Genome Informatics Vol. 14 (2003)

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Genome Informatics Vol. 14 (2003)

Presented at the 14th International Conference on Genome Informatics
December 14-17, 2003, Pacifico Yokohama, Japan

Published as: M. Gribskov, M. Kanehisa, S. Miyano, and T. Takagi (eds.)
"Genome Informatics 2003"
Universal Academy Press, Tokyo, 2003

Preface by M. Gribskov and M. Kanehisa

Program Committee

 


 

Full Talk Papers

Computational Inference of Regulatory Pathways in Microbes: an Application to Phosphorus Assimilation Pathways in Synechococcus sp. WH8102
Zhengchang Su, Phuongan Dam, Xin Chen, Victor Olman, Tao Jiang, Brian Palenik, Ying Xu
Genome Informatics 14: 3-13 (2003)
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A Case Study of Object-Oriented Bio-Chemistry: A Unified Specification of the Coagulation Cascade
Jacqueline Signorini, Patrick Greussay
Genome Informatics 14: 14-22 (2003)
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MetaFluxNet, a Program Package for Metabolic Pathway Construction and Analysis, and Its Use in Large-Scale Metabolic Flux Analysis of Escherichia coli
Sang Yup Lee, Dong-Yup Lee, Soon Ho Hong, Tae Yong Kim, Hongsoek Yun, Young-Gyun Oh, Sunwon Park
Genome Informatics 14: 23-33 (2003)
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Reducing False Positives in Molecular Pattern Recognition
Xijin Ge, Shuichi Tsutsumi, Hiroyuki Aburatani, Shuichi Iwata
Genome Informatics 14: 34-43 (2003)
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On Combining Multiple Microarray Studies for Improved Functional Classification by Whole-Dataset Feature Selection
See-Kiong Ng, Soon-Heng Tan, V.S. Sundararajan
Genome Informatics 14: 44-53 (2003)
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Statistical Inference Methods for Detecting Altered Gene Associations
Sang-Heon Yoon, Je-Suk Kim, Hae-Hiang Song
Genome Informatics 14: 54-63 (2003)
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Splice Site Detection with a Higher-Order Markov Model Implemented on a Neural Network
Loi Sy Ho, Jagath C. Rajapakse
Genome Informatics 14: 64-72 (2003)
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On Selecting Features from Splice Junctions: An Analysis Using Information Theoretic and Machine Learning Approaches
Christina L. Zheng, Virginia R. de Sa, Michael Gribskov, T. Murlidharan Nair
Genome Informatics 14: 73-83 (2003)
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An In-Silico Method for Prediction of Polyadenylation Signals in Human Sequences
Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong
Genome Informatics 14: 84-93 (2003)
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Construction of Genetic Network Using Evolutionary Algorithm and Combined Fitness Function
Ando Shin, Hitoshi Iba
Genome Informatics 14: 94-103 (2003)
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Layout Search of a Gene Regulatory Network for 3-D Visualization
Naoki Hosoyama, Noman Nasimul, Hitoshi Iba
Genome Informatics 14: 104-113 (2003)
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Neural-Network-Based Parameter Estimation in S-System Models of Biological Networks
Jonas S. Almeida, Eberhard O. Voit
Genome Informatics 14: 114-123 (2003)
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Finding Optimal Gene Networks Using Biological Constraints
Sascha Ott, Satoru Miyano
Genome Informatics 14: 124-133 (2003)
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Efficient Tree-Matching Methods for Accurate Carbohydrate Database Queries
Kiyoko F. Aoki, Atsuko Yamaguchi, Yasushi Okuno, Tatsuya Akutsu, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka
Genome Informatics 14: 134-143 (2003)
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Heuristics for Chemical Compound Matching
Masahiro Hattori, Yasushi Okuno, Susumu Goto, Minoru Kanehisa
Genome Informatics 14: 144-153 (2003)
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Processing Sequence Annotation Data Using the Lua Programming Language
Yutaka Ueno, Masanori Arita, Toshitaka Kumagai, Kiyoshi Asai
Genome Informatics 14: 154-163 (2003)
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PatternHunter II: Highly Sensitive and Fast Homology Search
Ming Li, Bin Ma, Derek Kisman, John Tromp
Genome Informatics 14: 164-175 (2003)
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On Half Gapped Seed
Wei Chen, Wing-kin Sung
Genome Informatics 14: 176-185 (2003)
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Clone-Array Pooled Shotgun Mapping and Sequencing: Design and Analysis of Experiments
Miklós Csürös, Bingshan Li, Aleksandar Milosavljevic
Genome Informatics 14: 186-195 (2003)
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Prediction and Analysis of β-Turns in Proteins by Support Vector Machine
Tho Hoan Pham, Kenji Satou, Tu Bao Ho
Genome Informatics 14: 196-205 (2003)
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Multi-Class Protein Fold Classification Using a New Ensemble Machine Learning Approach
Aik Choon Tan, David Gilbert, Yves Deville
Genome Informatics 14: 206-217 (2003)
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Multi-Class Support Vector Machines for Protein Secondary Structure Prediction
Minh N. Nguyen, Jagath C. Rajapakse
Genome Informatics 14: 218-227 (2003)
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Development of an ab initio Protein Structure Prediction System ABLE
Takashi Ishida, Takeshi Nishimura, Makoto Nozaki, Tsuyoshi Inoue, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
Genome Informatics 14: 228-237 (2003)
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Docking Unbound Proteins with MIAX: A Novel Algorithm for Protein-Protein Soft Docking
Carlos A. Del Carpio Muñoz, Tobias Peissker, Atsushi Yoshimori, Eiichiro Ichiishi
Genome Informatics 14: 238-249 (2003)
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A Domain Combination Based Probabilistic Framework for Protein-Protein Interaction Prediction
Dongsoo Han, Hong-Soog Kim, Jungmin Seo, Woohyuk Jang
Genome Informatics 14: 250-259 (2003)
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Keynote Address

On the Art of Modeling; Illustrated with the Analysis of the Golf Swing Motion
Hirotugu Akaike
Genome Informatics 14: 263-265 (2003)
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Predicting Nucleic Acid Hybridization and Melting Profiles
Michael Zuker
Genome Informatics 14: 266-268 (2003)
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Orthologous Sets of Functional Networks: Inference, Mining and Visualization
Charles DeLisi
Genome Informatics 14: 269-269 (2003)
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Software Demonstration Abstracts

CADLIVE System: Map-Based Dynamic Simulation of Biochemical Networks
Hiroyuki Kurata, Rei Iwasaki, Kouichi Masaki, Takayuki Tanaka, Kouji Mitsukiyo, Yoshiyuki Sumida
Genome Informatics 14: 270-271 (2003)
