Genome Informatics 1999 Genome Informatics 1999 Published as: Asai, K. and Miyano, S. and Takagi, T. (eds.); "Genome Informatics 1999" Universal Academy Press, Tokyo, 1999.
Preface by Kiyoshi Asai
[GIW99F01] Carlos A. Del Carpio Munoz, Atsushi Yoshimori; "MIAX: A Novel System for Assessment of Macromolecular Interaction in Condensed Phases. 1) Description of the Interaction Model and Simulation Algorithm" [pdf]
[GIW99F02] Chungfan Kim, Akihiko Konagaya, Kiyoshi Asai; "A Generic Criterion for Gene Recognitions in Genomic Sequences" [pdf]
[GIW99F03] Tatsuya Akutsu, Kim Lan Sim; "Protein Threading Based on Multiple Protein Structure Alignment" [pdf]
[GIW99F04] Xiaohong Li, Pedro Romero, Meeta Rani, A. Keith Dunker, Zoran Obradovic; "Predicting Protein Disorder for N-, C-, and Internal Regions" [pdf]
[GIW99F05] Ethan Garner, Pedro Romero, A. Keith Dunker, Celeste Brown, Zoran Obradovic; "Predicting Binding Regions within Disordered Proteins" [pdf]
[GIW99F06] Xin Chen, Sam Kwong, Ming Li; "A Compression Algorithm for DNA Sequences and Its Applications in Genome Comparison" [pdf]
[GIW99F07] Hirotada Kobayashi, Hiroshi Imai; "An EM-type Algorithm for Ordered Restriction Map Alignment" [pdf]
[GIW99F08] Koichiro Doi, Hiroshi Imai; "A Greedy Algorithm for Minimizing the Number of Primers in Multiple PCR Experiments" [pdf]
[GIW99F09] Nadia El-Mabrouk, David Sankoff; "On the Reconstruction of Ancient Doubled Circular Genomes Using Minimum Reversals" [pdf]
[GIW99F10] Mitsuteru Nakao, Hidemasa Bono, Shuichi Kawashima, Tomomi Kamiya, Kazushige Sato, Susumu Goto, Minoru Kanehisa; "Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG" [pdf]
[GIW99F11] See-Kiong Ng, Marie Wong; "Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts" [pdf]
[GIW99F12] Masanori Arita, Kiyoshi Asai, Takaaki Nishioka; "Finding Precursor Compounds in Secondary Metabolism" [pdf]
[GIW99F13] Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe, Akihiko Konagaya; "Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA for Hunting Pathogenic DNA Molecular Changes" [pdf]
[GIW99F14] Masao Nagasaki, Shuichi Onami, Satoru Miyano, Hiroaki Kitano; "Bio-calculus: Its Concept and Molecular Interaction" [pdf]
[GIW99F15] Tomohiro Yasuda, Hideo Bannai, Shuichi Onami, Satoru Miyano, Hiroaki Kitano; "Towards Automatic Construction of Cell-Lineage of C. elegans from Nomarski DIC Microscope Images" [pdf]
[GIW99F16] Akihiro Nakaya, Haretugu Hishigaki, Shinichi Morishita; "Tracing Synergetic Behavior of the QTLs Affecting Oral Glucose Tolerance in the OLETF Rat" [pdf]
[GIW99F17] Yutaka Ueno, Kiyoshi Asai, Masanori Arita; "Integrating Application Programs for Bioinformatics Using a Web Browser" [pdf]
[GIW99F18] Aaron Stokes, Hideo Matsuda, Akihiro Hashimoto; "Making High-level Queries on Diverse Genome Data: A Structured Genome Document Database System Based on GXML and GQL" [pdf]
[GIW99F19] Tomohiro Moriyama, Ayumi Shinohara, Masayuki Takeda, Osamu Maruyama, Takao Goto, Satoru Miyano, Satoru Kuhara; "A System to Find Genetic Networks Using Weighted Network Model" [pdf]
[GIW99D01] Yutaka Akiyama, Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando; "PAPIA (Parallel Protein Information Analysis) System and MolTreC Parallel Molecular Dynamics Simulator Running on a Compact 8-node Linux PC Cluster" [pdf]
