW98P20] Naoko Kasahara, Naoyuki Harada, Keiichi Nagai; "Detection of Frame-Shift Error in the Yeast Genome Sequences" [pdf]

[GIW98P21] Katsuhiko Murakami, Toshihisa Takagi; "Clustering and Detection of 5'Splice Sites of mRNA by k Weight Matrix Model" [pdf]

[GIW98P22] Masanori Arita; "Automated Metabolic Reconstruction at the Molecular Level" [pdf]

[GIW98P23] Yoshiaki Hojo, Ikuo Uchiyama, Yataro Daigo, Yusuke Nakamura, Toshihisa Takagi; "Correlation between Exon and Dispersed Repetitive DNA Distributions on the Human Genome" [pdf]

[GIW98P24] Mikio Yoshida, Kenichiro Fukuda, Toshihisa Takagi; "Automatic Construction of Biological Abbreviation Dictionary from Abstracts of Biomedical Papers" [pdf]

[GIW98P25] Kenichiro Fukuda, Mikio Yoshida, Toshihisa Takagi; "A Workbench for Systematic Construction of Signal Transduction Pathways: Ontologies and Architectures" [pdf]

[GIW98P26] Tomoko Okazaki-Ohta, Toshihisa Takagi; "Development of Information Extraction Tool: Toward Construction of Protein-Protein Interaction Database" [pdf]

[GIW98P27] Masao Fukagawa, Tatsuhiko Tsunoda, Toshihisa Takagi; "Palindrome Analysis: Distribution of Complete-Matched Inverted Repeats with a Moderate Length Spacer" [pdf]

[GIW98P28] Takeaki Taniguchi, Minoru Kanehisa; "Construction of Ortholog/Paralog Group Table for PTS" [pdf]

[GIW98P29] Kiminobu Sato, Minoru Kanehisa; "A Library of Protein-Ligand Interaction Sites for de novo Ligand Design" [pdf]

[GIW98P30] Wataru Fujibuchi, Hiroyuki Ogata, Hideo Matsuda, Minoru Kanehisa; "Automatic Detection of Gene Clusters by P-Quasi Complete Linkage Grouping" [pdf]

[GIW98P31] Yoshinobu Igarashi, Minoru Kanehisa; "The Construction of the Knowledge Base of Immune System" [pdf]

[GIW98P32] Hiroyuki Ogata, Wataru Fujibuchi, Minoru Kanehisa; "Detection of Co-regulated Genes by Comparative Analysis of Microbial Genomes" [pdf]

[GIW98P33] Shuichi Kawashima, Hiroyuki Ogata, Minoru Kanehisa; "Extracting Regulatory Signals from the Upstream Region of Co-expressed Genes Derived from DNA Microarray Experiments" [pdf]

[GIW98P34] Fumi Takazawa, Masaki Sasaki, Minoru Kanehisa; "Protein Folding Simulation and Self-Consistent Potential Functions" [pdf]

[GIW98P35] Atsushi Ogiwara; "Systematic Classification of B. subtilis Genes and Construction of a Knowledge Base to Represent Functional Information" [pdf]

[GIW98P36] Takaaki Nishioka, Kimito Funatsu; "Search Pathways for Secondary Metabolites Based on Genome Analysis and Chemical Knowledge on Metabolism" [pdf]

[GIW98P37] Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto; "A Method for Querying Complete Genomes by Viewing Them as Structured Documents" [pdf]

[GIW98P38] Masako Kaizawa, Satoru Watanabe, Takahiro Nobukuni, Masami Horikoshi, Hiroshi Handa, Yoshiyuki Kuchino, Takao Sekiya, Hiroshi Mizushima; "Maintenance of Transcription Factor DataBase TFDB by TFDB Maintenance System" [pdf]

[GIW98P39] Mika Hirakawa, Kensaku Imai, Hiroko Yamaguchi, Junko Shimada, Kazuo Takehana, Katsuji Matsumura, Takehiko Itoh, Masako Kuroda; "ALIS: Data Management Systems for Human Genome Sequencing" [pdf]

[GIW98P40] Yoshifumi Fukunishi, Hideaki Konno, Yoshihide Hayashizaki; "Automatic cDNA classification System for Mouse Genome Project" [pdf]

