Genome Informatics Vol. 13 (2002)

Presented at the 13th International Conference on Genome Informatics
December 16-18, 2002, The Garden Hall, Yebisu Garden Place, Tokyo, Japan

Published as: R. Lathrop, K. Nakai, S. Miyano, T. Takagi, and M. Kanehisa (eds.)
"Genome Informatics 2002"
Universal Academy Press, Tokyo, 2002

Preface by Kenta Nakai and Richard H. Lathrop

Program Committee


Full Talk Papers

A String Pattern Regression Algorithm and Its Application to Pattern Discovery in Long Introns
Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano
Genome Informatics 13: 3-11 (2002)
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A Novel Bioinformatic Strategy for Unveiling Hidden Genome Signatures of Eukaryotes: Self-Organizing Map of Oligonucleotide Frequency
Takashi Abe, Shigehiko Kanaya, Makoto Kinouchi, Yuta Ichiba, Tokio Kozuki, Toshimichi Ikemura
Genome Informatics 13: 12-20 (2002)
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Detection of Periodicity in Eukaryotic Genomes on the Basis of Power Spectrum Analysis
Atsushi Fukushima, Toshimichi Ikemura, Taku Oshima, Hirotada Mori, Shigehiko Kanaya
Genome Informatics 13: 21-29 (2002)
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Analysis of Common k-mers for Whole Genome Sequences Using SSB-Tree
Jeong-Hyeon Choi, Hwan-Gue Cho
Genome Informatics 13: 30-41 (2002)
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Large Scale Statistical Prediction of Protein-Protein Interaction by Potentially Interacting Domain (PID) Pair
Wan Kyu Kim, Jong Park, Jung Keun Suh
Genome Informatics 13: 42-50 (2002)
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A Comparative Study on Feature Selection and Classification Methods Using Gene Expression Profiles and Proteomic Patterns
Huiqing Liu , Jinyan Li, Limsoon Wong
Genome Informatics 13: 51-60 (2002)
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Extraction of Organism Groups from Phylogenetic Profiles Using Independent Component Analysis
Yoshihiro Yamanishi, Masumi Itoh, Minoru Kanehisa
Genome Informatics 13: 61-70 (2002)
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Origin of Most Primitive mRNAs and Genetic Codes via Interactions between Primitive tRNA Ribozymes
Koji Ohnishi, Shouken Hokari, Hiroshi Shutou, Madoka Ohshima, Naotaka Furuichi, Masaki Goda
Genome Informatics 13: 71-81 (2002)
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Very Fast Algorithms for Evaluating the Stability of ML and Bayesian Phylogenetic Trees from Sequence Data
Peter J. Waddell, Hirohisa Kishino, Rissa Ota
Genome Informatics 13: 82-92 (2002)
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An Algorithmic Analysis of the Role of Unequal Crossover in Alpha Satellite DNA Evolution
Can Alkan, Jeffrey A. Bailey, Evan E. Eichler, S. Cenk Sahinalp, Eray Tuzun
Genome Informatics 13: 93-102 (2002)
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Genomic Sorting with Length-Weighted Reversals
Ron Y. Pinter, Steven Skiena
Genome Informatics 13: 103-111 (2002)
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Marginalized Kernels for RNA Sequence Data Analysis
Taishin Kin, Koji Tsuda, Kiyoshi Asai
Genome Informatics 13: 112-122 (2002)
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Aligning Multiple Protein Sequences by Parallel Hybrid Genetic Algorithm
Hung Dinh Nguyen, Ikuo Yoshihara, Kunihito Yamamori, Moritoshi Yasunaga
Genome Informatics 13: 123-132 (2002)
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Inference of Euler Angles for Single Particle Analysis by Using Genetic Algorithms
Shusuke Saeki, Kiyoshi Asai, Katsutoshi Takahashi, Yutaka Ueno, Katsunori Isono, Hitoshi Iba
Genome Informatics 13: 133-142 (2002)
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Point Matching Under Non-Uniform Distortions and Protein Side Chain Packing Based on an Efficient Maximum Clique Algorithm
Dukka Bahadur K. C., Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki, Asao Fujiyama
Genome Informatics 13: 143-152 (2002)
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The Role of DNA Deformation Energy at Individual Base Steps for the Identification of DNA-Protein Binding Sites
Nicholas R. Steffen, Scott D. Murphy, Richard H. Lathrop, Michael L. Opel, Lorenzo Tolleri, G. Wesley Hatfield
Genome Informatics 13: 153-162 (2002)
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Folding Pattern Recognition in Proteins Using Spectral Analysis Methods
Carlos A. Del Carpio-Munoz, Julio Cesar Carbajal L.