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Selection of Causal Gene Sets from Gene Expression Profiles Using GeneFis®, New Software Based on FNN
Hiroyuki Honda, Takeshi Kobayashi
Genome Informatics 14: 272-273 (2003)
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Development of an Integrated System for Genetic Network Analysis and Microarray Data Management
Ji-Hung Kim, Kyung-Shin Lee, Pan-Gyu Kim, Hwan-Gue Cho
Genome Informatics 14: 274-275 (2003)
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An Open Source Client-Server System for the Analysis of Affymetrix Microarray Data
Lars Martin Jakt, Mitsuhiro Okada, Shin-Ichi Nishikawa
Genome Informatics 14: 276-277 (2003)
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ASIAN: A Web Site for Network Inference
Katsuhisa Horimoto, Hiroyuki Toh, Sachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Shigeru Saito, Kousuke Goto, Masaki Fumoto
Genome Informatics 14: 278-279 (2003)
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Netview: Application Software for Constructing and Visually Exploring Phylogenetic Networks
Kirill Kryukov, Naruya Saitou
Genome Informatics 14: 280-281 (2003)
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Integrated System for Inference of Gene Expression Network
Masahiko Nakatsui, Takanori Ueda, Masahiro Okamoto
Genome Informatics 14: 282-283 (2003)
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MutationView : An Integrated Knowledge Base for Mutations and Polymorphisms in Human Disease Genes -- Automatical Extraction of Disease-Associated Knowledge --
Masafumi Ohtsubo, Susumu Mitsuyama, Takashi Kawamura, Nobuyoshi Shimizu, Shinsei Minoshima
Genome Informatics 14: 284-285 (2003)
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BirdsAnts: Bringing Informative Rules from a Database System, Aimed at Novel Targets Search
Motoi Tobita, Ken Horiuchi, Kenji Araki, Masashi Nemoto, Tetsuo Nishikawa
Genome Informatics 14: 286-287 (2003)
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Ecell2d : Distributed E-CELL2
Andrew Stubbings, Naota Ishikawa, Takashi Yamazaki, Ariya Fujita, Iriko Kaneko, Yoshinari Fukui, Toshikazu Ebisuzaki
Genome Informatics 14: 288-289 (2003)
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Integrated Distributed Computing Environment on the G-Language GAE v.2
Ryo Hattori, Kazuharu Arakawa, Hayataro Kouchi, Masaru Tomita
Genome Informatics 14: 290-291 (2003)
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SuperNORM: A Computer Program for the Parametric Normalization of Microarray Data
Tomokazu Konishi, Masanori Yoshida, Kenya Shibahara
Genome Informatics 14: 292-293 (2003)
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E-CELL System Version 3: A Software Platform for Integrative Computational Biology
Kouichi Takahashi, Takeshi Sakurada, Kazunari Kaizu, Tomoya Kitayama, Satya Arjunan, Tatsuya Ishida, Gabor Bereczki, Daiki Ito, Masahiro Sugimoto, Takashi Komori, Ohta Seiji, Masaru Tomita
Genome Informatics 14: 294-295 (2003)
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BPE: Biopathway Executer for Large-Scale Biopathway Modeling and Simulation
Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Eri Torikai, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 14: 296-297 (2003)
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Bioinformatics and Computational Biology with Biopython
Michiel J.L. de Hoon, Brad Chapman, Iddo Friedberg
Genome Informatics 14: 298-299 (2003)
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Representing Metabolic Networks by the Substrate-Product Relationships
Masanori Arita
Genome Informatics 14: 300-301 (2003)
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Poster Abstracts

Comprehensive Analysis of Delay in Transcriptional Regulation Using Expression Profiles
Koji Ota, Takuji Yamada, Yoshihiro Yamanishi, Susumu Goto, Minoru Kanehisa
Genome Informatics 14: 302-303 (2003)
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Prediction of Glycan Structures from Glycosyltransferase Expression Profiles
Shin Kawano, Yasushi Okuno, Kosuke Hashimoto, Harumi Yamamoto, Hiromu Takematsu, Yasunori Kozutsumi, Susumu Goto, Minoru Kanehisa
Genome Informatics 14: 304-305 (2003)
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Statistical Analysis of the Relationship between Gene Expression and Location
Sachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Katsuhisa Horimoto
Genome Informatics 14: 306-307 (2003)
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Detection of Genes with Tissue-Specific Patterns Using Akaike's Information Criterion
Koji Kadota, Katsutoshi Takahashi
Genome Informatics 14: 308-309 (2003)
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Operon Prediction by DNA Microarray: An Approach with a Bayesian Network Model
Hitoshi Shimizu, Shigeyuki Oba, Shin Ishii
Genome Informatics 14: 310-311 (2003)
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Automatic Extraction of Expression-Related Features Shared by a Given Group of Genes
Takuya Oyama, Mikio Yoshida, Satoshi Kamegai, Kagehiko Kitano, Fumihito Miura, Noriko Kawaguchi, Miyuki Onda, Kenji Satou, Takashi Ito
Genome Informatics 14: 312-313 (2003)
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Dynamics of Repressilator: From Noise to Coherent Oscillation
Tomohiro Ushikubo, Wataru Inoue, Masaki Sasai
Genome Informatics 14: 314-315 (2003)
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Gene Expression Analysis Refining System (GEARS) via Statistical Approach: A Preliminary Report
Chen-Hsin Chen, Henry Horng-Shing Lu, Chen-Tuo Liao, Chun-houh Chen, Ueng-Cheng Yang, Yun-Shien Lee
Genome Informatics 14: 316-317 (2003)
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CAPIES: DNA Microarray-Based Class Prediction System for Computational Diagnostics
Sung Geun Lee, Bonghee Seo, Yang Seok Kim
Genome Informatics 14: 318-319 (2003)
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Gene Screening Method for Prognostic Prediction Using Projective ART Model
Hiro Takahashi, Takeshi Kobayashi, Hiroyuki Honda
Genome Informatics 14: 320-321 (2003)
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Features of Gene Extraction by Nonlinear Support Vector Machines in Gene Expression Analysis
Daisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara
Genome Informatics 14: 322-323 (2003)
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Prognosis Prediction by Microarray Gene Expression Using Support Vector Machine
Chihoko Tago, Taizo Hanai, Masahiro Okamoto
Genome Informatics 14: 324-325 (2003)
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Automatically Finding Good Clusters with Seed K-Means
Miyoung Shin, Eun Mi Kang, Seon Hee Park
Genome Informatics 14: 326-327 (2003)
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Analysis of DNA Microarray Data by Using Self-Organizing Maps
Tomoyuki Kato, Kikuo Fujimura, Heizo Tokutaka, Yasushi Kawata, Masaaki Ohkita
