Genome Informatics Vol. 12 (2001)

Presented at the 12th International Conference on Genome Informatics
December 17-19, 2001, The Garden Hall, Yebisu Garden Place, Tokyo, Japan

Published as: H. Matsuda, S. Miyano, T. Takagi, and L. Wong (eds.)
"Genome Informatics 2001"
Universal Academy Press, Tokyo, 2001

Preface by Hideo Matsuda and Limsoon Wong

Program Committee


Full Talk Papers

Emerging Patterns and Gene Expression Data
Jinyan Li, Limsoon Wong
Genome Informatics 12: 3-13 (2001)
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Selecting Informative Genes with Parallel Genetic Algorithms in Tissue Classification
Juan Liu, Hitoshi Iba, Mitsuru Ishizuka
Genome Informatics 12: 14-23 (2001)
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Minimum Spanning Trees for Gene Expression Data Clustering
Ying Xu, Victor Olman, Dong Xu
Genome Informatics 12: 24-33 (2001)
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Characterizing the Relationship between Protein-Fusion and Gene Co-Expression
Cary S. Gunther, Terry Gaasterland
Genome Informatics 12: 34-43 (2001)
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Extraction of Correlated Gene Clusters by Multiple Graph Comparison
Akihiro Nakaya, Susumu Goto, Minoru Kanehisa
Genome Informatics 12: 44-53 (2001)
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XML Documentation of Biopathways and Their Simulations in Genomic Object Net
Hiroshi Matsuno, Atsushi Doi, Yuichi Hirata, Satoru Miyano
Genome Informatics 12: 54-62 (2001)
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Estimation of Bidirectional Metabolic Fluxes from MS and NMR Data Using Positional Representations
Marcos J. Arauzo-Bravo, Kazuyuki Shimizu
Genome Informatics 12: 63-72 (2001)
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A Multi-Queue Branch-and-Bound Algorithm for Anytime Optimal Search with Biological Applications
Richard H. Lathrop, Anton Sazhin, Ye Sun, Nick Steffen, Sandra S. Irani
Genome Informatics 12: 73-82 (2001)
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Local Multiple Alignment of Numerical Sequences: Detection of Subtle Motifs from Protein Sequences and Structures
Tatsuya Akutsu, Katsuhisa Horimoto
Genome Informatics 12: 83-92 (2001)
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A Graph-Based Clustering Method for a Large Set of Sequences Using a Graph Partitioning Algorithm
Hideya Kawaji, Yosuke Yamaguchi, Hideo Matsuda, Akihiro Hashimoto
Genome Informatics 12: 93-102 (2001)
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Prediction of Subcellular Localizations Using Amino Acid Composition and Order
Yukiko Fujiwara, Minoru Asogawa
Genome Informatics 12: 103-112 (2001)
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Automatic Epitope Recognition in Proteins Oriented to the System for Macromolecular Interaction Assessment MIAX
Atsushi Yoshimori, Carlos A. Del Carpio
Genome Informatics 12: 113-122 (2001)
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The Potential Use of SUISEKI as a Protein Interaction Discovery Tool
Christian Blaschke, Alfonso Valencia
Genome Informatics 12: 123-134 (2001)
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Conservation of Protein Interaction Network in Evolution
Jong Park, Dan Bolser
Genome Informatics 12: 135-140 (2001)
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A Phylogenetic Foundation for Comparative Mammalian Genomics
Peter J. Waddell, Hirohisa Kishino, Rissa Ota
Genome Informatics 12: 141-154 (2001)
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Bacterial Molecular Phylogeny Using Supertree Approach
Vincent Daubin, Manolo Gouy, Guy Perriere
Genome Informatics 12: 155-164 (2001)
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Optimally Separating Sequences
Gene Myers
Genome Informatics 12: 165-174 (2001)
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Indexing Huge Genome Sequences for Solving Various Problems
Kunihiko Sadakane, Tetsuo Shibuya
Genome Informatics 12: 175-183 (2001)
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A Mini-greedy Algorithm for Faster Structural RNA Stem-Loop Search
Jan Gorodkin, Rune B. Lyngso, Gary D. Stormo
Genome Informatics 12: 184-193 (2001)
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High-Throughput Identification, Database Storage and Analysis of SNPs in EST Sequences
Francisco Jose Useche, Guang Gao, Mike Hanafey, Antoni Rafalski
Genome Informatics 12: 194-203 (2001)
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Bioinformatics Issues for Automating the Annotation of Genomic Sequences
Kim Carter, Akira Oka, Gen Tamiya, Matthew I. Bellgard
Genome Informatics 12: 204-211 (2001)
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DNAinsight: A Web Based Image Processing System for Large Scale RLGS Analysis
Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe
Genome Informatics 12: 212-221 (2001)
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Software Demonstration Abstracts

GeneSpringTM: Tools for Analyzing Microarray Expression Data
Lillian Chu, Eric Scharf, Takashi Kondo
Genome Informatics 12: 227-229 (2001)
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SSDB: Sequence Similarity Database in KEGG
Yoko Sato, Akihiro Nakaya, Kotaro Shiraishi, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa
Genome Informatics 12: 230-231 (2001)
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READ: Practical Analysis System of Mouse Transcriptome with the FANTOM Database
Hidemasa Bono, Takeya Kasukawa, Nikaido Itoshi, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki
Genome Informatics 12: 232-233 (2001)
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KMDB / MutationView : An Integrated Knowledge Base for Mutations and Polymorphisms in Human Disease Genes - Data Expansion and Further Functional Development -
Shinsei Minoshima, Saho Ohno, Masafumi Ohtsubo, Susumu Mitsuyama, Takashi Kawamura, Sachiko Ito, Fumiaki Ito, Nobuyoshi Shimizu
Genome Informatics 12: 234-236 (2001)
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The Gene Resource Locator: Integrated Annotation of the Draft Human Genome
Toshihiko Honkura, Jun Ogasawara, Tomoyuki Yamada, Shinichi Morishita
Genome Informatics 12: 237-238 (2001)
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Genomic Object Net: XML Visualization of Simulation Results from Biological Modeling on Hybrid Functional Petri Net
Hiroshi Matsuno, Atsushi Doi, Sachie Fujita, Makiko Sasaki, Yuichi Hirata, Satoru Miyano
Genome Informatics 12: 239-240 (2001)
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Poster Abstracts

Detecting Transcriptional cis-Regulation from Gene Expression Data
Yoshinobu Igarashi, Yasushi Okuno, Jean-Philippe Vert, Minoru Kanehisa
Genome Informatics 12: 241-242 (2001)
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Extraction of Related Genes in the Vesicular Transport by Simultaneous Comparison of Two-Hybrid and Microarray Data
Akiyasu C. Yoshizawa, Akihiro Nakaya, Susumu Goto, Minoru Kanehisa
Genome Informatics 12: 243-244 (2001)
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Gene Expression Analysis Using Fuzzy ART
Shuta Tomida, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi
Genome Informatics 12: 245-246 (2001)
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Prognostic Prediction of Lymphoma by Gene Expression Profiling Using FNN
Tatsuya Ando, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi
Genome Informatics 12: 247-248 (2001)
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A Clustering Method for Discovering Patterns Using Gene Regulatory Processes
Siyoung Park, Daewoo Choi, Chi-Hyuck Jun
Genome Informatics 12: 249-251 (2001)
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DNA Microarray Data Analysis for Cancer Classification Based on Stepwise Discriminant Analysis and Bayesian Decision Theory
Sungwoo Kwon, Young-Hwan Chu, Heui-Seok Yi, Chonghun Han
Genome Informatics 12: 252-254 (2001)
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Blind Gene Classification - An Application of a Signal Separation Method
Gen Hori, Masato Inoue,, Shin-ichi Nishimura,, Hiroyuki Nakahara
Genome Informatics 12: 255-256 (2001)
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Improvement of Chemosensitivity Prediction by Transcriptional Profiling in Hepatoma Cells
Yujin Hoshida, Masaru Moriyama, Motoyuki Otsuka,, Naoya Kato, Yasushi Shiratori, Naohiko Seki, Masao Omata
Genome Informatics 12: 257-258 (2001)
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Highly Specific and Quantitative Gene Expression Profiling Based on DNA Computing
Nao Nishida, Masatoshi Wakui, Katushi Tokunaga, Akira Suyama
Genome Informatics 12: 259-260 (2001)
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A Network-Based Array Data Interpreter
Kotoko Nakata, Kyoko Toda, Eiichiro Ichiishi, Tsuguchika Kaminuma
Genome Informatics 12: 261-262 (2001)
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Statistical Comparison of Expression Profiles of Genes
Hijiri Maeno, Shin-ichi Matsusaki, Yasushi Masuda, Taku Oshima, Hiroko Asahi, Shigehiko Kanaya, Hirotada Mori
Genome Informatics 12: 263-265 (2001)
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Lag Analysis of Genetic Networks in the Cell Cycle of Budding Yeast
Mamoru Kato, Tatsuhiko Tsunoda, Toshihisa Takagi
Genome Informatics 12: 266-267 (2001)
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Correspondence between a Genetic Network Inferred from Expression Profiles by Strategic Gene Disruptions and the Known Regulatory Relationships