Genome Informatics 13: 163-172 (2002)
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Comparative Analysis of the Genomes of Cyanobacteria and Plants
Naoki Sato
Genome Informatics 13: 173-182 (2002)
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A Novel Index which Precisely Derives Protein Coding Regions from Cross-Species Genome Alignments
Hideki Noguchi, Tetsushi Yada, Yoshiyuki Sakaki
Genome Informatics 13: 183-191 (2002)
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Using Feature Generation and Feature Selection for Accurate Prediction of Translation Initiation Sites
Fanfan Zeng, Roland H. C. Yap, Limsoon Wong
Genome Informatics 13: 192-200 (2002)
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Automatic Ontology Construction from the Literature
Christian Blaschke, Alfonso Valencia
Genome Informatics 13: 201-213 (2002)
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In Silico Metabolic Pathway Analysis and Design: Succinic Acid Production by Metabolically Engineered Escherichia coli as an Example
Sang Yup Lee, Soon Ho Hong, Soo Yun Moon
Genome Informatics 13: 214-223 (2002)
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Physical Modeling of the Cellular Arrangement in C. elegans Early Embryo: Effect of Rounding and Stiffening of the Cells
Atsushi Kajita, Masayuki Yamamura, Yuji Kohara
Genome Informatics 13: 224-232 (2002)
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Keynote Address

Comparative Genomics for Understanding Ourselves
Yoshiyuki Sakaki
Genome Informatics 13: 235-235 (2002)
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Inferring Gene Transcription Networks: The Davidson Model
Vladimir Filkov, Sorin Istrail
Genome Informatics 13: 236-239 (2002)
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Software Demonstration Abstracts

E-CELL2: E-CELL Simulation System for Windows
Kouichi Takahashi, Naota Ishikawa, Yasuhiro Sadamoto, Hiroyuki Sasamoto, Seiji Ohta, Akira Shiozawa, Fumihiko Miyoshi, Yasuhiro Naito, Yoichi Nakayama, Masaru Tomita
Genome Informatics 13: 240-241 (2002)
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SANAC: Mathematical Simulator for Elucidating the Architecture of Biochemical Networks
Hiroyuki Kurata, Hiroaki Kitano
Genome Informatics 13: 242-243 (2002)
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KnowledgeEditor: A Tool for Interactive Modeling and Analyzing Biological Pathways Based on Microarray Data
Tetsuro Toyoda, Katsura Hirosawa, Akihiko Konagaya
Genome Informatics 13: 244-245 (2002)
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Pedigree Analysis Programme GTree 1.0
Daisuke Ogino, Shiro Mori, Masato Nose, Hideki Sawada
Genome Informatics 13: 246-247 (2002)
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BioRuby: Object Oriented Open Source Library for Bioinformatics
Toshiaki Katayama, Shuichi Kawashima, Naohisa Goto, Mitsuteru C. Nakao, Yoshinori K. Okuji, Minoru Kanehisa
Genome Informatics 13: 248-249 (2002)
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Open Source Clustering Software
Michiel J. L. de~Hoon, Seiya Imoto, Satoru Miyano
Genome Informatics 13: 250-251 (2002)
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Genomic Object Net in JAVA: A Platform for Biopathway Modeling and Simulation
Masao Nagasaki, Atsushi Doi, Makiko Sasaki, Christopher J. Savoie, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 13: 252-253 (2002)
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Hi-per BLAST: High Performance BLAST on PC Cluster System
Akira Naruse, Naoki Nishinomiya, Kouichi Kumon, Masahito Yamaguchi
Genome Informatics 13: 254-255 (2002)
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Poster Abstracts

Correlation-Based Cluster Analysis Using Mixture of Constrained PCAs
Taku Yoshioka, Natsuko Kawase, Shin Ishii
Genome Informatics 13: 256-257 (2002)
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Hybrid Clustering Method for DNA Microarray Data Analysis
Sungwoo Kwon, Chonghun Han
Genome Informatics 13: 258-259 (2002)
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Development of Clustering and Leaf Ordering Tool for Gene Expression Profiles
Sang Soo Yeo, Jung Won Rhee, Sung Kwon Kim
Genome Informatics 13: 260-261 (2002)
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A Novel Clustering Algorithm with Map Energy Minimization
Takatoshi Kawai, Yasuto Yokoi, Yuji Miura, Tsuyoshi Tabata, Takeshi Nagasu, Ken Aoshima
Genome Informatics 13: 262-263 (2002)
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Characteristics of Support Vector Machines in Gene Expression Analysis
Daisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Shigeo Ihara
Genome Informatics 13: 264-265 (2002)
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Quick Learning for Batch-Learning Self-Organizing Map
Makoto Kinouchi, Naoshi Takada, Yoshihiro Kudo, Toshimichi Ikemura
Genome Informatics 13: 266-267 (2002)
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Precise Gene Expression Measurement with Outlier Detection
Jan Dupac, Chihiro Uematsu, Meishan Shen, Vaclav Hlavac, Hideki Kambara, Kazunori Okano
Genome Informatics 13: 268-269 (2002)
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Global Gene Expression Profiling of E. coli and Its Mutant Unable to Produce Acetate
Won Jae Heo, Sung Ho Yoon, Sang Yup Lee
Genome Informatics 13: 270-271 (2002)
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Gene Expression Analysis of Heat Shock Response Using Fuzzy ART
Naoki Kato, Takeshi Kobayashi, Hiroyuki Honda
Genome Informatics 13: 272-273 (2002)
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A Novel Algorithm to Test Significant Differences in Microarray Experiments
Kyoko Toda, Seiichi Ishida, Yuzuru Hayashi, Kotoko Nakata, Rieko Matsuda, Yukari Shigemoto-Mogami, Kayoko Fujishita, Shogo Ozawa, Jun-ichi Sawada, Kazuhide Inoue, Koichi Shudo
Genome Informatics 13: 274-275 (2002)
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Gene Selection Using Gene Expression Data in a Virtual Environment
Kunihiro Nishimura, Shumpei Ishikawa, Shuichi Tsutsumi, Hiroyuki Aburatani, Koichi Hirota, Michitaka Hirose
Genome Informatics 13: 276-277 (2002)