Genome Informatics 14: 328-329 (2003)
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Clustering Method Based on Onset and Cessation of Gene Expression
Kazumi Hakamada, Taizo Hanai, Masahiro Okamoto
Genome Informatics 14: 330-331 (2003)
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Significance Test of Clusters in Gene Expression Profile Data
Natsuko Kawase, Shigeyuki Oba, Shin Ishii
Genome Informatics 14: 332-333 (2003)
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Gene Expression Analysis Using Fuzzy K-Means Clustering
Chinatsu Arima, Taizo Hanai, Masahiro Okamoto
Genome Informatics 14: 334-335 (2003)
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A Method for Normalization of Gene Expression Data
Makoto Kano, Hisashi Kashima, Tetsuo Shibuya, Kaori Ide, Aiko Kashihara, Noriko Nakagawa, Mariko Hatakeyama, Seiki Kuramitsu, Akihiko Konagaya
Genome Informatics 14: 336-337 (2003)
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Normalization of Target Fluorescence Using Reference Fluorescence for cDNA Microarray Method
Yu Suzuki, Kenji Hatano, Shigehiko Kanaya, Shunsuke Uemura
Genome Informatics 14: 338-339 (2003)
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A System for Visualizing Gene Expressions Using Metabolic Networks
Ryoko Tamaru, Toshiyuki Amagasa, Shigehiko Kanaya, Shunsuke Uemura
Genome Informatics 14: 340-341 (2003)
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Image Preprocessing for cDNA Microarray Using Deconvolution Method
Hyo Jung Ban, Myungguen Chung, Yong Sung Lee, Jin Hyuk Kim, Young Seek Lee
Genome Informatics 14: 342-343 (2003)
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On Visualization, Screening, and Classification of Cell Cycle-Regulated Genes in Yeast
Henry Horng-Shing Lu, Han-Ming Wu
Genome Informatics 14: 344-345 (2003)
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A PCA Based Method of Gene Expression Visual Analysis
Kunihiro Nishimura, Koji Abe, Shumpei Ishikawa, Shuichi Tsutsumi, Koichi Hirota, Hiroyuki Aburatani, Michitaka Hirose
Genome Informatics 14: 346-347 (2003)
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Bioinformatics for Oncogenomic Target Identification
Masaru Katoh
Genome Informatics 14: 348-349 (2003)
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Multiscale Bootstrap Analysis of Gene Networks Based on Bayesian Networks and Nonparametric Regression
Takeshi Kamimura, Hidetoshi Shimodaira, Seiya Imoto, SunYong Kim, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
Genome Informatics 14: 350-351 (2003)
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Combining Gene Expression Data with DNA Sequence Information for Estimating Gene Networks Using Bayesian Network Model
Yoshinori Tamada, SunYong Kim, Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
Genome Informatics 14: 352-353 (2003)
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Enumeration of Likely Gene Networks and Network Motif Extraction for Large Gene Networks
Sascha Ott, Satoru Miyano
Genome Informatics 14: 354-355 (2003)
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Genetic Networks with Stochastic Fluctuations
Luonan Chen, Ruiqi Wang, Kazuyuki Aihara
Genome Informatics 14: 356-357 (2003)
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Integrative Method for Identifying Combinatorial Regulation of Transcription Factors
Mamoru Kato, Naoya Hata, Nila Banerjee, Michael Q. Zhang
Genome Informatics 14: 358-359 (2003)
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Pathways/Networks to Syndrome X
Tsuguchika Kaminuma, Masumi Yukawa, Naomi Komiyama, Kotoko Nakata, Hiroki Momose, Yoshitomo Tanaka, Hiroshi Tanaka
Genome Informatics 14: 360-361 (2003)
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Identification of Regulation Networks of Lipid Metabolism by Nuclear Receptors
Yoshitomo Tanaka, Tsuguchika Kaminuma, Hiroki Momose, Kotoko Nakata, Hiroshi Tanaka
Genome Informatics 14: 362-363 (2003)
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Analysis of Gene Regulation Network by Nuclear Receptor PPAR
Hiroki Momose, Tsuguchika Kaminuma, Yoshitomo Tanaka, Kotoko Nakata, Hiroshi Tanaka
Genome Informatics 14: 364-365 (2003)
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Analysis of Reactive Modules in the Metabolic Pathways
Masaaki Kotera, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
Genome Informatics 14: 366-367 (2003)
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Metabolic Pathway Reconstruction for Malaria Parasite Plasmodium falciparum
Vachiranee Limviphuvadh, Yasushi Okuno, Toshiaki Katayama, Susumu Goto, Akiyasu C. Yoshizawa, Minoru Kanehisa
Genome Informatics 14: 368-369 (2003)
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Extraction of a Thermodynamic Property for Biochemical Reactions in the Metabolic Pathway
Michihiro Tanaka, Yasushi Okuno, Takuji Yamada, Susumu Goto, Shunsuke Uemura, Minoru Kanehisa
Genome Informatics 14: 370-371 (2003)
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Crosstalk between Metabolic and Regulatory Pathways
Min Kyung Kim, Hyun Seok Park, Seong Joon Yoo
Genome Informatics 14: 372-373 (2003)
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An Efficient Pathway Search Using an Indexing Scheme for RDF
Akiyoshi Matono, Toshiyuki Amagasa, Masatoshi Yoshikawa, Shunsuke Uemura
Genome Informatics 14: 374-375 (2003)
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Graph Complexity of Chemical Compounds in Biological Pathways
Atsuko Yamaguchi, Kiyoko F. Aoki, Hiroshi Mamitsuka
Genome Informatics 14: 376-377 (2003)
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M³: Merging Module Model for a Network with Scale-Free Properties and Modularity
Kazuhiro Takemoto, Chikoo Oosawa
Genome Informatics 14: 378-379 (2003)
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Comparative Analysis Workbench for Genetic Networks
Pan-Gyu Kim, Kyung-Shin Lee, Hwan-Gue Cho, Seon-Hee Park, Miyoung Shin, Eun-Mi Kang
Genome Informatics 14: 380-381 (2003)
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KAREIDMAP: A System for Predicting and Mining Gene Regulatory Networks
Hironori Mizuguchi, Dai Kusui, Taku Oshima, Shigehiko Kanaya, Hirotada Mori
Genome Informatics 14: 382-383 (2003)
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Development of a New Gene-Network Estimation System
Shigeyuki Mitsui, Hiroya Nobori, Tuyoshi Takada, Kunihiro Kishida, Yoshiki Miura, Hiroshi Ikawa
Genome Informatics 14: 384-385 (2003)
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3-D Visualization Software of a Gene Regulatory Network
Kouichi Okada, Nasimul Noman, Naoki Hosoyama, Hitoshi Iba
Genome Informatics 14: 386-387 (2003)
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CADLIVE Automatic Visualizing System for Large-Scale Biochemical Maps
Weijiang Li, Hiroyuki Kurata
Genome Informatics 14: 388-389 (2003)