[GIW99D02] Susumu Goto, Kotaro Shiraishi, Kayo Okamoto, Hiroko Ishida, Toshi Nakatani, Tomoko Deno, Minoru Kanehisa; "Ortholog Identifiers for Integration of Genomic and Pathway Information in KEGG" [pdf]
[GIW99D03] Yasuhiko Kitamura, Tetsuro Nanbu, Shoji Tatsumi; "A Keyword Recommendation System for GenBank" [pdf]
[GIW99D04] Ken Kurokawa, Yoshitaka Hasegawa, Kenichi Kawashima, Toshiyuki Okumura, Tatsuya Takagi, Teruo Yasunaga; "GeneAlign: Java Application Software for Multiple Sequence Alignment Editor" [pdf]
[GIW99D05] Shinsei Minoshima, Susumu Mitsuyama, Saho Ohno, Takashi Kawamura, Nobuyoshi Shimizu; "KMDB: Keio Mutation Database for Human Disease Gene" [pdf]
[GIW99D06] Tadasu Shin-i, Yuji Kohara; "NEXTDB: The Expression Pattern Map Database for C. elegans" [pdf]
[GIW99D07] Yoshinori Tamada, Satoshi Matsumoto, Osamu Maruyama, Satoru Miyano; "ViewDesigner: A Tool for Designing Viewscopes in Discovery System HypothesisCreator" [pdf]
[GIW99D08] Atsushi Doi, Rainer Drath, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano; "Protein Dynamics Observations of Lambda Phage by Hybrid Petri Net" [pdf]
[GIW99D09] Miyako Tanaka, Sanae Nakazono, Hiroshi Matsuno, Satoru Miyano; "An Intelligent Tool for Selecting Abstracts in MEDLINE" [pdf]
[GIW99P01] Koji Kadota, Rika Miki, Yasushi Okazaki, Kentaro Shimizu, Yoshihide Hayashizaki; "Development of an Efficient Data Processing Method for cDNA Microarray and Its Application to Tissue Expression Profiling" [pdf]
[GIW99P02] Kyotetsu Kanaya, Akira Ohyama, Tatsuya Akutsu, Asao Fujiyama; "DDGEL/DDCHIP: Web-Based Systems for Analysis of 2-D Gel Electrophoresis Images and DNA Macro/Micro Array Images" [pdf]
[GIW99P03] Ken-ichi Kurata, Akira Suyama; "Probe Design for DNA Chips" [pdf]
[GIW99P04] Tatsuhiko Tsunoda, Yoshiaki Hojo, Chikashi Kihara, Norihiko Shiraishi, Osamu Kitahara, Kenji Ono, Toshihiro Tanaka, Toshihisa Takagi, Yusuke Nakamura; "Discrimination of Drug Sensitivity of Cancer Using cDNA Microarray and Multivariate Statistical Analysis" [pdf]
[GIW99P05] Jianghong An, Takao Nakama, Yasushi Kubota, Hiroshi Wako, Akinori Sarai; "Construction of an Integrated Environment for Sequence, Structure, Property and Function Analysis of Proteins" [pdf]
[GIW99P06] Carlos Adriel Del Carpio Munoz; "Recent Improvements in the Automatic System for Protein Tertiary Structure Prediction GAX" [pdf]
[GIW99P07] Hiroaki Kato, Yoshimasa Takahashi, Hidetsugu Abe; "Development of an Automated Identification Program for Three-Dimensional Protein Motifs" [pdf]
[GIW99P08] Makiko Suwa, Henrik T. Yudate, Yasuhiko Masuho, Asaf A. Salamov, Christine A. Orengo, Mark B. Swindells; "Genius: System for Assigning Protein Coding Regions to 3D Structures" [pdf]
[GIW99P09] Shouji Tatsumoto, Kenji Satou; "A System for Displaying Protein Structure Information Based on Sequence Fragment Similarity" [pdf]
[GIW99P10] Junichi Uechi, Takatsugu Hirokawa, Makiko Suwa, Shigeki Mitaku; "An Automated Structure Prediction System by Lattice Model for Seven-Helix-Type Membrane Proteins" [pdf]
[GIW99P11] Yutaka Ueno, Katsutoshi Takahashi, Kiyoshi Asai, Chikara Sato; "BESPA: Software Tools for Three-dimensional Structure Reconstruction from Single Particle Images of Proteins" [pdf]