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Selection of Causal Gene Sets from Transcriptional Profiling by FNN Modeling and Prediction of Lymphoma Outcome
Tatsuya Ando, Miyuki Katayama, Masao Seto, Takeshi Kobayashi, Hiroyuki Honda
Genome Informatics 13: 278-279 (2002)
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Parametric Treatment of cDNA Microarray Data
Tomokazu Konishi
Genome Informatics 13: 280-281 (2002)
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Designing of a High-Sensitivity and Low-Background cDNA Microarray
Tadasu Shin-i, Toshifumi Tsukahara, Yasuhiro Kuroda, Ichizo Nishino
Genome Informatics 13: 282-283 (2002)
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Modification of ASIAN: Deduction of a Framework of Gene Regulatory Systems from Expression Profile Data
Katsuhisa Horimoto, Sachiyo Aburatani, Satoru Kuhara, Hiroyuki Toh
Genome Informatics 13: 284-285 (2002)
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A Method for Gene Regulations Inference from Gene Expression Data of Multiple Deletions Mutants
Kotaro Baba, Koji Kyoda, Hiroaki Kitano, Shuichi Onami
Genome Informatics 13: 286-287 (2002)
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Assignment of Direct Binding in Gene Regulatory Systems from Expression Profiles
Sachiyo Aburatani, Satoru Kuhara, Hiroyuki Toh, Katsuhisa Horimoto
Genome Informatics 13: 288-289 (2002)
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Ribozyme and Macroarray: Identification of AP-2-Regulated Genes by Macroarray Profiling of Gene Expression
Hiroshi Minoshima, Eigo Suyama, Hiroaki Kawasaki, Kazunari Taira
Genome Informatics 13: 290-292 (2002)
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New Training Method for Computational Identification of Promoter
Jung Won Rhee, Sang Soo Yeo, Kyung Rak Na, Sung Kwon Kim
Genome Informatics 13: 293-294 (2002)
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Collection and Analysis of Eukaryotic Promoter Regions: DBTSS (DataBase of Transcriptional Start Sites)
Riu Yamashita, Yutaka Suzuki, Toshihisa Takagi, Sumio Sugano, Kenta Nakai
Genome Informatics 13: 295-296 (2002)
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Prediction of Co-Regulated Genes in Eubacterial Genomes by Phylogenetic Footprinting
Yuko Makita, Goro Terai, Shigeki Mitaku, Toshihisa Takagi, Kenta Nakai
Genome Informatics 13: 297-298 (2002)
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Development of an Efficient Method to Search Conserved Noncoding Sequences
Hangil Chang
Genome Informatics 13: 299-300 (2002)
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Building Common Patterns for Transcription Factor Binding Sites of Escherichia coli
Weijiang Li, Hiroyuki Kurata
Genome Informatics 13: 301-302 (2002)
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Inferring Combinatorial Regulation of Binding Sites and Transcription Factors on Gene Expression
Mamoru Kato, Naoya Hata, Nila Banerjee, Michael Q. Zhang
Genome Informatics 13: 303-304 (2002)
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Target Prediction of Transcription Factors: Application of Structure-Based Method to Yeast Genome
Akinori Sarai, Samuel Selvaraj, Michael M. Gromiha, Joerg-Gerald Siebers, Ponraj Prabakaran, Hidetoshi Kono
Genome Informatics 13: 305-307 (2002)
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Prediction of DNA Binding in Proteins from Composition, Sequence and Structure
Shandar Ahmad, Michael M. Gromiha, Akinori Sarai
Genome Informatics 13: 308-309 (2002)
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Analysis of Complementarity of Protein-DNA Interactions Using the Electrostatic Potential and the Molecular Surface Geometry
Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura
Genome Informatics 13: 310-311 (2002)
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Analysis of Protein-RNA Interactions at Atomic Level
Hyunwoo Kim, Euna Jeong, Seong-Wook Lee, Kyungsook Han
Genome Informatics 13: 312-313 (2002)
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Classification of C2H2 Zinc Finger Domains Using Support Vector Machines
Takafumi Nagano, Makiko Suwa, Kiyoshi Asai
Genome Informatics 13: 314-315 (2002)
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The Role of Electrostatics in Discrimination of Adenine and Guanine by Proteins
Dakshanamurthy Sivanesan, Gautam Basu, Nobuhiro Go
Genome Informatics 13: 316-317 (2002)
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Protein Interactions in the Whole Human Genome
Kyungsook Han, Byunggyu Park, Hyongguen Kim, Hong-Jin Kim, Jong Park
Genome Informatics 13: 318-319 (2002)
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Putative Protein Interactome Database
Chung-Yen Lin, Chi-Shang Cho, Chen-Zen Lo, Chao A. Hsiung
Genome Informatics 13: 320-321 (2002)
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Prediction of Protein-Protein Interaction Sites Using Support Vector Machines
Yohei Minakuchi, Kenji Satou, Akihiko Konagaya, Takashi Ito
Genome Informatics 13: 322-323 (2002)
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Interaction Generality, a Measurement to Assess the Reliability of a Protein-Protein Interaction
Rintaro Saito, Masaru Tomita, Harukazu Suzuki, Yoshihide Hayashizaki
Genome Informatics 13: 324-325 (2002)
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Towards a Functional Claasification of ARE Protein Interactoins
Jorg Hackermuller, Nicole-Claudia Meisner, Andras Aszodi, Manfred Auer, Markus Jaritz
Genome Informatics 13: 326-327 (2002)
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Indirect Relations in Yeast Protein Interactome
Akihiro Nakaya, Akiyasu C. Yoshizawa, Susumu Goto, Minoru Kanehisa
Genome Informatics 13: 328-329 (2002)
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Searching for Common Protein Networks in Neurodegenerative Disorders
Vachiranee Limviphuvadh, Susumu Goto, Seigo Tanaka, Kunihiro Ueda, Minoru Kanehisa
Genome Informatics 13: 330-331 (2002)
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Combining MIAX-Based In-Silico-Peptide-Chips with Membrane-Support Peptide-Array-Chips Oriented to Novel Drug Discovery
Carlos A. Del Carpio-Munoz, William Campbell, Mitoshi Kunimatsu