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Transcriptome Profiling and Deciphering the Regulatory Role of Global Transcription Factor fadR
Byung Hun Kim, Si Jae Park, Sang Yup Lee
Genome Informatics 14: 390-391 (2003)
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Conservation of DNA Curvature Signals in Gene Regulatory Regions
Ruy Jauregui, Enrique Merino
Genome Informatics 14: 392-393 (2003)
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Large Scale Analysis of Transcriptional and Translational Control Mechanism in Human Ribosomal Proteins
Kyota Ishii, Tamayo Uechi, Takanori Washio, Maki Yoshihama, Naoya Kenmochi, Masaru Tomita
Genome Informatics 14: 394-395 (2003)
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Regulator Identification by Expression Profiles of Transcriptional Factor Mutants and Promoter Sequence in Bacillus subtilis
Nobuyuki Fujii, Joe Akitomi, Kazuo Kobayashi, Naotake Ogasawara, Shigehiko Kanaya
Genome Informatics 14: 396-397 (2003)
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Developing Genome-Scale Prediction System for Transcription Factors and Their Targets
Akinori Sarai, Shandar Ahmad, Michael M. Gromiha, M. D. Shaji Kumar, Abdulla Bava, Hidetoshi Kono
Genome Informatics 14: 398-399 (2003)
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Prediction of Transcription Factor Binding Sites with Suffix Arrays
Myung Eun Lim, Jeong Seop Sim, Myung Geun Chung, Sun Hee Park
Genome Informatics 14: 400-401 (2003)
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Phylogenetic Analysis of Eubacterial Transcriptional Systems Based on the DBTBS Database of B. subtilis Transcription Factors and Promoters
Yuko Makita, Naotake Ogasawara, Kenta Nakai
Genome Informatics 14: 402-403 (2003)
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Genome Wide Analysis Reveals Strong Correlation between CpG Islands and Tissue-Specificity
Riu Yamashita, Yutaka Suzuki, Toshihisa Takagi, Sumio Sugano, Kenta Nakai
Genome Informatics 14: 404-405 (2003)
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Extraction of Biological Motifs by Gibbs Sampler from the Promoters of Homo Sapiens, Saccharomyces cerevisiae and Bacillus subtilis
Natalia Poluliakh, Kenta Nakai
Genome Informatics 14: 406-407 (2003)
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Detection of Tissue Specific Genes by Putative Regulatory Motifs in Human Promoter Sequences
Katsuhiko Murakami, Toshio Kojima, Yoshiyuki Sakaki
Genome Informatics 14: 408-409 (2003)
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Statistical Analysis of Symmetric Exon Sets in Eukaryotic Genes
Yiyu Jia, Chee Keong Kwoh, Meena K. Sakharkar, Pandjassarame Kangueane
Genome Informatics 14: 410-411 (2003)
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Human Full-Length Pre-mRNA Sequence Dataset for Computational Gene Prediction and Alternative Splicing Analysis
Masahiko Mizuno, Osamu Gotoh, Makiko Suwa
Genome Informatics 14: 412-413 (2003)
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Detect of Novel Alternative Form at Development Stages in Brain
SungHun Lee, MyungGuen Chung, SungHee Park, SooJun Park, SeonHee Park
Genome Informatics 14: 414-415 (2003)
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Splice Variant Search with Gene Expression Data
Tadashi Kadowaki, Satoshi Shiojima, Gozoh Tsujimoto
Genome Informatics 14: 416-417 (2003)
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Mapping Database of cDNA and Genome Designed to Use for Various Applications
Akifumi Yamashita, Ken Kurokawa, Teruo Yasunaga
Genome Informatics 14: 418-419 (2003)
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Finding Significant Patterns Characterizing Types of Alternative Splicing
Hiroki Sakai, Osamu Maruyama
Genome Informatics 14: 420-421 (2003)
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Towards Splicing Pattern Detection Based on cDNA Sequences
Tomohiro Yasuda, Koichi Kimura, Tetsuo Nishikawa
Genome Informatics 14: 422-423 (2003)
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An Algorithm for Classification of Alternative Splicing and Transcriptional Initiation and Its Genome-Wide Application
Hideki Nagasaki, Makiko Suwa, Osamu Gotoh
Genome Informatics 14: 424-425 (2003)
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Detection of the Splicing Sites with Kernel Method Approaches Dealing with Nucleotide Doublets
Masaki Yamamura, Osamu Gotoh
Genome Informatics 14: 426-427 (2003)
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Identifying Potential Regulatory Sequences of Alternative Splicing
Hitomi Itoh, Takanori Washio, Masaru Tomita
Genome Informatics 14: 428-429 (2003)
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A cDNA Evaluation System for Highly Efficient Sequencing of Splicing Variant cDNAs
Jun-ichi Yamamoto, Naoto Hatano, Kenji Araki, Hiroshi Makita, Kouichi Kimura, Ai Wakamatsu, Shizuko Ishii, Tetsuo Nishikawa, Takao Isogai
Genome Informatics 14: 430-431 (2003)
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Self-Nonself Discrimination Based on Incompatibility of Amino Acid Sequences of Human and Viruses
Wataru Honda, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 14: 432-433 (2003)
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Analysis of Domain Combinations in Eukaryotic Genomes
Masumi Itoh, Akiyasu C. Yoshizawa, Shujiro Okuda, Susumu Goto, Minoru Kanehisa
Genome Informatics 14: 434-435 (2003)
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Comprehensive Survey of Intracellular Transport System-Related Proteins in Complete Genomes and Draft Genomes
Akiyasu C. Yoshizawa, Masumi Itoh, Shujiro Okuda, Vachiranee Limviphuvadh, Tadahiko Sakiyama, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 14: 436-437 (2003)
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Extraction of Organism Groups from Whole Genome Comparisons
Yoshihiro Yamanishi, Akiyasu C. Yoshizawa, Masumi Itoh, Toshiaki Katayama, Minoru Kanehisa
Genome Informatics 14: 438-439 (2003)
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Identifying Obscure Periodic Patterns in Genomic DNA Sequence
Hiroo Murakami, Natsuhiro Ichinose, Tetsushi Yada, Sachiyo Abratani, Nobuyoshi Sugaya, Makihiko Sato, Katsuhisa Horimoto
Genome Informatics 14: 440-441 (2003)
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Distribution of Chromophore-Binding GAF Domains in Genome Sequence
Shinobu Okamoto, Masayuki Ohomori
Genome Informatics 14: 442-443 (2003)
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Newly Identified Motifs within PAS Domains of Filamentous Cyanobacteria
Rei Narikawa, Shinobu Okamoto, Masahiko Ikeuchi, Masayuki Ohmori
Genome Informatics 14: 444-445 (2003)
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Translational Efficiency Prediction Using Structural Learning Method
Koya Mori, Rintaro Saito, Shinichi Kikuchi, Masaru Tomita
Genome Informatics 14: 446-447 (2003)