[GIW99P12] Takaaki Nishioka, Kimito Funatsu; "Chemical Knowledge for Predicting Biosynthetic Pathways of Secondary Metabolites" [pdf]
[GIW99P13] Atsushi Ogiwara; "Prediction of Secondary Metabolism Pathways from Genomic Information and Compounds Data" [pdf]
[GIW99P14] Akinori Sarai, Hidetoshi Kono, Michael Gromiha, Fabio Pichierri, Kenji Sayano, Misako Aida; "Methods for Predicting Target Sites of Transcription Factors" [pdf]
[GIW99P15] Goro Terai, Takeshi Mizuno, Toshihisa Takagi; "Evaluation of a Method for Predicting Transcription Factors" [pdf]
[GIW99P16] Yifei Wang, Akinori Sarai; "Prediction of Cooperative Binding Sites for Multiple Transcription Factors" [pdf]
[GIW99P17] Yukihiro Maki, Shoji Watanabe, Yukihiro Eguchi, Daisuke Tominaga, Masahiro Okamoto; "AIGNET: A System That Infers Large Scale Genetic Networks" [pdf]
[GIW99P18] Osamu Gotoh; "Coherent Structural Prediction of a Set of Paralogous Genes on a Eukaryotic Genome" [pdf]
[GIW99P19] Haretsugu Hishigaki, Toshihide Ono, Akira Tanigami, Toshihisa Takagi; "Interaction-based Analysis of Protein Function and Network" [pdf]
[GIW99P20] Hideki Noguchi, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi; "Prediction of MHC Class II-Peptide Interaction Using Fuzzy Neural Network" [pdf]
[GIW99P21] Keun-Joon Park, Minoru Kanehisa; "Prediction of Nuclear Localization Signals by HMM" [pdf]
[GIW99P22] Atsushi Yoshimori, Carlos Adriel Del Carpio Munoz; "A Novel System for Assessment of Macromolecular Interaction in Condensed Phases. 2) Interaction Site Inference by Molecular Shape and Electrostatic Complementarity" [pdf]
[GIW99P23] Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, P. Prabakaran, Akinori Sarai; "Progress of ProTherm: Theromodynamic Database for Proteins and Mutants" [pdf]
[GIW99P24] Masahiro Hattori, Minoru Kanehisa; "Detection of Apoptotic Domains Against KEGG Database by the HMM Search" [pdf]
[GIW99P25] Masako Kaizawa, Satoru Watanabe, Takahiro Nobukuni, Masami Horikoshi, Hiroshi Handa, Yoshiyuki Kuchino, Takao Sekiya, Hiroshi Mizushima; "Maintenance of Transcription Factor DataBase TFDB" [pdf]
[GIW99P26] Akihiro Kawaguchi, Kenji Satou; "A Database System for the Management and Karyotype Analysis of Chromosome Image Data" [pdf]
[GIW99P27] Shuichi Kawashima, Takeshi Kawashima, Hiroki Nishida, Kazuhiro W. Makabe, Minoru Kanehisa; "MAGEST: ESTs and Gene Expression Pattern Database for Halocynthia roretzi Maternal cDNA" [pdf]
[GIW99P28] Yoshiyuki Mukai, Hideki Nagasaki, Baltazar A. Antonio, Katsumi Sakata, Yasumichi Sakai, Takuji Sasaki; "INE: The Rice Genome Sequence Database" [pdf]
[GIW99P29] Kotoko Nakata, Takako Takai, Tsuguchika Kaminuma; "Receptor Database (RDB) in 1999" [pdf]
[GIW99P30] P. Prabakaran, Jianghong An, Michael Gromiha, S. Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai; "Thermodynamic Database for Protein-Nucleic Acid Interactions" [pdf]
[GIW99P31] Christian Schönbach, Vladimir Brusic, Judice L.Y. Koh; "SLAD - An Integrated Swine MHC Database: A Case Study of Data Warehousing in Molecular Immunology" [pdf]
[GIW99P32] Kim Lan Sim, Tomoyuki Uchida, Satoru Miyano; "PDB-DO: Database of Disorder" [pdf]
[GIW99P33] Takashi Yamanaka, Tetsushi Yada, Kenta Nakai; "An Aberrant Splicing Database for Finding Rules of Splice-Site Selection" [pdf]