Genome Informatics 13: 332-333 (2002)
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Identification and Classification of Eukaryotic GPCRs by Binary Topology Pattern
Yasuhito Inoue, Masami Ikeda, Toshio Shimizu
Genome Informatics 13: 334-335 (2002)
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Application of Covariation Analysis in 3D Structure Prediction of G-Protein Coupled Receptors
Wataru Nemoto, Takashi Imai, Takeshi Kikuchi, Norihisa Fujita
Genome Informatics 13: 336-337 (2002)
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Analysis of the Evolutionary Relationships of the PDZ Domains
Masaki Yamamura, Tatsuya Akutsu, Susumu Goto
Genome Informatics 13: 338-339 (2002)
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Protein Structure Analysis Using Continuous Density Hidden Markov Models
Morihiro Hayashida, Nobuhisa Ueda, Katsuhisa Horimoto, Tatsuya Akutsu
Genome Informatics 13: 340-341 (2002)
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Identification of Ortholog Groups in KEGG/SSDB by Considering Domain Structures
Masumi Itoh, Akihiro Nakaya, Minoru Kanehisa
Genome Informatics 13: 342-343 (2002)
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FROG (Fitted Rotation and Orientation of protein structure by means of real-coded Genetic algorithm): Asynchronous Parallelizing for Protein Structure-Based Comparison on the Basis of Geometrical Similarity
Sung-Joon Park, Masayuki Yamamura
Genome Informatics 13: 344-345 (2002)
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Formulation of the Energy Distribution among a Globular Protein Structure Ensemble for the High-through-Put Screening of Sequences
Takuyo Aita, Yuzuru Husimi
Genome Informatics 13: 346-347 (2002)
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Importance of Long-Range Interactions for Determining the Folding Rate and Transition State Structures of Two-state Proteins
Michael M. Gromiha, Samuel Selvaraj
Genome Informatics 13: 348-349 (2002)
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Pathways - a Unifying Framework for Systems Biology Data
Michael A. Gibson, Richard Messenger, Jun Qian, Lingyan Zhu, Christophe Beaumont, Steve Anderson, Joseph A. Borkowski
Genome Informatics 13: 350-350 (2002)
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Generalized Representation of Metabolic and Regulatory Pathways
Min Kyung Kim, Hyun Seok Park
Genome Informatics 13: 351-352 (2002)
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Extraction of Modules from the Metabolic Pathways with Phylogenetic Profile
Takuji Yamada, Yoshihiro Yamanishi, Susumu Goto, Minoru Kanehisa
Genome Informatics 13: 353-354 (2002)
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Vzyme: A Template-Based Method to Predict Reactions between Two Chemical Compounds
Yasushi Okuno, Masahiro Hattori, Masaaki Kotera, Yoshinobu Igarashi, Susumu Goto, Minoru Kanehisa
Genome Informatics 13: 355-356 (2002)
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Candidate Genes at Locus Heterogeneity Closely Lying on Metabolic Pathway: A Hypothesis Test toward Phenotype-to-Genes Search
Eli Kaminuma, Tetsuro Toyoda, Akihiko Konagaya
Genome Informatics 13: 357-358 (2002)
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A Mathematical Modeling of Signal Transduction Cascade on Raf-Akt Cross-Talk
Mariko Hatakeyama, Shuhei Kimura, Noriko Yumoto, Mio Ichikawa, Takuji Kawasaki, Takashi Naka, Akihiko Konagaya
Genome Informatics 13: 359-360 (2002)
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Computer Modeling of Ras-MAPK Signal Transduction Pathway
Satoshi Yamada, Akihiko Yoshimura
Genome Informatics 13: 361-362 (2002)
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Exploring Flux Distribution Profiles for Switching Pathways Using Multiobjective Flux Balance Analysis
Dong-Yup Lee, Young-gyun Oh, Hongseok Yoon, Sang Yup Lee, Sunwon Park
Genome Informatics 13: 363-364 (2002)
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Discovery of Analogous Enzymes in Thiamin Biosynthesis by Anticorrelation
Enrique Morett, Jan O. Korbel, Emmanuvel Rajan, Gloria Saab-Rincon, Leticia Olvera, Maricela Olvera, Steffen Schmidt, Berend Snel, Peer Bork
Genome Informatics 13: 365-366 (2002)
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Genome-Wide Search of Human Genes Implicated in WNT Signaling Pathway Using Bioinformatics
Masaru Katoh
Genome Informatics 13: 367-368 (2002)
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Bootstrap Analysis of Gene Networks Based on Bayesian Netowrks and Nonparamatric Regression
Seiya Imoto, SunYong Kim, Hidetoshi Shimodaira, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
Genome Informatics 13: 369-370 (2002)
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Dynamic Bayesian Network and Nonparametric Regression Model for Inferring Gene Networks
SunYong Kim, Seiya Imoto, Satoru Miyano
Genome Informatics 13: 371-372 (2002)
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An Analysis of Cancer Microarrays in the Pathway Context Using Bayesian Networks
Yohsuke Minowa, Susumu Goto, Minoru Kanehisa
Genome Informatics 13: 373-374 (2002)
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Statistical Properties of Randomly Constructed Boolean Networks that Resemble the Transcription Factor Network of Escherichia coli
Chikoo Oosawa, Michael A. Savageau
Genome Informatics 13: 375-376 (2002)
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Genetic Network Analysis Using F2DMatrix
Hiro Takahashi, Shuta Tomida, Takeshi Kobayashi, Hiroyuki Honda
Genome Informatics 13: 377-379 (2002)
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Comparison between Two Different Genetic Network Inferring Models on Expression Profiles in S. cerevisiae
Yoriko Takahashi, Yuji Arikawa, Shoji Watanabe, Yukihiro Maki, Sachiyo Aburatani, Satoru Kuhara, Yukihiro Eguchi
Genome Informatics 13: 380-381 (2002)
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Inference of Genetic Network Using the Expression Profile Time Course Data of Mouse P19 Cells
Yukihiro Maki, Takanori Ueda, Masahiro Okamoto, Naoya Uematsu, Kentaro Inamura, Kazuhiko Uchida, Yoriko Takahashi, Yukihiro Eguchi
Genome Informatics 13: 382-383 (2002)