Sachiryo Aburatani, Katsuhisa Horimoto, Hiroyuki Toh, Ayumi Shinohara, Keisuke Iida, Kosuke Tashiro, Satoru Kuhara
Genome Informatics 12: 268-269 (2001)
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ASIAN: Automatic System for Inferring a Network from Gene Expression Profiles
Katsuhisa Horimoto, Hiroyuki Toh
Genome Informatics 12: 270-271 (2001)
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Identifying Genetic Network Using Experimental Time Series Data by Boolean Algorithm
Kazumi Hakamada, Taizo Hanai,, Hiroyuki Honda, Takeshi Kobayashi
Genome Informatics 12: 272-273 (2001)
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Inference of a Gene Network from the Experimentally Observed Expression Data by Using AIGNET
Yuji Arikawa, Yoriko Takahashi, Shoji Watanabe, Yukihiro Maki, Masahiro Okamoto, Yukihiro Eguchi
Genome Informatics 12: 274-275 (2001)
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Evolutionary Inference of a Biological Network as Differential Equations by Genetic Programming
Erina Sakamoto, Hitoshi Iba
Genome Informatics 12: 276-277 (2001)
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Interactive Evolution of a Gene Regulatory Network Model
Atsushi Mimura, Hitoshi Iba
Genome Informatics 12: 278-279 (2001)
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Computational Analysis of SOS Response in Ultraviolet-Irradiated Escherichia coli
Junji Kitagawa, Kenji Yamamoto, Hitoshi Iba
Genome Informatics 12: 280-281 (2001)
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Computer Modeling of JAK/STAT Signal Transduction Pathway
Satoshi Yamada, Akihiko Yoshimura
Genome Informatics 12: 282-283 (2001)
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BIOCAD Project for Constructing a Biological System in Silico
Tadashi Adachi, Nana Matoba, Hiroyuki Kurata
Genome Informatics 12: 284-285 (2001)
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Simulation and System Analysis of Gene Regulatory Networks Using the Two-phase Partition Method
Hiroyuki Kurata, Takahiro Inoue, Yoshiyuki Sumida, Shin Tanaka, Takashi Ohashi
Genome Informatics 12: 286-287 (2001)
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Simulation of the Pattern Formation in Multicellular Organism by Genomic Object Net
Atsushi Doi, Rie Yamane, Naoyuki Yamasaki, Haruka Yoshimori, Ryutaro Murakami, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 12: 288-289 (2001)
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Biopathway Model Conversion from E-CELL to Genomic Object Net
Mika Matsui, Atsushi Doi, Hiroshi Matsuno, Yuichi Hirata, Satoru Miyano
Genome Informatics 12: 290-291 (2001)
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Genomic Object Net: Petri Net Enhancement for Multi-Cellular Processes
Yuichi Hirata, Hiroshi Matsuno, Makiko Sasaki, Satoru Miyano
Genome Informatics 12: 292-293 (2001)
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Gene Toggle Switches Only with Positive Feedback Loops
Tetsuya Kobayashi, Luonan Chen, Kazuyuki Aihara
Genome Informatics 12: 294-295 (2001)
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Regulation Analysis by Combining the Information Obtained from the mRNA Expression, Protein Expression and Metabolic Fluxes
Chen Yang,, Qiang Hua, Kazuyuki Shimizu
Genome Informatics 12: 296-297 (2001)
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In Silico Metabolic Pathway Modeling and Analysis of Mycoplasma pneumoniae
Jin Sik Kim, Sang Yup Lee
Genome Informatics 12: 298-299 (2001)
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Circadian Oscillation and Stochastic Noises
Nobukazu Ohki, Masatoshi Hagiwara
Genome Informatics 12: 300-301 (2001)
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A Study of Spatial Formation of Immune Cells
Shin I. Nishimura
Genome Informatics 12: 302-303 (2001)
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Pathway Finding from Given Time-Courses Using Genetic Algorithm
Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Masaru Tomita
Genome Informatics 12: 304-305 (2001)
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Modeling Photorespiration Pathway through E-CELL
Pawan Dhar, Emily Wang, Yoichi Nakayama, Masaru Tomita
Genome Informatics 12: 306-307 (2001)
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Estimation of Genetic Networks of the Circadian Rhythm in Cyanobacterium Using the E-CELL System
Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita
Genome Informatics 12: 308-309 (2001)
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A Simulation Model of Diabetes Using E-CELL System
Yasuhiro Naito, Hiroshi Ohno, Sae Seno, Yuki Oguchi, Atsumi Sano, Hiromu Nakajima, Masaru Tomita
Genome Informatics 12: 310-311 (2001)
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Towards Simulation of Whole Metabolic Pathways in Human Erythrocyte