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Identification of Non-Coding RNAs in the Escherichia coli Genome Using Sequence Specificity Index (SSI)
Nozomu Yachie, Koji Numata, Rintaro Saito, Akio Kanai, Masaru Tomita
Genome Informatics 14: 448-449 (2003)
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Heterogeneity in Synonymous Codon Usage among Genes of Diverse Bacterial Genomes
Haruo Suzuki, Rintaro Saito, Masaru Tomita
Genome Informatics 14: 450-451 (2003)
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Detection of Processed Pseudogenes Based on cDNA Mapping to the Human Genome
Hiroaki Sakai, Kanako O. Koyanagi, Takeshi Itoh, Tadashi Imanishi, Takashi Gojobori
Genome Informatics 14: 452-453 (2003)
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Improvement in the Accuracy of Gene Prediction in Human cDNA Sequences
Fusano Todokoro, Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima, Tadashi Imanishi, Takashi Gojobori
Genome Informatics 14: 454-455 (2003)
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The Translated Region Inspector for cDNA Sequences
Kouichi Kimura, Tetsuo Nisikawa, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
Genome Informatics 14: 456-457 (2003)
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Characterization of One-Pass and Full-Length Sequences of Oligo-Capping cDNA Clones by Genome Mapping
Tetsuo Nishikawa, Kouichi Kimura, Tomohiro Yasuda, Jun-ichi Yamamoto, Ai Wakamatsu, Shizuko Ishii, Masashi Nemoto, Jun-ichi Uechi, Yutaka Suzuki, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
Genome Informatics 14: 458-459 (2003)
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Mapping the Genome Sequences on Self Organizing Maps
Hiroshi Dozono, Hisao Tokushima, Yoshio Noguchi
Genome Informatics 14: 460-461 (2003)
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Mapping of Artificial Nucleosome Positioning Sequences to the Saccharomyces cerevisiae Genome
Vorathaya Tantoolvesm, Yoichi Takenaka, Satoshi Harashima, Hideo Matsuda
Genome Informatics 14: 462-463 (2003)
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Analysis of Tandem Repeats Detected in Prokaryotic Genomes
Hikaru Munakata, Abulimiti Aimaiti, Akito Taneda, Kenji Oosawa, Toshio Shimizu
Genome Informatics 14: 464-465 (2003)
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Genome-Scale Detection of Tandemly-Duplicated Gene Structures
Keisuke Onishi, Hao Zhang, Takuro Tamura, Takashi Gojobori, Shintaroh Ueda
Genome Informatics 14: 466-467 (2003)
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Estimation of the Number of Orphan Genes in the Genome Sequences
Satoshi Fukuchi, Ken Nishikawa
Genome Informatics 14: 468-469 (2003)
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A Comparative Study on Formal Grammars for Pseudoknots
Yuki Kato, Hiroyuki Seki, Tadao Kasami
Genome Informatics 14: 470-471 (2003)
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Analysis of 3'/5' Ratio of Actin and Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)
Yasuo Oshima, Akio Fujimura
Genome Informatics 14: 472-473 (2003)
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MGAlign, a Reduced Search Space Approach to the Alignment of mRNA Sequences to Genomic Sequences
Shoba Ranganathan, Bernett T. K. Lee, Tin Wee Tan
Genome Informatics 14: 474-475 (2003)
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Development of Efficient Designing Method for Target Specific Probe Sets
So Young Yoo, Hyeong Jun An, Doheon Lee, Sang Yup Lee
Genome Informatics 14: 476-477 (2003)
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IMPORT - Integrated Massive Probe's Optimal Recognition Tools
Cheng Tao Wu, Chung Ya Liao, Hung Ju Su, Shiu Chieh Lan, Yu Yu Lin, Yu Ching Chang
Genome Informatics 14: 478-479 (2003)
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Algorithms for Computing an Optimal Protein Threading with Profiles and Distance Restraints
Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto
Genome Informatics 14: 480-481 (2003)
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Development of Residue Look-Up Tables and Graphical Representation of Solvent Accessibility in Proteins
Shandar Ahmad, Jung-Ying Wang, M. Michael Gromiha, Hamed Fawareh, Akinori Sarai
Genome Informatics 14: 482-483 (2003)
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Refinement of Comparative-Modeling Structures by Multicanonical Molecular Dynamics
Wei Cao, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
Genome Informatics 14: 484-485 (2003)
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Molecular Modeling for Generation of Structural and Molecular Electronic Descriptors for QSAR Using Quantum Mechanical Semiempirical and ab initio Methods
Mohd. Shahid Khan, Zahid H. Khan
Genome Informatics 14: 486-487 (2003)
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Maximum Likelihood Superposition of Protein Structures
Tsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai
Genome Informatics 14: 488-489 (2003)
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Prediction from Sequence to Structure at Oligonucleotide Level by MD Simulations
Manish Biyani, Koichi Nishigaki
Genome Informatics 14: 490-491 (2003)
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A Protein Structure Retrieval System Using Atom-Atom Bond-Line Histogram
Sung-hee Park, Soo-jun Park, Sung-hun Lee, Sun-hee Park
Genome Informatics 14: 492-493 (2003)
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A Combined Experimental and Inferring Interactomes
Chung-Yen Lin, Chi-Shiang Cho, Li-Ming Wang, Chia-Ling Chen, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung
Genome Informatics 14: 494-495 (2003)
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Prediction of Protein-Protein Interactions from Phylogenetic Trees Using Partial Correlation Coefficient
Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Hiroyuki Toh, Minoru Kanehisa
Genome Informatics 14: 496-497 (2003)
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Prediction of Protein Functions Based on K-Cores of Protein-Protein Interaction Networks and Amino Acid Sequences
Md. Altaf-Ul-Amin, Kensaku Nishikata, Toshihiro Koma, Teppei Miyasato, Yoko Shinbo, Md. Arifuzzaman, Chieko Wada, Maki Maeda, Taku Oshima, Hirotada Mori, Shigehiko Kanaya
Genome Informatics 14: 498-499 (2003)
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Prediction of Protein Interaction Sites and Protein-Protein Interaction Pairs Using Support Vector Machines
Asako Koike, Toshihisa Takagi
Genome Informatics 14: 500-501 (2003)
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Support Vector Machines for Predicting Protein-Protein Interactions
Shinsuke Dohkan, Asako Koike, Toshihisa Takagi
Genome Informatics 14: 502-503 (2003)
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Inferring Strengths of Protein-Protein Interactions Using Linear Programming
Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu