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An Inference Engine for Gene Network Determination by Means of Optical Array Logic
Kouichi Nitta, Jun Tanida
Genome Informatics 13: 384-385 (2002)
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Development of System Identification Technique Based on Real-Coded Genetic Algorithm
Takanori Ueda, Isao Ono, Masahiro Okamoto
Genome Informatics 13: 386-387 (2002)
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A Fast Clustering System for a Huge Number of Nucleotide Sequences
Tomohiro Yasuda, Tetsuo Nishikawa
Genome Informatics 13: 388-389 (2002)
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Computational Structural Genomics of a Complete Minimal Organism
John-Marc Chandonia, David E. Konerding, Darryl G. Allen, In-Geol Choi, Hisao Yokota, Steven E. Brenner
Genome Informatics 13: 390-391 (2002)
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Global Analysis of Distribution and Preference of A-Tract in Bacteria and Archaea Genomes
Takeshi Ozaki, Atsushi Fukushima, Hayato Kimura, Taku Oshima, Shigehiko Kanaya, Hirotada Mori
Genome Informatics 13: 392-393 (2002)
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Prediction of Target Substrates of Transporters in Escherichia coli
Shin-ichi Matsusaki, Hidemi Watanabe, Taku Oshima, Shigehiko Kanaya, Hirotada Mori
Genome Informatics 13: 394-395 (2002)
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Comparison of SVM-Based Methods for Remote Homology Detection
Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu, Nobuhisa Ueda
Genome Informatics 13: 396-397 (2002)
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Improvement in Performance of Homology-Based Prediction of Human Gene Organizations
Osamu Gotoh, Kaoru Sugimori
Genome Informatics 13: 398-399 (2002)
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Comprehensive Analysis of Tandem Repeat Sequences in Cyanobacteria Genome
Toshiaki Katayama, Shinobu Okamoto, Rei Narikawa, Takatomo Fujisawa, Shuichi Kawashima, Masumi Itoh, Masayuki Ohmori, Minoru Kanehisa
Genome Informatics 13: 400-401 (2002)
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CYORF: Community Annotation of Cyanobacteria Genes
Miho Furumichi, Yoko Sato, Tatsuo Omata, Masahiko Ikeuchi, Minoru Kanehisa
Genome Informatics 13: 402-403 (2002)
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Comparative Analysis of Rab GTPases and SNAREs in Eukaryotic Genomes
Akiyasu C. Yoshizawa, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 13: 404-405 (2002)
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Correlation Analysis between tRNA Composition and Codon Usage Using Diversity and Equitability Index
Haruo Susuki, Kazuharu Arakawa, Tatekimi Matsuzaki, Rintaro Saito, Masaru Tomita
Genome Informatics 13: 406-407 (2002)
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Tandem Repeats in Prokaryotic Genomes
Jiewen Liu, Hikaru Munakata, Abulimiti Aimaiti, Akito Taneda, Kenji Oosawa, Toshio Shimizu
Genome Informatics 13: 408-409 (2002)
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Dot Plot Detects Repetitive Structures in DNA Sequences
Akito Taneda, Toshio Shimizu
Genome Informatics 13: 410-411 (2002)
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Power Spectra of DNA Sequences in Phage and Tumor Suppressor Genes (TSG)
Eisei Takushi
Genome Informatics 13: 412-413 (2002)
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Prediction of RNA Pseudoknots -- Comparative Study of Genetic Algorithms
Dongkyu Lee, Kyungsook Han
Genome Informatics 13: 414-415 (2002)
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Transmembrane-Protein-Gene Clusters in Prokaryotic Genomes
Tsutomu Yokoyama, Toshio Shimizu
Genome Informatics 13: 416-417 (2002)
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Classification of Transmembrane Protein Families Based on Topological Similarity
Hironori Mitsuke, Yoshiaki Sugiyama, Toshio Shimizu
Genome Informatics 13: 418-419 (2002)
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Comprehensive Functional Classification/Identification of Prokaryotic Transmembrane Proteins by Sequence and Topology Similarities
Yoshiaki Sugiyama, Masafumi Arai, Toshio Shimizu
Genome Informatics 13: 420-421 (2002)
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Analysis of Asymmetry of Membrane Proteins by Evolutionary Trace
Hisako Ichihara, Hiromi Daiyasu, Hiroyuki Toh
Genome Informatics 13: 422-423 (2002)
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Analysis of Aberrant Splicing Data
Yoshinori Tamada, Sascha Ott, Hideo Bannai, SunYong Kim, Kenta Nakai, Satoru Miyano
Genome Informatics 13: 424-425 (2002)
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Positional Correlations in Splicing Patterns ---Its Application to Prediction of Splice Sites
Takumi Watanabe, Yumi Kudo, Toshio Shimizu
Genome Informatics 13: 426-427 (2002)
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Distribution Analysis of the Oligonucleotide around 5' Splice Sites in H. sapiens, M. musculus, D. melanogaster and A. thaliana pre-mRNAs
Sumie Kitamura-Abe, Nobuyuki Takahashi, Hitomi Itoh, Atsushi Sakurai, Rintaro Saito, Takanori Washio, Masaru Shimbo, Akihiro Tsutsumi, Masaru Tomita
Genome Informatics 13: 428-429 (2002)
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Parameter Landscape Analysis for Improving the Performance of Common Motif Detection Algorithms
Natalia Poluliakh, Michiko Konno, Toshihisa Takagi, Kenta Nakai
Genome Informatics 13: 430-431 (2002)
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A Method for the Best Model Selection for Single and Paired Motifs
Daisuke Shinozaki, Osamu Maruyama
Genome Informatics 13: 432-433 (2002)
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NJML+P: A Hybrid Algorithm of the Maximum Likelihood and Neighbor-Joining Methods Using Parallel Computing
Satoshi OOta, Naruya Saitou
Genome Informatics 13: 434-435 (2002)
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Gapless Local Alignment of Multiple Sequences
Martin C. Frith, Joel H. Graber, Zhiping Weng, John L. Spouge
Genome Informatics 13: 436-437 (2002)
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Weak Homology Detection by Profile-Profile Comparison