[GIW98P41] Hideaki Konno, Yuichi Sugahara, Yoshifumi Fukunishi, Kazuhiro Shibata, Yoshihide Hayashizaki; "Automated cDNA Information System for Large Scale cDNA Project" [pdf]

[GIW98P42] Yuichi Sugahara, Yoshihide Hayashizaki; "Application of the RLGS Image Analysis Tool (RAT) to the Construction of a Genetic Linkage Map of Recombinant Inbred Strain SMXA" [pdf]

[GIW98P43] Jianghong An, Takao Nakama, Yasushi Kubota, Akinori Sarai; "3DinSight: An Integrated Database and Search Tool for Structure, Function and Property of Biomolecules" [pdf]

[GIW98P44] M. Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, Akinori Sarai; "ProTherm: Thermodynamic Database for Proteins and Mutants" [pdf]

[GIW98P45] Hidetoshi Kono, Akinori Sarai; "Prediction of DNA target Sites by Regulatory Proteins Based on Structure-Derived Potential" [pdf]

[GIW98P46] Osamu Maruyama, Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano; "Genomic Hypothesis Creator: A Multi-Strategic View Creator for Sequences" [pdf]

[GIW98P47] Kyotetsu Kanaya, Akira Ohyama, Tatsuya Akutsu, Asao Fujiyama; "Development of Web Interface of Image Analysis System DDGEL for 2D Gel Electrophoresis" [pdf]

[GIW98P48] Tatsuya Akutsu; "Subcubic Time Algorithms for RNA Secondary Structure Prediction" [pdf]

[GIW98P49] Satoshi OOta; "ThreeTree: A New Method to Reconstruct Phylogenetic Trees" [pdf]

[GIW98P50] Fengrong Ren, Hiroshi Tanaka; "Efficiency of Model-Based Complexity Method for Estimating Unrooted Multifurcate Phylogenetic Tree" [pdf]

[GIW98P51] Yukio Kobayashi, Nobuhiko Saito; "Secondary Structure Prediction Based on Statistical Mechanics" [pdf]

[GIW98P52] Kiyoshi Asai, Katunobu Itou, Tetsushi Yada; "Integrating Multiple Evidences by Hidden Markov Models" [pdf]

[GIW98P53] Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Takahiro Ishii, Kenta Nakai; "Modeling Transcriptional Units of E. coli Genes Using HMM" [pdf]

[GIW98P54] Takahiro Ishii, Kenta Nakai; "A Database of B. subtilis Promoters and Transcription Factors" [pdf]

[GIW98P55] Jun-Ichi Sagara, Shugo Nakamura, Mitsunori Ikeguchi, Kentaro Shimizu; "A Study Using Sequence Comparison to Investigate the Molecular Evolution of Mitochondrial tRNA Genes" [pdf]

[GIW98P56] Tetsuo Nishikawa, Toshio Ota, Takao Isogai; "Prediction of Initiation Codons in cDNA Fragments Using Statistical Information and Similarity with Protein Sequences" [pdf]

[GIW98P57] Asaf A. Salamov, Makiko Suwa, Christine A. Orengo, Mark B. Swindells; "Genome Analysis: Assigning Protein Coding Regions to 3D Structures" [pdf]

[GIW98P58] Makoto Hirosawa, Osamu Ohara, Katsumi Isono; "A Novel Application of GeneMark-RC to the Analysis of Prokaryotic Genomes and Human cDNAs: Sequence Data with Statistical Deviations Are Rich in Important Biological Information" [pdf]

[GIW98P59] Yasukazu Nakamura, Shusei Sato, Satoshi Tabata; "Annotation and Presentation Systems for Arabidopsis Genome Sequencing Project at Kazusa DNA Research Institute" [pdf]

[GIW98P60] Masahiro Gomi, Takatsugu Hirokawa, Shigeki Mitaku; "Charge Distribution of Signal Peptides and Signal Anchor Type II" [pdf]

[GIW98P61] Koji Kadota, Hiroyuki Sasamoto, Takatsugu Hirokawa, Shigeki Mitaku; "Topology Prediction of Membrane Proteins Based on a Modified ``Positive-Inside'' Rule" [pdf]