Genome Informatics 14: 504-505 (2003)
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Prediction of Residues in Protein-RNA Interaction Sites by Neural Networks
Euna Jeong, I-Fang Chung, Satoru Miyano
Genome Informatics 14: 506-507 (2003)
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Positive Charge Cores in DNA-Binding Proteins
Kimiko Horibe, Shigeki Mitaku
Genome Informatics 14: 508-509 (2003)
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Structure-Thermodynamic Relationship in Protein-DNA Binding: Heat Capacity Changes
Hatsuho Uedaira, Hidetoshi Kono, Prabakaran Ponraj, Koji Kitajima, Akinori Sarai
Genome Informatics 14: 510-511 (2003)
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Prediction of Interfaces for GPCR Oligomer
Wataru Nemoto, Hiroyuki Toh
Genome Informatics 14: 512-513 (2003)
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Predict Functionally Important Residues Responsible for Estrogen Receptor Subtype Divergence
Feng Wang, Hirohisa Kishino, Yasuhiko Wada
Genome Informatics 14: 514-515 (2003)
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Protein Classification via Kernel Matrix Completion
Taishin Kin, Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
Genome Informatics 14: 516-517 (2003)
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On Improving Protein Functional Identification in Pattern Recognition Based on Continuous Density HMM
Dooil Kim, Dae-Sil Lee
Genome Informatics 14: 518-519 (2003)
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Protein Family Classification Using Second-Order Recurrent Neural Networks
Jinmiao Chen, Narendra S. Chaudhari
Genome Informatics 14: 520-521 (2003)
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Profile-Profile Comparison Based on Hidden Markov Model Profiles
Makihiko Sato, Nobuyoshi Sugaya, Hiroo Murakami, Sachiyo Aburatani, Katsuhisa Horimoto
Genome Informatics 14: 522-523 (2003)
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Genome Scale Classification of Extended Proteins by a Predictor SOSUIdumbbell
Nobuyuki Uchikoga, Ke Rungcong, Fumitsugu Akazawa, Masashi Sonoyama, Shigeki Mitaku
Genome Informatics 14: 524-525 (2003)
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A New Method for Characterizing Functionally-Unknown Proteins Using Specific Amino Acid Frequency and Periodicity at the Proteome Level
Kosuke Fujishima, Jun Imoto, Akio Kanai, Masaru Tomita
Genome Informatics 14: 526-527 (2003)
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Classification of Protein Sequences into Paralog and Ortholog Clusters Using Sequence Similarity Profiles of KEGG/SSDB
Yohsuke Minowa, Toshiaki Katayama, Akihiro Nakaya, Susumu Goto, Minoru Kanehisa
Genome Informatics 14: 528-530 (2003)
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Detection of Remote Homologue Using Predicted Structural Information
Daisuke Ishibe, Katsunori Uehara, Takeshi Kawabata, Nobuhiro Go
Genome Informatics 14: 531-532 (2003)
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RiceBLAST: A Comprehensive Homology Search for Rice Specific Sequences
Yoshiaki Nagamura, Baltazar A. Antonio, Hisataka Numa, Ikuo Horiuchi, Manabu Akimoto, Shigehiro Honda, Koichi Sugioka, Nana Matoba, Yuji Shimizu, Katsuaki Watanabe, Takuji Sasaki, Kenichi Higo
Genome Informatics 14: 533-534 (2003)
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Scalable BLAST Service in OBIGrid Environment
Fumikazu Konishi, Yukimasa Shiroto, Ryo Umetsu, Akihiko Konagaya
Genome Informatics 14: 535-536 (2003)
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Protein-Ligand Interactions: ProLINT Database and QSAR Analysis
Shandar Ahmad, Kouji Kitajima, Samuel Selvaraj, Hideo Kubodera, Shinji Sunada, Jianghong An, Akinori Sarai
Genome Informatics 14: 537-538 (2003)
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In Silico Prediction of Peroxisomal Proteins in Mouse
Igor V. Kurochkin, Christian Schönbach, Akihiko Konagaya
Genome Informatics 14: 539-540 (2003)
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A Proteomic Approach to Engineer Improved Cell Growth and Increased Production of Serine-Rich Proteins in Escherichia coli
Mee-Jung Han, Jong-Shin Yoo, Sang Yup Lee
Genome Informatics 14: 541-542 (2003)
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Genome-Wide Functional Classification/Identification of Prokaryotic Transmembrane Proteins Based on Transmembrane Topology Similarity
Masafumi Arai, Kosuke Okumura, Masanobu Satake, Toshio Shimizu
Genome Informatics 14: 543-544 (2003)
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Transmembrane Protein Evolution by Internal Gene Duplication
Hironori Mitsuke, Keisuke Noto, Masafumi Arai, Toshio Shimizu
Genome Informatics 14: 545-546 (2003)
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Comprehensive Functional Identification of Transmembrane Proteins Using the BTP Method
Yasuhito Inoue, Toshio Shimizu
Genome Informatics 14: 547-548 (2003)
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Inner Residues in the Transmembrane Helix Bundle are More Conservative
Sukenobu Konishi, Takuhiro Nishio, Toshio Shimizu
Genome Informatics 14: 549-550 (2003)
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The Clusters of Transmembrane Protein Genes in Prokaryotic Genomes
Ichitaro Oya, Satoshi Mizuta, Toshio Shimizu
Genome Informatics 14: 551-552 (2003)
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A Consensus Transmembrane Topology Prediction Method of High-Reliability
Jun-Xiong Xia, Toshio Shimizu
Genome Informatics 14: 553-554 (2003)
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Bioinformatics Studies on Transmembrane Strand Proteins
M. Michael Gromiha, Shandar Ahmad, Makiko Suwa
Genome Informatics 14: 555-556 (2003)
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On the Accuracy of Transmembrane Segment Prediction of Helical Integral Membrane Proteins
Shin Tanimoto, Gautam Basu, Takeshi Kawabata, Nobuhiro Go
Genome Informatics 14: 557-558 (2003)
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PLOC: Prediction of Subcellular Location of Proteins
Keun-Joon Park, Minoru Kanehisa, Yutaka Akiyama
Genome Informatics 14: 559-560 (2003)
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Gene-Distribution Patterns on Cyanobacterial Genomes
Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Satoh, Sachiyo Aburatani, Katsuhisa Horimoto
Genome Informatics 14: 561-562 (2003)
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Omic Space and Totalomics
Tetsuro Toyoda, Akiyoshi Wada
Genome Informatics 14: 563-564 (2003)
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Correlated Mutation Analysis of C2H2 Zinc Finger Domains
Takafumi Nagano, Makiko Suwa, Kiyoshi Asai
Genome Informatics 14: 565-566 (2003)
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Analysis of Horizontal Gene Transfer and Clustering of Microbial ORFs by Use of a GRID Environment