Ayako Kinoshita, Yoichi Nakayama, Masaru Tomita
Genome Informatics 12: 312-313 (2001)
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An Electrophysiological Simulation Model of the Myocardial Cell Using E-CELL System
Motohiro Yoneda, Yasuhiro Naito, Shoko Miyamoto, Sayaka Ishinabe, Shinobu Kuratomi, Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma, Masaru Tomita
Genome Informatics 12: 314-315 (2001)
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Design and Development of Software Environment for Whole-Cell Simulation
Yusuke Saito, Kenta Hashimoto, Takeshi Sakurada, Yuki Fujita, Kouichi Takahashi, Masaru Tomita
Genome Informatics 12: 316-317 (2001)
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E-CELL Simulation Environment Version 3: System Architecture of Simulation Engine
Kouichi Takahashi, Takeshi Sakurada, Yohei Yamada, Tomoya Kitayama, Masaaki Kawata, Masaru Tomita
Genome Informatics 12: 318-319 (2001)
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Computer Simulation of the Asymmetric Cell Division in Early Development of C. elegans Embryo Using E-CELL System,
Azusa Kuroki, Akio Kanai, Masaru Tomita
Genome Informatics 12: 320-321 (2001)
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Modeling Environment for Large-Scale Models Using the E-CELL System
Yoichi Nakayama, Katsuyuki Yugi, Yohei Yamada, Masaru Tomita
Genome Informatics 12: 322-323 (2001)
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Development of the Bacteria Analysis System on G-Language Genome Analysis Environment
Koya Mori, Kazuharu Arakawa, Masaru Tomita
Genome Informatics 12: 324-325 (2001)
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G-Language Genome Analysis Environment
Kazuharu Arakawa, Koya Mori, Masaru Tomita
Genome Informatics 12: 326-327 (2001)
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Prediction System for Dumbbell-Type Proteins: SOSUIdumbbell
Nobuyuki Uchikoga, Shun-ya Takahashi, Ke Runcong, Fumitsugu Akazawa, Masashi Sonoyama, Shigeki Mitaku
Genome Informatics 12: 328-329 (2001)
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Molecular Dynamics Simulation of Protein Translocation across a Membrane
Mitsuharu Okazaki, Tomoki Watanabe, Naohito Urakami, Takashi Yamamoto
Genome Informatics 12: 330-331 (2001)
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Classification and Analysis of Inter-Helical Loop Segments in Membrane Proteins
Takatsugu Hirokawa, Makiko Suwa, Yutaka Akiyama
Genome Informatics 12: 332-333 (2001)
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Comprehensive Functional Identification of Prokaryotic Transmembrane Proteins by Binary Topology Pattern
Yoshiaki Sugiyama, Masafumi Arai, Toshio Shimizu
Genome Informatics 12: 334-335 (2001)
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Classification of Eukaryotic 7-tms Transmembrane Proteins by Binary Topology Pattern
Yasuhito Inoue, Yoshiaki Sugiyama, Masami Ikeda, Toshio Shimizu
Genome Informatics 12: 336-337 (2001)
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Comprehensive Analysis of Transmembrane Protein Sequences in 39 Microbial Genomes
Masafumi Arai, Keisuke Noto, Demelo Madrazo Lao, Masami Ikeda, Toshio Shimizu
Genome Informatics 12: 338-339 (2001)
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Methods for Detecting the Signal Peptide in Transmembrane and Globular Proteins
Demelo Madrazo Lao, Toshio Shimizu
Genome Informatics 12: 340-342 (2001)
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Detection of Hidden Periodicity in Protein Sequences and Its Correlation with Structure and Function of Proteins
Andrew A. Laskin, Eugene V. Korotkov, Nikolai A.Kudryashov
Genome Informatics 12: 343-344 (2001)
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Analysis of Complementarity of Protein-Protein and Protein-DNA Interactions Using the Molecular Surface Database, eF-site
Kengo Kinoshita, Yuko Tsuchiya, Haruki Nakamura
Genome Informatics 12: 345-347 (2001)
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Functional Proteomics in Silico: Putative Protein Interaction Analysis
Chung-Yen Lin, Chen-Zen Lo, Chao A. Hsiung
Genome Informatics 12: 348-349 (2001)
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Protein Classification Comparison Server
Jun-Hyung Park, Sung-Ryong Ryu, Cheolmin Kim, InSong Koh, Jong Park
Genome Informatics 12: 350-351 (2001)
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Discovery and Classification of Peptide Family G-Protein Coupled Receptors in the Human Genome Sequence
Maria E. Levchenko, Toshiaki Katayama, Minoru Kanehisa
Genome Informatics 12: 352-353 (2001)
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A Novel Protein Soft Docking Algorithm Based on Spectral Analysis of Shape Complementarity
Atsushi Yoshimori, Carlos A. Del Carpio M.