Masashi Fujita, Tatsuya Akutsu, Susumu Goto, Minoru Kanehisa
Genome Informatics 13: 438-439 (2002)
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Building a Better BLAST: A Systematic Comparison of BLAST Implementations
Alan Kilian, Kosuke Goto, Yasuhiro Kuroda, Daniel Naimey
Genome Informatics 13: 440-440 (2002)
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Improvement of PSORT II Protein Sorting Prediction for Mammalian Proteins
Mitsuteru C. Nakao, Kenta Nakai
Genome Informatics 13: 441-442 (2002)
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Finding Conserved Amino Acid Sequences among Prokaryotic Proteomes
Naohisa Goto, Ken Kurokawa, Teruo Yasunaga
Genome Informatics 13: 443-444 (2002)
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A Visualization Tool for Gene Network Discovery - G.NET
Ken Aoshima, Masayuki Ikawa, Satoshi Tanaka, Koji Yanagisawa, Kim Sun Yong, Naoki Nariai, Seiya Imoto, Satoru Miyano
Genome Informatics 13: 445-446 (2002)
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BiopathwayBuilder: Nested 3D Visualization System for Complex Molecular Interactions
Changsu Lee, Jinah Park, Jong C. Park
Genome Informatics 13: 447-448 (2002)
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Genome Visualization by Isometric Projection Focused on Replication Origins and Termini, and Genome Instability
Hirokazu Nishio, Ken-nosuke Wada, Yoshiko Wada, Atsushi Fukushima, Toshimichi Ikemura, Hirotada Mori, Taku Oshima, Shigehiko Kanaya
Genome Informatics 13: 449-450 (2002)
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Complexity of Pedigree Analysis
Daisuke Ogino, Hideki Sawada
Genome Informatics 13: 451-452 (2002)
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Experimental Observations and Simulations by Genomic Object Net of Notch Signaling in Drosophila Multicellular Systems
Hiroshi Matsuno, Ryutaro Murakami, Rie Yamane, Naoyuki Yamasaki, Sachie Fujita, Haruka Yoshimori, Satoru Miyano
Genome Informatics 13: 453-454 (2002)
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Development of Genomic Object Net Builder for Supporting XML Design for Visualization
Toshinori Tanaka, Hironori Kitakaze, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 13: 455-456 (2002)
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XML Pathway File Conversion between Genomic Object Net and SBML
Masafumi Nakano, Hironori Kitakaze, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 13: 457-458 (2002)
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A Computational Model of Mammalian Cell Cycle Using Petri Nets
Shuji Kotani, Takashi Yoshioka, Akihiko Konagaya
Genome Informatics 13: 459-460 (2002)
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Protein Explorer: A Petaflops Special-Purpose Computer for Molecular Dynamics Simulations
Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada, Akihiko Konagaya
Genome Informatics 13: 461-462 (2002)
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Development of Biochemical System Simulator with Parameter Estimator
Takuji Kawasaki, Shuhei Kimura, Mariko Hatakeyama, Takashi Naka, Akihiko Konagaya
Genome Informatics 13: 463-464 (2002)
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A Study of Development Scheme of Biosimulator
Shigeyuki Mitsui, Hideko Urushihara, Kazuko Hagiwara, Hiroya Nobori, Hiroyuki Watanabe, Katsumi Sakata
Genome Informatics 13: 465-466 (2002)
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BIOCAD Project for Synthesis and Analysis of Gene Regulatory Networks
Hiroyuki Kurata, Yoshiyuki Sumida, Shin Tanaka, Kouichi Masaki, Takayuki Tanaka, Yuki Urago, Ken Ohashi
Genome Informatics 13: 467-468 (2002)
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A -Calculus Model of the Na Pump
Gabriel Ciobanu, Vlad Ciubotariu, Bogdan Tanasa
Genome Informatics 13: 469-471 (2002)
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Theoretical Analyses of Circadian Oscillation Regulated by mRNA Half-Life
Nobukazu Ohki, Masatoshi Hagiwara
Genome Informatics 13: 472-473 (2002)
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Bifurcation Diagram Analyzer for Differential Equations of Biological Models
Rikuhiro Yamada, Minoru Kanehisa
Genome Informatics 13: 474-475 (2002)
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Electrophysiological Simulation of Myocardial Cell Using E-CELL System
Shoko Miyamoto, Yasuhiro Naito, Motohiro Yoneda, Sayaka Ishinabe, Shinobu Kuratomi, Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma, Masaru Tomita
Genome Informatics 13: 476-477 (2002)
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Construction of a Simulation Model of Diabetes for Pathophysiological Analysis Using E-Cell System
Yasuhiro Naito, Hiroshi Ohno, Atsumi Sano, Hiromu Nakajima, Masaru Tomita
Genome Informatics 13: 478-479 (2002)
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A Simulation Model of Cardiovascular System for Diabetes Pathophysiological Model Using E-Cell System
Atsumi Sano, Yasuhiro Naito, Hiroshi Ohno, Hiromu Nakajima, Masaru Tomita
Genome Informatics 13: 480-481 (2002)
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Automatic Transformation of Kinetic Equations into S-System and GMA Forms
Yohei Yamada, Ayako Kinoshita, Yoichi Nakayama, Masaru Tomita
Genome Informatics 13: 482-483 (2002)
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OBIGrid: A New Computing Platform for Bioinformatics
Fumikazu Konishi, Akinobu Fukuzaki, Kenji Satou, Tomoyuki Yamamoto, Xavier Defago, Akihiko Konagaya
Genome Informatics 13: 484-485 (2002)
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Development of Database Systems by Integrating Heterogeneous Metabolic Databases
Jin Sik Kim, Sung Ho Yoon, Doheon Lee, Sang Yup Lee
Genome Informatics 13: 486-487 (2002)
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New Features of PDBj-ML, an XML format for Protein Data Bank
Nobutoshi Ito, Hisashi Sakamoto, Kaori Kobayashi, Yoshikazu Kaneta, Yohei Kawaguchi, Takenao Ohkawa, Haruki Nakamura
Genome Informatics 13: 488-489 (2002)
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Classification and Analysis of KEGG/REACTION Database