Hideaki Sugawara, Yoji Nakamura, Kazuho Ikeo, Satoru Miyazaki, Takashi Gojobori, Kenji Satou, Akihiko Konagaya
Genome Informatics 14: 567-568 (2003)
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Real-Time Mapping System of cDNAs and Genomes Using Grid Computing
Yusuke Saito, Manabu Gomi, Hideo Matsuda, Naohisa Goto, Ken Kurokawa, Teruo Yasunaga
Genome Informatics 14: 569-570 (2003)
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Space-Gene : Microbial Gene Prediction System Based on Linux Clustering
Jong-won Chang, Chungoo Park, Dong Soo Jung, Mi-hwa Kim, Jae-woo Kim, Seung-sik Yoo, Hong Gil Nam
Genome Informatics 14: 571-572 (2003)
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Pedigree Analysis Programme GTree 1.2 and Its Application
Daisuke Ogino, Shiro Mori, Masato Nose, Hideki Sawada
Genome Informatics 14: 573-574 (2003)
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Self-Organizing Clustering: A Novel Non-Hierarchical Method for Clustering Large Amount of DNA Sequences
Kou Amano, Hidemitsu Nakamura, Hiroaki Ichikawa
Genome Informatics 14: 575-576 (2003)
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PFcDNA: Prediction of a Full Length Gene from Partial Sequence
SooYoung Cho, Myungguen Chung, Seung-baek Han, Hyun Kim, YoungSeek Lee
Genome Informatics 14: 577-578 (2003)
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Statistical Significance of Tree Similarity Scores
Kiyoko F. Aoki, Atsuko Yamaguchi, Yasushi Okuno, Tatsuya Akutsu, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka
Genome Informatics 14: 579-580 (2003)
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Systematic Analyses of P-Loop Containing Nucleotide Triphosphate Hydrolase Superfamily Based on Sequence, Structure and Function
Yoichi Kawamura, Kiyoshi Asai, Shin Ishii, Nozomi Nagano
Genome Informatics 14: 581-582 (2003)
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TTOP : A System for Phylogenetic Tree Editing and Evolutionary Annotation of Genes
Srinesh Kundu, Masato Hagiwara, Kanako O. Koyanagi, Tadashi Imanishi, Takeshi Itoh
Genome Informatics 14: 583-584 (2003)
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Gclust: Genome-Wide Clustering of Protein Sequences for Identification of Photosynthesis-Related Genes Resulting from Massive Horizontal Gene Transfer
Naoki Sato
Genome Informatics 14: 585-586 (2003)
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Comparative Genomics between Drosophila and Human
Masuko Katoh, Masaru Katoh
Genome Informatics 14: 587-588 (2003)
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Novel Types of Two-Domain Multi-Copper Oxidases: Possible Missing Links in the Evolution
Kensuke Nakamura, Takeshi Kawabata, Kei Yura, Nobuhiro Go
Genome Informatics 14: 589-590 (2003)
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SNPAnalyzer: Web-Based Workbench for the SNPs Analysis
Jihho Yoo, Bonghee Seo, Yangseok Kim
Genome Informatics 14: 591-592 (2003)
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Artificial Neural Network Model for Prediction of Childhood Allergic Asthma Using Single Nucleotide Polymorphism Data
Yasuyuki Tomita, Shuta Tomida, Yoichi Suzuki, Taro Shirakawa, Takeshi Kobayashi, Hiroyuki Honda
Genome Informatics 14: 593-594 (2003)
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NAMIHEI: A Novel Algorithm for Genomic Polymorphism Detection from DNA Sequence
Go Maeno, Tomohiro Isobe, Yuko Tokoro, Yuki Ejiri, Nobutaka Mitsuhashi, Tokuki Sakiyama, Ken Aoshima
Genome Informatics 14: 595-596 (2003)
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Drug Screening of GPCR Using Active Learning
Yukiko Fujiwara, Yoshiko Yamashita, Tsutomu Osoda, Minoru Asogawa, Shun Doi, Masaaki Asao, Emi Kushiyama, Kazuya Nakao, Masataka Kuroda, Kazuteru Wada, Takanori Ogaru, Chiaki Fukushima, Ryo Shimizu
Genome Informatics 14: 597-598 (2003)
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An Integrated Database of Interaction between Human Proteins and Commonly Used Drugs
Masashi Nemoto, Kenji Araki, Ken Horiuchi, Motoi Tobita, Tetsuo Nishikawa
Genome Informatics 14: 599-600 (2003)
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Common Features in Substrates of Multidrug Resistance Transporters
Yoshinobu Igarashi, Yasushi Okuno, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
Genome Informatics 14: 601-602 (2003)
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Computational Models of Calcium Signaling in the Pancreas - Temporal and Spatial Regulations
Kojiro Yano, Ole H. Petersen, Alexei V. Tepikin
Genome Informatics 14: 603-604 (2003)
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Model Analysis of Helper T Cell Differentiation
Satoshi Yamada, Akihiko Yoshimura
Genome Informatics 14: 605-606 (2003)
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Kinetics Behavior of G1-to-S Cell Cycle Phase Transition Model
Yoshihiko Tashima, Taizo Hanai, Hiroyuki Hamada, Masahiro Okamoto
Genome Informatics 14: 607-608 (2003)
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CADLIVE-Based Analysis for the Budding Yeast Cell Cycle
Natsumi Shimizu, Shunsuke Yamamichi, Hiroyuki Kurata
Genome Informatics 14: 609-610 (2003)
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Deterministic and Stochastic Models Analyze the Robustness of Circadian Rhythms
Yoshiyuki Sumida, Fumitaka Ohnishi, Hiroyuki Kurata
Genome Informatics 14: 611-612 (2003)
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Integration of Postgenomic Data for GMA to Simulate a Metabolic Circuit
Takayuki Tanaka, Hiroyuki Kurata
Genome Informatics 14: 613-614 (2003)
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Xenopus Cell Cycle Pathway for Simulating Cell Division Processes by Genomic Object Net
Mika Matsui, Sachie Fujita, Shun-ichi Suzuki, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 14: 615-616 (2003)
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Simulation of Drosophila Boundary Cell Formation in Forced-Expression of NotchΔE
Rie Yamane, Junko Umezaki, Hiroshi Matsuno, Ryutaro Murakami, Naoyuki Yamasaki, Satoru Miyano
Genome Informatics 14: 617-618 (2003)
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Distributed Client-Server System Architecture for High Performance Simulations on Genomic Object Net
Tomokazu Kono, Ryuhei Noda, Hironori Kitakaze, Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 14: 619-620 (2003)
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OBIYagns: A Biochemical Simulator in Grid Environment
Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya
Genome Informatics 14: 621-622 (2003)
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Computer Simulation System for Modeling of Reaction-Diffusion of Biochemical Pathways
Ryuzo Azuma, Yoshiki Yamaguchi, Tetsuji Kitagawa, Akihiko Konagaya
Genome Informatics 14: 623-624 (2003)
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Parallelized Simulation of Molecular Dynamics with a Special-Purpose Computer: MDGRAPE-2