Genome Informatics 12: 354-355 (2001)
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Scoring Protein-Substrate Complex Decoys Based on Electrostatic and Hydrophobic Complementarities: Evaluation of Hormone-Receptor Interactions
Yoshihiro Katsuta, Atsushi Yoshimori, Carlos A. Del Carpio M.
Genome Informatics 12: 356-357 (2001)
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Protein Folding Recognition Based on Amino Acid Physicochemical Property Profiles
Daisuke Komatsu, Atsushi Yoshimori, Carlos A. Del Carpio M.
Genome Informatics 12: 358-359 (2001)
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A Bioinformatic Approach for RNA 3D Structure Prediction: Development of a Knowledge-Base for 2D-to-3D Structural Elements Compatibility Analysis
Yoshimitsu Shigenobu, Carlos A. Del Carpio
Genome Informatics 12: 360-361 (2001)
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Conformational Search and Potential Energy Analysis of Protein beta-Hairpin Formations by Parallel Exhaustive Tree Search
Makoto Ando, Yutaka Akiyama, Hideo Matsuda
Genome Informatics 12: 362-363 (2001)
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Comparative Analysis of Protein Charge Distribution in Genome Scale
Ke Runcong, Shigeki Mitaku
Genome Informatics 12: 364-365 (2001)
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PepAssem, a Peptide Assembly Algorithm for a Complex Protein Mixture
Sang-Hee Shim, Doo Soo Chung
Genome Informatics 12: 366-367 (2001)
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Multiple Zinc Finger Motifs with Comparison of Plant and Insect
Nobuyuki Kawagashira, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Kenichi Higo
Genome Informatics 12: 368-369 (2001)
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Analysis of Amino Acid Substitution Rate in Proteins between Hyperthermophilic and Mesophilic Organisms Using Complete Genome Data
Tomoya Yamashita, Goki Kashima, Akio Kanai, Asako Sato, Kenji Higashi, Takanori Washio, Masaru Tomita
Genome Informatics 12: 370-371 (2001)
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Structural Affectivity of Protein Chain Growth by t-RNA System
Yasuo Yonezawa, Sadaharu Ueno
Genome Informatics 12: 372-373 (2001)
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An Approach for Homology Search with Reconfigurable Hardware
Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya
Genome Informatics 12: 374-375 (2001)
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Aligning and Scoring Motifs based on Secondary Characteristics
Pedro Gonnet, Frederique Lisacek
Genome Informatics 12: 376-377 (2001)
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Heuristic Probe Mining Based on Multiple Sequence Analysis
Byeong-Chul Kang, Heung-Soo Park, Ho-Young Kang, Hee-Kyung Park, Cheolmin Kim
Genome Informatics 12: 378-379 (2001)
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Amino Acid Substitution Matrices Estimated by Maximum Likelihood
Leonardo de Oliveira Martins, Paolo M. de A. Zanotto
Genome Informatics 12: 380-381 (2001)
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A Web Server for Multiple Sequence Alignment Using Genetic Algorithm
Tsutomu Yokoyama, Takumi Watanabe, Akito Taneda, Toshio Shimizu
Genome Informatics 12: 382-383 (2001)
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Target Prediction of Transcription Factors: Refinement of Structure-Based Method
Akinori Sarai, Samuel Selvaraj, M. Michael Gromiha, Joerg-Gerald Siebers, Ponraj Prabakaran, Hidetoshi Kono
Genome Informatics 12: 384-385 (2001)
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Analysis of the Maternal mRNAs Encoding DNA-Binding Motifs in the Ascidian Egg Using SSDB
Shuichi Kawashima, Takeshi Kawashima, Akihiro Nakaya, Kazuhiro W. Makabe, Susumu Goto, Minoru Kanehisa
Genome Informatics 12: 386-387 (2001)
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"Melina" - Novel Tool for Elucidation of Consensus Motif in the Promoter Regions of Functionally Related DNA Sequences
Natalia Poluliakh, Michiko Konno, Toshihisa Takagi, Kenta Nakai
Genome Informatics 12: 388-389 (2001)
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Identification and Phylogenetic Analysis of Schizophrenia Associated Retrovirus (SZRV) Element in the Human GenBank Database
Jun-Seop Kim, Sang-Bae Kim, InSong Koh
Genome Informatics 12: 390-391 (2001)
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The Origin and Evolution of Eukaryotic Protein Kinases
Asako Koike, Kenta Nakai, Toshihisa Takagi