[GIW98P62] Shigeki Mitaku, Takatsugu Hirokawa, Mitsuo Ono; "Classification of Membrane Proteins by Types of Transmembrane Helices Using SOSUI System" [pdf]

[GIW98P63] Shigehiko Kanaya, Yoshihiro Kudo, Takashi Abe, Takanori Okazaki, Carlos Del Carpio, Toshimichi Ikemura; "Gene Classification by Self-Organization Mapping of Codon Usage in Bacteria with Completely Sequenced Genome" [pdf]

[GIW98P64] Carlos A. Del Carpio; "GAFLEX: A Hybrid GA Engine for Mapping the Configuration Hyper-Space of Organic Compounds in Solution" [pdf]

[GIW98P65] Atsushi Yoshimori, Carlos A. Del Carpio; "DYNAX: A New System for Biomolecular Dynamics Simulation in Solution" [pdf]

[GIW98P66] Masachika Azuma, Taiki Kojima, Masaki Kobayashi, Carlos Adriel Del Carpio; "Development of an Antibacterial MAP Homologous to a Loop Region in Human Lactoferrin" [pdf]

[GIW98P67] Hiromi Nakatake, Carlos Adriel Del Carpio; "MOLDEX:A Computer System for Drug Design. 4)A Combined Electro-Geometric Method for the Identification of Pharmacophoric Structural Patterns in Drugs" [pdf]

[GIW98P68] Tomoko Hara, Carlos Adriel Del Carpio; "A Simulated Annealing Algorithm for Geometrical Assessment of Macromolecular Hydrophobic Interaction" [pdf]

[GIW98P69] Katsuhisa Yamaguchi, Carlos Adriel Del Carpio; "A Genetic Programming Based System for the Prediction of Secondary and Tertiary Structures of RNA" [pdf]

[GIW98P70] Todd Taylor, Masahira Hattori, Kiyoteru Noguchi, Tomomi Shobu, Kazuo Ishii, Atsushi Toyoda, Yoshiyuki Sakaki; "Detailed Sequence Analysis of the Distal Down Syndrome Critical Region and the SOD1/AML1 Region on Chromosome 21" [pdf]

[GIW98P71] Camelia B. Gogonea, M. Y. Ali, Tetsunari Fukushige, M. Afaq Shakir, Takashi Matsuo, Shahid S. Siddiqui; "Genome Wide Survey of the Entire C. elegans alpha-Tubulin Gene Family: cDNA Cloning, Expression, and Structure-Function Analysis" [pdf]

[GIW98P72] Nobuyuki Uchikoga, Akira Suyama; "Gene Has Its Inherent Significantly Repetitive Tuples" [pdf]

[GIW98P73] Hiroshi Nakashima, Motonori Ota, Ken Nishikawa, Tatsuo Ooi; "Nucleotide Sequence of a Gene Encodes Characteristic Features of an Organism as Well as an Amino Acid Sequence" [pdf]

[GIW98P74] Chindo Hicks, Eiji Kobayashi, Masahiro Satoh, Kazuo Ishii, Tsutomu Furukawa; "Application Computer Software in Mapping Quantitative Trait Loci" [pdf]

[GIW98P75] Koji Ohnishi; "Phosphoglycerate-transporter Protein B as a Most Primitive Protein Predicted by the Poly-tRNA Theory" [pdf]

[GIW98P76] Takayoshi Sasano, Jun-Ichi Sagara, Shugo Nakamura, Mitsunori Ikeguchi, Kentaro Shimizu; "Sequence Analysis of the IRES-Loop III Region of Hepatitis C Virus" [pdf]

[GIW98P77] Kenji Suzuki, Takeshi Ara, Hideo Matsuda, Hirotada Mori; "ORF Clustering Analysis of 17 Complete Genomes" [pdf]

Invited Talks

[GIW98I01] Shun-ichi Amari; "Information Geometry and Neural Networks" [pdf]

[GIW98I02] Eugene V. Koonin; "Comparative Genomics: Is It Changing the Paradigm of Evolutionary Biology?" [pdf]