Masaaki Kotera, Yasushi Okuno, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
Genome Informatics 13: 490-491 (2002)
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Improvement of the LIGAND Chemical Database
Rumiko Yamamoto, Tomoko Komeno, Susumu Goto, Yasushi Okuno, Masahiro Hattori, Minoru Kanehisa
Genome Informatics 13: 492-493 (2002)
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The Construction and Analysis of the Multidrug Resistance Transporter Knowledge-Base
Yoshinobu Igarashi, Yasushi Okuno, Susumu Goto, Minoru Kanehisa
Genome Informatics 13: 494-495 (2002)
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Database of Operons in Bacillus subtilis
Shujiro Okuda, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 13: 496-497 (2002)
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Development of a Protein-Ligand Interaction Database, ProLINT, and Its Application to QSAR Analysis
Kouji Kitajima, Shandar Ahmad, Samuel Selvaraj, Hideo Kubodera, Shinji Sunada, Jianghong An, Akinori Sarai
Genome Informatics 13: 498-499 (2002)
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Recent Developments in ProTherm: Thermodynamic Database for Proteins and Mutants
K. Abdulla Bava, Michael M. Gromiha, Hatsuho Uedaira, Koji Kitajima, Akinori Sarai
Genome Informatics 13: 500-501 (2002)
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Progress of ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions
Hatsuho Uedaira, Ponraj Prabakaran, Michael M. Gromiha, Kouji Kitajima, Akinori Sarai
Genome Informatics 13: 502-503 (2002)
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Kinase Pathway Database: An Integrated Resource of Automatically Extracted Information and Sequence Analysis
Asako Koike, Yoshiyuki Kobayashi, Toshihisa Takagi
Genome Informatics 13: 504-505 (2002)
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Database of Human UV-Regulated Genes
Goro Terai, Makoto Yamazaki, Yoshinori Sugiyama, Hiroko Ao, Shintaro Inoue, Toshihisa Takagi
Genome Informatics 13: 506-507 (2002)
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An Integrated Database System for Full-Length Human cDNA in NEDO Full-Length Human cDNA Sequencing Project
Tetsuo Nishikawa, Kouichi Kimura, Tomohiro Yasuda, Keiichi Nagai, Sumio Sugano, Takao Isogai
Genome Informatics 13: 508-510 (2002)
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SEVENS: A Comprehensive Collection of Human Seven Transmembrane Helix Receptors
Makiko Suwa, Masanori Arita, Shinichi Matsumoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Kiyoshi Asai,Yutaka Akiyama
Genome Informatics 13: 511-512 (2002)
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Construction of Human Pathogenic Bacterial DB and Integration of Oligonucleotide Probe Selection Tools
Byeong-Chul Kang, Heung-Soo Park, Jun-Hyung Park, Hyun-Jung Jang, Hyuk-Jin Choi, Ho-Young Kang, Chang-Jin Shin, Hee-Kyung Park, Cheolmin Kim
Genome Informatics 13: 513-514 (2002)
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A Nuclear Receptor Database that Maps Pathways to Diseases
Kotoko Nakata, Masumi Yukawa, Naomi Komiyama, Tatsuya Nakano, Tsuguchika Kaminuma
Genome Informatics 13: 515-516 (2002)
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GENIUS II: A Database System Including Complete Genome ORFs that are Assigned to Protein Three-Dimensional Domains
Yukimitsu Yabuki, Yuri Mukai, Makiko Suwa
Genome Informatics 13: 517-518 (2002)
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ProMode: A Database of Normal Mode Analysis of Proteins
Hiroshi Wako, Shigeru Endo
Genome Informatics 13: 519-520 (2002)
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RAD: Rice Annotation Database
Yuichi Ito, Isamu Ohta, Yoshiyuki Mukai, Shinji Naito, Baltazar A. Antonio, Atsuko Shimano, Masayoshi Masukawa, Michie Shibata, Mayu Yamamoto, Kohji Arikawa, Yasumichi Sakai, Kazuyoshi Makino, Katsumi Sakata, Nobukazu Namiki, Takashi Matsumoto, Takuji Sasaki
Genome Informatics 13: 521-522 (2002)
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Development of a Database Platform for the Rice Genome Project
Minoru Yoshikawa, Masakazu Inaba, Kiyoshi Matsubara, Hideaki Koike
Genome Informatics 13: 523-524 (2002)
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A New Method for Database Searching: The BlastNP
Jan Charles Biro
Genome Informatics 13: 525-526 (2002)
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Design of Various High Quality Random Libraries for in vitro Protein Evolution
Sayaka Soramoto, Shingo Ueno, Ichiro Tabuchi, Yuzuru Husimi
Genome Informatics 13: 527-528 (2002)
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Development and Implementation of the G-Language Genome Analysis Environment Version 2
Kazuharu Arakawa, Koya Mori, Tatekimi Matsuzaki, Ryo Hattori, Yohei Yamada, Masaru Tomita
Genome Informatics 13: 529-530 (2002)
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Development of Comparative Genome Analysis System (COMGA) on the G-Language Genome Analysis Environment
Seira Nakamura, Tatekimi Matsuzaki, Kazuharu Arakawa, Koya Mori, Yoichi Nakayama, Masaru Tomita
Genome Informatics 13: 531-532 (2002)
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Development of Chi Sequence Analysis System on the G-Language Genome Analysis Environment
Daisuke Kyuma, Kazuharu Arakawa, Reina Uno, Yoichi Nakayama, Masaru Tomita
Genome Informatics 13: 533-534 (2002)
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System for Extraction of Protein Interaction Based on Aging-Related Corpus
Hyuk-Gyu Cho, Dae Ui Park, Hyuk-Chul Kwon, Hea Young Chung
Genome Informatics 13: 535-536 (2002)
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AgingDB: Aging-Related Signal Pathway Imagemap and Protein Interaction Visualization
Dae Ui Park, Chul Hong Kim, Seong Eui Hong, Byung Pal Yu, Hea Young Chung
Genome Informatics 13: 537-538 (2002)
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A Legume Lotus japonicus Genome Annotation
Yasukazu Nakamura, Erika Asamizu, Takakazu Kaneko, Tomohiko Kato, Shusei Sato, Satoshi Tabata
Genome Informatics 13: 539-540 (2002)
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A High-Throughput Annotation System of Rice Genome Sequence at RGP