Genome Informatics 12: 392-393 (2001)
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Evolution of the MIR Elements Located in Coding Regions of Human Genome
Maria Chaley, Eugene Korotkov, Nicolai Kudryashov
Genome Informatics 12: 394-395 (2001)
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Comparison between Linear Chromosomes in Terms of Duplicate Genes: Implication of Whole Genome Duplication in Yeast
Satoshi Fukuchi, Ken Nishikawa, Katsuhisa Horimoto
Genome Informatics 12: 396-397 (2001)
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Relation between Restriction Modification Genes and Genome Rearrangements Suggested from Genome Sequence Comparison within Genus Neisseria
Keiichirou Nakao, Akito Chinen, Ayaka Nobusato, Youhei Fujitani, Ikuo Uchiyama, Ichizo Kobayashi
Genome Informatics 12: 398-399 (2001)
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Analysis of Dictyostelium discoideum cDNA Obtained from Multicellular and Unicellular Stages
Masumi Itoh, Yoshinori K. Okuji, Susumu Goto, Hideko Urushihara, Mineko Maeda, Yoshimasa Tanaka, Minoru Kanehisa
Genome Informatics 12: 400-401 (2001)
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Maintenance of Microbial Genome Architecture
Kentaro Mori, Katsuhisa Horimoto, Satoshi Fukuchi, Ken Nishikawa
Genome Informatics 12: 402-403 (2001)
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Comparative Analysis on the Conservation of Two Orthologous Genome Regions
Taehyung Kim, Kyeyoung Cho, Hojin Jung, InSong Koh, Jong H. Park
Genome Informatics 12: 404-405 (2001)
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Development of a Novel Functional Gene Discovery System by Hybrid-Ribozyme Libraries in the Post Genome Era
Hiroaki Kawasaki,, Eigo Suyama,, Reiko Onuki,, Kazunari Taira
Genome Informatics 12: 406-408 (2001)
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ParalogCluster: Classifying Paralogs in a Genome into Paralogous Groups
Kiyoshi Yamazaki, Makoto Ohnishi, Ken Kurokawa, Teruo Yasunaga
Genome Informatics 12: 409-410 (2001)
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Toward Chromosome-Level Comparative Analysis of Vertebrate Genomes
Katsuhiko Murakami, Hideki Noguchi, Yasushi Totoki, Tetsushi Yada, Atsushi Toyoda, Masahira Hattori, Yoshiyuki Sakaki
Genome Informatics 12: 411-412 (2001)
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Symbolical Kernel-Based Reasoning: Its Application to the Rule Extraction in Dictyostelium discoideum DNA
Moritoshi Yasunaga, Kentaro Ushiyama, Ikuo Yoshihara, Jung Hwan Kim
Genome Informatics 12: 413-414 (2001)
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Distribution Analysis of 5' Splice Site-Like Sequences in Human and Mouse pre-mRNAs
Sumie Kitamura-Abe,, Nobuyuki Takahashi, Atsushi Sakurai, Takanori Washio, Mineichi Kudo, Masaru Shimbo, Akihiro Tsutsumi, Masaru Tomita
Genome Informatics 12: 415-416 (2001)
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Guide of Putative Alternative Splicing Database
Jiunn-Jei Lai, Yen-hua Hunang, Yu-tin Chen, Ueng-Cheng Yang
Genome Informatics 12: 417-419 (2001)
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Feature Extraction from Genome Sequence Using Multi-Modal Neural Network
Ikuo Yoshihara, Yoshiyuki Kamimai, Moritoshi Yasunaga
Genome Informatics 12: 420-422 (2001)
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Dataset Construction for Gene Structure Prediction and Alternative Splicing Analysis
Masahiko Mizuno, Hideki Nagasaki, Makiko Suwa
Genome Informatics 12: 423-424 (2001)
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An Automated System for Finding Seven Transmembrane Helix Receptors from Human Genome
Makiko Suwa, Toshiyuki Sato, Ikuo Okouchi, Masanori Arita, Shinichi Matsumoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Kiyoshi Asai, Yutaka Akiyama
Genome Informatics 12: 425-426 (2001)
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Prediction of Co-Regulated Genes in Prokaryotic Genomes on the Basis of Upstream Elements Conserved Across Closely Related Species
Yuko Makita, Goro Terai, Shigeki Mitaku, Toshihisa Takagi, Kenta Nakai
Genome Informatics 12: 427-428 (2001)
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Prediction of Co-Regulated Genes in Bacillus subtilis Based on the Conserved Upstream Elements across Three Closely Related Species
Goro Terai, Toshihisa Takagi, Kenta Nakai
Genome Informatics 12: 429-430 (2001)
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Detection of tRNA Genes with Introns from DNA Sequences of Archaea