[GIW99P34] Hideaki Konno, Yoshifumi Fukunishi, Toshinori Endo, Yoshihide Hayashizaki; "Construction and Application of Mouse Full-length cDNA Database" [pdf]
[GIW99P35] Katsutoshi Ibushi, Nigel Collier, Jun'ichi Tsujii; "Classification of MEDLINE Abstracts" [pdf]
[GIW99P36] Hisao Imai, Nigel Collier, Jun'ichi Tsujii; "A Combined Query Expansion Approach for Information Retrieval" [pdf]
[GIW99P37] Tomoko Ohta, Yuka Tateisi, Nigel Collier, Chikashi Nobata, Katsutoshi Ibushi, Jun'ichi Tsujii; "A Semantically Annotated Corpus from MEDLINE Abstracts" [pdf]
[GIW99P38] Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi; "Automatic Extraction of Information on Protein-Protein Interaction from Scientific Literature" [pdf]
[GIW99P39] Yuka Tateisi, Tomoko Ohta, Takako Takai, Jun'ichi Tsujii; "An Ontology for Biological Reaction Events" [pdf]
[GIW99P40] Bal A. Antonio, Zhiwei Fang, Hector Sanchez, Mary Polacco, Su-Shing Chen, Katsumi Sakata, Isamu Ohta, Yoshiyuki Mukai, E. Jr. Coe, Takuji Sasaki; "An Object-Protocol Model Multidatabase Query System for Rice and Maize" [pdf]
[GIW99P41] Ken-ichiro Fukuda, Toshihisa Takagi; "A Preliminary Study in Data Management and Visualization of Signal Transduction Pathway Data -- Viewing Interaction Data" [pdf]
[GIW99P42] Yoshiki Fuseda, Kenji Satou; "Toward a Data Mining Service from Large and Heterogeneous Genome Databases in GenomeNet" [pdf]
[GIW99P43] David P. Hansen, Thure Etzold, Guenther Kurapkat; "Cross Database Visualization" [pdf]
[GIW99P44] Takao Kataoka, Kenji Satou; "A Full-Text Search System Covering the Whole GenomeNet" [pdf]
[GIW99P45] Kazuo Takehana, Takehiko Ito, Tetsushi Yada, Mika Hirakawa, Hiroko Yamaguchi, Junko Shimada, Katsuji Matsumura, Masako Kuroda; "WEB Based GENOME Analysis Tools in ALIS Project" [pdf]
[GIW99P46] Tetsuro Toyoda, Akiko Itai; "Global Integration of Gene Databases by Eigen-ID Method" [pdf]
[GIW99P47] Takashi Abe, Shigehiko Kanaya, Makoto Kinouchi, Yoshihiro Kudo, Hirotada Mori, Hideo Matsuda, Carlos Del Carpio, Toshimichi Ikemura; "Gene Classification Method Based on Batch-Learning SOM" [pdf]
[GIW99P48] Mamoru Kato, Akira Suyama; "Synonymous Codon Usage Based on Codon-Anticodon Interaction Energy and Gene Expression Level" [pdf]
[GIW99P49] Jun-Ichi Sagara, Kentaro Shimizu; "Analysis of Molecular Evolution in Mitochondorial tRNA Gene Sequences" [pdf]
[GIW99P50] Kiminobu X. Sato, Susumu Goto, Minoru Kanehisa; "Unit-Based de novo Drug Design Using a Library of Protein-Ligand Interaction Sites" [pdf]
[GIW99P51] Yumi Tamada, Toshio Shimizu; "Characterization and Classification of Splicing Patterns" [pdf]
[GIW99P52] Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto; "Application to Gene Cluster Analysis of Inductive Inference of Languages over Patterns with Conceptual Hierarchy" [pdf]
[GIW99P53] Takeshi Ara, Kenji Suzuki, Hideo Matsuda, Hirotada Mori; "Distribution of Species Specific Gene Family in Microorganisms" [pdf]
[GIW99P54] Yosuke Ozawa, Satoshi Hanaoka, Rintaro Saito, Masaru Tomita; "Differences of Translation Termination Sites Among the Three Stop Codons" [pdf]
[GIW99P55] Hiroaki Sakai, Chiaki Imamura, Hiroshi Ohno, Takanori Washio, Masaru Tomita; "Fop Values, Start Codons, SD Sequence Conservation, and Their Correlation to Gene Expression Level" [pdf]