Atsuko Idonuma, Nobukazu Namiki, Takashi Matsumoto, Satoshi Nobushima, Shigehiro Honda, Takuji Sasaki
Genome Informatics 13: 541-542 (2002)
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ETools: Tools to Handle Biological Sequences and Alignments for Evolutionary Studies
Toshinori Endo, Soichi Ogishima, Hiroshi Tanaka
Genome Informatics 13: 543-544 (2002)
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An Extracting System of Accurate ORFs from cDNA Sequences
Tetsuo Nishikawa, Katsuhiko Murakami, Koji Hayashi, Hiroyuki Sato, Tetsuji Otsuki, Naoko Kasahara, Tomohiro Yasuda, Kouichi Kimura, Keiichi Nagai, Ryotaro Irie, Tomoyasu Sugiyama, Takao Isogai
Genome Informatics 13: 545-547 (2002)
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Intris: A Viewer for cDNA-Genome Alignments Enabling Efficient Detection of Splicing Variants and Expression Profiles
Kouichi Kimura, Tetsuo Nishikawa, Keiichi Nagai, Sumio Sugano, Takao Isogai
Genome Informatics 13: 548-550 (2002)
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Prediction of Random PCR Products and Its Inverse Problem
Ayumu Saito, Koichi Nishigaki
Genome Informatics 13: 551-552 (2002)
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BioTags: A JSP Tag Library for Bioinformatics Website Construction
Aki Hasegawa, Ryo Umetsu, Akihiko Konagaya
Genome Informatics 13: 553-554 (2002)
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A Web Site for Location to Location Correspondence (L2LC): Circular Genome Comparison from Related Gene Configuration
Kentaro Mori, Satoshi Fukuchi, Ken Nishikawa, Katsuhisa Horimoto
Genome Informatics 13: 555-556 (2002)
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Genome Scenario: The Integrated Environment for Genome Analysis
Toshiyuki Koike, Akiko Inoue, Kazuo Takehana, Katsuji Matsumura, Jiro Araki, Takehiko Ito, Masako Kuroda
Genome Informatics 13: 557-558 (2002)
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A Web Based Mutation Analysis System for BRCA Genes
Jun-Hyung Park, Byeong-Chul Kang, Heung-Soo Park, Hee-Kyung Park, Cheol-Min Kim
Genome Informatics 13: 559-560 (2002)
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An Application of Special Function Units of the CRAY SV1 System to a Contamination Problem of Human Chromosome 21 and 11
Akira Iida, Kenji Oosawa, Asao Fujiyama
Genome Informatics 13: 561-562 (2002)
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THEMATICS as a Tool for Functional Genomics
Mary Jo Ondrechen
Genome Informatics 13: 563-564 (2002)
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FAMS and FAMSBASE: Modeling of All the Genomes and Database
Mitsuo Iwadate, Shigetsugu Kawakita, Hideaki Umeyama
Genome Informatics 13: 565-566 (2002)
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Using Unlabeled MEDLINE Abstracts for Biological Named Entity Classification
Manabu Torii, K. Vijay-Shanker
Genome Informatics 13: 567-568 (2002)
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Construction of User Model Using Behavior of Retrieved Ontology
Masaru Takeya, Hisataka Numa, Kotaro Baba
Genome Informatics 13: 569-570 (2002)
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Extracting Biological Keywords from Scientific Text
Wen-Juan Hou, Hsin-Hsi Chen
Genome Informatics 13: 571-573 (2002)
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A Text Mining Middleware for Life Science
Harunobu Kubo, Naohiko Uramoto, Stephan Grell, Hirofumi Matsuzawa
Genome Informatics 13: 574-575 (2002)
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Toward Ontology-Based Knowledge Extraction from Biomedical Literature
Satoshi Kamegai, Kenji Satou, Akihiko Konagaya
Genome Informatics 13: 576-577 (2002)
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Sense Disambiguation in PubMed Abstracts Using Text and Data Mining
Yun Jeong Choi, Seung Soo Park, Min Kyung Kim, Hyun Seok Park
Genome Informatics 13: 578-579 (2002)
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AGEV: Automated Gene Extraction through Literature Mining and Visualization of Gene Structure
Seong-Eui Hong, Dae-Ui Park, Chul-Hong Kim, Byung-Pal Yu, Hae-Young Chung
Genome Informatics 13: 580-581 (2002)
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Identification of Novel Genes Associated with Rat Leukemogenesis by Clustering Analysis
Kenichi Koami, Shinya Yamakita, Tamotsu Irino, Mitsuhiko Osaka
Genome Informatics 13: 582-583 (2002)
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Understanding the Genetic Information Process at Giant DNA Chain Aggregate with Spermidine, ATP and Mg++ as Biological Conditions
Yasuo Yonezawa, Hidetoshi Kuramochi, Sinobu Nagano
Genome Informatics 13: 584-586 (2002)
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Comparison of Transcript Levels by DNA Microarray and Metabolic Flux Based on Flux Analysis for the Production of Poly- -Glutamic Acid in Recombinant Escherichia coli
Sung Ho Yoon, Sang Yup Lee
Genome Informatics 13: 587-588 (2002)
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Design of ITS and 23S rDNA-Targeted Probes and Its Usefulness for the Identification of Bacterial Pathogens
So Young Yoo, Kyung Hee Chang, Seung Min Yoo, Sun Young Park, Nae Choon Yoo, Ki Chang Keum, Won Min Yoo, June Myung Kim, Sang Yup Lee
Genome Informatics 13: 589-590 (2002)
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Whole Genome PCR Scanning Analyzer and Its Application to Bacterial Genome
Masatomo Najima, Ken Kurokawa, Makoto Ohnishi, Tetsuya Hayashi, Teruo Yasunaga
Genome Informatics 13: 591-592 (2002)
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Combined Metabolome and Transcriptome Analysis of Bacillus subtilis Cells Cultured on Different Carbon Sources
Keiko Matsuda, Hirotake Yamaguchi, Yuki Ueno, Tomoyoshi Soga, Yasutaro Fujita, Takaaki Nishioka
Genome Informatics 13: 593-594 (2002)
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A New Method for Phenome Analysis of Arabidopsis thaliana: Collection of Morphological Information by Using 3-Dimensional Laser Scanner
Tetsuro Toyoda, Naohiko Heida, Eli Kaminuma, Akihiko Konagaya, Naoki Okamoto, Minami Matsui
Genome Informatics 13: 595-596 (2002)
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