Makoto Kinouchi,, Yoshihiro Kudo
Genome Informatics 12: 431-432 (2001)
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Skew of Mononucleotide Frequencies, Relative Abundance of Dinucleotides, and DNA Strand Asymmetry
Chiharu Shioiri, Takahata Naoyuki
Genome Informatics 12: 433-434 (2001)
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Statistical Analysis of Genomic Information: Various Periodicities in DNA Sequence
Atsushi Fukushima, Makoto Kinouchi, Yoshihiro Kudo, Shigehiko Kanaya, Hirotada Mori, Toshimichi Ikemura
Genome Informatics 12: 435-436 (2001)
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Latent Periodicity of Many Genes
Eugene Korotkov,, Nikolay Kudryaschov
Genome Informatics 12: 437-439 (2001)
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Nonparametric Linkage Analysis for Complex Genetic Diseases with Linked Loci
Osamu Ogasawara, Toshihisa Takagi
Genome Informatics 12: 440-441 (2001)
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Adapting in Vitro Selected oligoDNAs for Recognition of Natural Sites and for Analysis of SNPs and Mutagenesis
Galina V. Orlova, Julia V. Ponomarenko, Anatoly S. Frolov, Mikhail P. Ponomarenko, Mikhail S. Gelfand
Genome Informatics 12: 442-444 (2001)
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Lorenz Curves and Statistical Distribution Functions on Frequency Repetition
Eugene Korotkov,, Nikolay Kudryaschov
Genome Informatics 12: 445-446 (2001)
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Revealing mRNA Translational Signals by Primary and Secondary Structure Analyses
Igor Titov, Alex Kochetov, Nikolay Kolchanov, Akinori Sarai
Genome Informatics 12: 447-448 (2001)
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Comparison of Methods for Probe Design
Noriyuki Hosaka, Ken-ichi Kurata, Hiroshi Nakamura
Genome Informatics 12: 449-450 (2001)
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Efficient Numerical Optimization Technique Based on Real-Coded Genetic Algorithm
Takanori Ueda, Nobuto Koga, Masahiro Okamoto
Genome Informatics 12: 451-453 (2001)
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More Speed and More Pattern Variations for Knowledge Discovery System BONSAI
Hideo Bannai, Keisuke Iida, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano
Genome Informatics 12: 454-455 (2001)
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Two-Layered Genetic Network Drawings with Minimum Edge Crossings
Atsuko Yamaguchi, Hiroyuki Toh
Genome Informatics 12: 456-457 (2001)
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Visualization for Comparison between Gene Clusters Generated from Different Sources
Shuichi Tsutsumi, Makoto Kano, Yutaka Midorikawa, Michitaka Hirose, Hiroyuki Aburatani
Genome Informatics 12: 458-459 (2001)
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ReView: A Viewer to Display the Relation of Protein-Coding Region and Repetitive Patterns
Yu-Tin Chen, Yu-Chung Chang, Yen-Hua Huang, Ueng-Cheng Yang
Genome Informatics 12: 460-461 (2001)
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3-D Visualization for Gene Rearrangement in Ternary Comparison
Naobumi Sasaki, Naoki Sato
Genome Informatics 12: 462-463 (2001)
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XPAK: A Visualization Toolkit for Transcriptome Analysis
Yasushi Masuda, Shigehiko Kanaya, Hirotada Mori
Genome Informatics 12: 464-465 (2001)
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gLdraw: A General Tool for a Comparison of Chromosome Maps
Yousuke Hayakawa, Kanako Koyanagi, Takuro Tamura, Takashi Gojobori, Tadashi Imanishi
Genome Informatics 12: 466-468 (2001)
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Ontology Based Corpus Annotation and Tools
Tomoko Ohta, Yuka Tateisi, Jin-Dong Kim, Hideki Mima, Jun'ichi Tsujii
Genome Informatics 12: 469-470 (2001)
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Graphical Representation of Gene Ontology in Scalable Vector Graphics
Junko Tanoue, Noboru Matoba, Masatoshi Yoshikawa, Shunsuke Uemura
Genome Informatics 12: 471-472 (2001)
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A System for Integration of Heterogeneous Biological XML Data
Noboru Matoba, Junko Tanoue, Masatoshi Yoshikawa, Shunsuke Uemura
Genome Informatics 12: 473-474 (2001)
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Toward an Ontological Classification and Mapping of Bioinformatics Fields
Tae-Hyung Kim, Gil-Mi Ryu,, InSong Koh, Jong Park
Genome Informatics 12: 475-477 (2001)