[GIW99P56] Reina Uno, Yoichi Nakayama, Kenji Yotsutani, Takehito Mogami, Kazuharu Arakawa, Masaru Tomita; "Computational Analysis of c Sequences" [pdf]
[GIW99P57] Yasuo Yonezawa, Hiroyuki Motohasi; "Zipf-Scaling Description in the DNA Sequences" [pdf]
[GIW99P58] Wayne Dawson, Kenji Yamamoto; "Toward Full 3D Structural Investigation of Intron Splicing in Human Cytochrome P450 2D6 pre-mRNA" [pdf]
[GIW99P59] Toshinori Endo, Yoshifumi Fukunishi, Hideaki Konno, Harukazu Suzuki, Yasuhiro Ozawa, Masayasu Yoshino, Kazuhiro Shibata, Masayoshi Itoh, Piero Carninci, Yasushi Okazaki, Yoshihide Hayashizaki; "Systematic Analyses on Mouse Encyclopedia" [pdf]
[GIW99P60] Masahiro Gomi, Shigeki Mitaku; "Sequence Analysis for Discrimination of Signal Peptides and Signal Anchor Sequences" [pdf]
[GIW99P61] Zhongmin Li, Yoshio Yoshioka, Toshio Shimizu; "Pairwise Alignment on the Loop Structured Computer" [pdf]
[GIW99P62] Yasukazu Nakamura, Satoshi Tabata; "A High-throughput Gene Discovery System for Arabidopsis Genome Sequencing Project" [pdf]
[GIW99P63] Ayaka Nobusato, Ikuo Uchiyama, Seishi Ohashi, Ichizo Kobayashi; "Insertion with Long Target Duplication: A Novel Mechanism for Bacterial Gene Mobility Suggested from Genome Comparison" [pdf]
[GIW99P64] Koji Ohnishi, Shoken Hokari; "Evolutionary Emergence of Early-Peptide-Synthesizing RNA Machines by Means of Hierarchical Sociogenesis of tRNA-Riboorganisms" [pdf]
[GIW99P65] Nobuyuki Uchikoga, Akira Suyama; "Distances between Completely Matched Tuples in the Modern Gene Sequences" [pdf]
[GIW99P66] Hiroyuki Kurata, Kazunari Taira, Hiroaki Kitano; "Synthesis and Analysis of a Biological System" [pdf]
[GIW99P67] Koji M. Kyoda, Michiko Muraki, Shugo Hamahashi, Mineo Morohashi, Shuichi Onami, Hiroaki Kitano; "BIODRIVE: Simulator for Biochemical and Genetic Networks" [pdf]
[GIW99P68] Kenta Hashimoto, Fumihiko Miyoshi, Sae Seno, Masaru Tomita; "Generic Gene Expression System for Modeling Complex Gene Regulation Network Using E-CELL System" [pdf]
[GIW99P69] Yusuke Saito, Kouichi Takahashi, Tomoharu Iwata, Tomohiko Aikawa, Masaru Tomita; "Parameter Estimation Mechanism of E-CELL Simulation Environment" [pdf]
[GIW99P70] Ryo Matsushima, Yoichi Nakayama, Natsumi Noguchi, Hironori Tanaka, Ayako Kinoshita, Masaru Tomita; "Pathological Analyses of Enzyme Deficiency in Human Erythrocyte Using E-CELL System" [pdf]
[GIW99P71] Fumihiko Miyoshi, Kenta Hashimoto, Yuki Fujita, Reina Matsuo, Youhei Yamada, Masaru Tomita; "Towards Kinetic Modeling of DNA Replication Using the E-CELL System" [pdf]
[GIW99P72] Yoichi Nakayama, Ryo Matsushima, Masaru Tomita; "Computer Simulation of Human Erythrocyte Using the E-CELL System" [pdf]
[GIW99P73] Masayuki Okayama, Motohiro Yoneda, Yusuke Saito, Kouichi Takahashi, Masaru Tomita; "Mathematical Analysis of Metabolic Networks Using the E-CELL Simulation Environment" [pdf]
[GIW99P74] Katsuyuki Yugi, Yuko Kanai, Masaru Tomita; "Kinetic Modelling of Energy Metabolism in Mitochondria" [pdf]
[GIW99I01] David Haussler; "Computational Analysis of High-throughput Genomics Data Using Hidden Markov Models and Support Vector Machines" [pdf]
[GIW99I02] Yusuke Nakamura; "Human Genome Analysis and Medicine in the 21st Century" [pdf]