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Bio-GilJabee: An Ontological Source Dictionary for Bioinformatics
Myungguen Chung, Kiho Park, InSong Koh, Jong Park
Genome Informatics 12: 478-479 (2001)
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An Integrated Bioinformatic Search Server: Sequences, Structure, Interaction, and Function of Proteins (SSIF) Server
Jae-Hyung Lee,In Song Koh, Jong Park
Genome Informatics 12: 480-481 (2001)
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Drug to SNP: A Pharmacogenomics Database for Linking Drug Response to SNPs
Ju-Youn Lee, In-Song Koh
Genome Informatics 12: 482-483 (2001)
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A Secondary Database for Journal Search Based on Experimental Materials and Methods in Alzheimer's Disease Research
Younghee Lee, Bumjin Kim, InSong Koh
Genome Informatics 12: 484-485 (2001)
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Database for Human UV-Regulated Genes
Makoto Yamazaki, Hiroko Ao, Goro Terai, Nobuo Kitamura, Toshihisa Takagi
Genome Informatics 12: 486-487 (2001)
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DBTSS: DataBase of Human Transcriptional Start Sites and Full-Length cDNA
Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai
Genome Informatics 12: 488-489 (2001)
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Current Status of ProTherm: Thermodynamic Database for Proteins and Mutants
M. Michael Gromiha, Hatsuho Uedaira, Jianghong An, Samuel Selvaraj, Ponraj Prabakaran, Akinori Sarai
Genome Informatics 12: 490-491 (2001)
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Database on mRNA-Located Eukaryotic Expression Signals Influencing Translation Efficiency and Specificity
Alex V. Kochetov, Dmitri Grogorovich, Nikolay A. Kolchanov, Akinori Sarai
Genome Informatics 12: 492-493 (2001)
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Recent Developments in ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions
Ponraj Prabakaran, Jianghong An, M. Michael Gromiha, Samuel Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai\
Genome Informatics 12: 494-495 (2001)
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RiceGAAS: An Automated Annotation System for Rice Genome
Hisataka Numa, Katsumi Sakata, Yoshiaki Nagamura, Baltazar A. Antonio, Atsuko Idonuma, Yuji Shimizu, Ikuo Horiuchi, Takashi Matsumoto, Takuji Sasaki, Kenichi Higo
Genome Informatics 12: 496-497 (2001)
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Towards a Unified Genome Database of Nitrogen Fixation and Photosynthesis Organisms
Yasukazu Nakamura, Satoshi Tabata
Genome Informatics 12: 498-499 (2001)
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Assessment of a Database System, On-Web GP, for Identifying Species
Mohammed Naimuddin, Mariko Kouduka, Ayumu Saito, Koichi Nishigaki
Genome Informatics 12: 500-501 (2001)
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CAMUS DB for Amino Acid Sequence Data
Sadahiko Misu, Takayasu Iizuka, Yuichi Kawanishi, Kaoru Fukami-Kobayashi, Naruya Saitou
Genome Informatics 12: 502-503 (2001)
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Construction of Database for Protein Classifications
Jiro Araki
Genome Informatics 12: 504-505 (2001)
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Rank Aggregation Method for Biological Databases
Jun Sese, Shinichi Morishita
Genome Informatics 12: 506-507 (2001)
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Development of PDBj-ML
Nobutoshi Ito, Hisashi Sakamoto, Kaori Kobayashi, Haruki Nakamura
Genome Informatics 12: 508-509 (2001)
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Quadtree Representation of DNA Sequences
Natsuhiro Ichinose, Tetsushi Yada, Toshihisa Takagi
Genome Informatics 12: 510-511 (2001)
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DNA Data Compression in the Post Genome Era
Hisahiko Sato, Takashi Yoshioka, Akihiko Konagaya, Tetsuro Toyoda
Genome Informatics 12: 512-514 (2001)
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Invited Talks

New Data Driven Research Pardigm for the Post Genome Era: A Transcription Regulation Example
Charles Lawrence
Genome Informatics 12: 225-225 (2001)
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Protein Interactions
David Eisenberg, Ioannis Xenarios, Joyce Duan, Lukasz Salwinski, Todd Yeates Matteo Pellegrini, Michael J. Thompson, Edward Marcotte
Genome Informatics 12: 226-226 (2001)
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