Naoki Takada, Noriyuki Futatsugi, Atsushi Suenaga, Tetsu Narumi, Noriaki Okimoto, Hidenori Hirano, Atsushi Kawai, Kenji Yasuoka, Toshikazu Ebisuzaki, Makoto Taiji, Akihiko Konagaya
Genome Informatics 14: 625-626 (2003)
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Quantifying the Spiral Leaf Trait of Arabidopsis from the 3D Shape Model Towards Computational Phenomics
Eli Kaminuma, Naohiko Heida, Yuko Tsumoto, Minami Matsui, Tetsuro Toyoda, Akihiko Konagaya
Genome Informatics 14: 627-628 (2003)
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BioRuby: Open-Source Bioinformatics Library
Naohisa Goto, Mitsuteru C. Nakao, Shiuichi Kawashima, Toshiaki Katayama, Minoru Kanehisa
Genome Informatics 14: 629-630 (2003)
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G-Language Genome Analysis Environment Version 2
Hayataro Kouchi, Kazuharu Arakawa, Ryo Hattori, Yohei Yamada, Yusuke Kobayashi, Atsuko Kishi, Kosaku Shinoda, Masaru Tomita
Genome Informatics 14: 631-632 (2003)
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Development of Bacteria Analysis System v.2 on the G-Language Genome Analysis Environment
Daisuke Kyuma, Kazuharu Arakawa, Koya Mori, Masaru Tomita
Genome Informatics 14: 633-634 (2003)
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Microarray Visualization System on the G-Language GAE
Yohei Yamada, Kazuharu Arakawa, Hirotada Mori, Masaru Tomita
Genome Informatics 14: 635-636 (2003)
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Prediction of Biochemical Reactions Using Genetic Programming
Masahiro Sugimoto, Shinichi Kikuchi, Masaru Tomita
Genome Informatics 14: 637-638 (2003)
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Automatic Generation of Cell-Wide Pathway Model from Complete Genome
Kazuharu Arakawa, Yohei Yamada, Hiromi Komai, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
Genome Informatics 14: 639-640 (2003)
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SIMDEB-ECS : E-CELL Static Model Debugger
Naota Ishikawa, Iriko Kaneko, Toshikazu Ebisuzaki
Genome Informatics 14: 641-642 (2003)
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In silico Simulation Represents Adenoviral Gene Knockdown of Myocardial Ventricular Cell
Yasuhiro Naito, Motohiro Yoneda, Sayaka Ishinabe, Shoko Miyamoto, Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma, Masaru Tomita
Genome Informatics 14: 643-644 (2003)
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Model Construction of the Energy Metabolism Pathway in Myocardial Cell
Motohiro Yoneda, Shoko Miyamoto, Yasuhiro Naito, Sayaka Ishinabe, Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma, Masaru Tomita
Genome Informatics 14: 645-646 (2003)
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FAMSBASE: Modeling Database of 161 Genomes
Mitsuo Iwadate, Kazuhiko Kanou, Daisuke Takaya, Katsuichiro Komatsu, Mayuko Takeda-Shitaka, Hideaki Umeyama
Genome Informatics 14: 647-648 (2003)
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GLYCAN: The Database of Carbohydrate Structures
Kosuke Hashimoto, Masami Hamajima, Susumu Goto, Shigekazu Masumoto, Masayuki Kawasima, Minoru Kanehisa
Genome Informatics 14: 649-650 (2003)
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HAPPY: Hypothetical and Putative Protein Database System
Takuya Murakami, Masatomo Najima, Michihiro Ogawa, Ken Kurokawa, Teruo Yasunaga
Genome Informatics 14: 651-652 (2003)
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The Construction of a Database for Ubiquitin Signaling Cascade
Tadahiko Sakiyama, Shuichi Kawashima, Akiyasu C. Yoshizawa, Minoru Kanehisa
Genome Informatics 14: 653-654 (2003)
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Development of HocDB (Homology-Based Clustering DataBase), a Sequence Classification System for Database Searching
Motokazu Ishikawa, Yoshinori Sato, Hiroyuki Toh
Genome Informatics 14: 655-656 (2003)
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Development of Community Annotation Databases for Linking Genomes to Cellular Functions
Miho Furumichi, Yoko Sato, Toshiaki Katayama, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 14: 657-658 (2003)
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Gene List of Sphingomonas chungbukensis DJ77
Kwon Hae-Ryong, Hyun-Ju Um, Jeong-Su Oh, Wan-Sup Cho, Young-Chang Kim
Genome Informatics 14: 659-660 (2003)
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Current Status of Rice Annotation Database (RAD)
Yuichi Ito, Isamu Ohta, Yoshiyuki Mukai, Baltazar A. Antonio, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Katsumi Sakata, Nobukazu Namiki, Takashi Matsumoto, Takuji Sasaki
Genome Informatics 14: 661-662 (2003)
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Improvements in ProMode (a Database of Normal Mode Analyses of Proteins)
Hiroshi Wako, Masaki Kato, Shigeru Endo
Genome Informatics 14: 663-664 (2003)
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Current Status of ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions
M.D. Shaji Kumar, Ponraj Prabakaran, M. Michael Gromiha, Hatsuho Uedaira, Kouji Kitajima, Akinori Sarai
Genome Informatics 14: 665-666 (2003)
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Latest Developments in ProTherm: Thermodynamic Database for Proteins and Mutants
K. Abdulla Bava, M. Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, Akinori Sarai
Genome Informatics 14: 667-668 (2003)
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Enhancement of the SOAP Server in DDBJ Web Services to Process Tsunami of Biological Data
Yasumasa Shigemoto, Masahito Yamaguchi, Satoru Miyazaki, Hideaki Sugawara
Genome Informatics 14: 669-670 (2003)
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A Prototype of PubMed Central Japan
Hideaki Sugawara, Takashi Gojobori, Takeshi Konno, Yasumasa Shigemoto, Masahito Yamaguchi
Genome Informatics 14: 671-672 (2003)
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KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System
Shuichi Kawashima, Toshiaki Katayama, Yoko Sato, Minoru Kanehisa
Genome Informatics 14: 673-674 (2003)
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GOODIES: GO Based Data Mining Tool for Characteristic Attribute Interpretation on a Group of Biological Entities
Sung Geun Lee, Wan Seon Lee, Yang Seok Kim
Genome Informatics 14: 675-676 (2003)
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Open Ontology Forge: A Tool for Ontology Creation and Text Annotation Applied to the Biomedical Domain
Ai Kawazoe, Tony Mullen, Koichi Takeuchi, Tuangthong Wattarujeekrit, Nigel Collier
Genome Informatics 14: 677-678 (2003)
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INOH: A Textual Knowledge Based Pathway Database
Satoko Yamamoto, Tatsuya Kushida, Naotaka Ono, Yuki Yamagata, Toshihisa Takagi, Ken-ichiro Fukuda
Genome Informatics 14: 679-680 (2003)
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UniPath: A Knowledge Representation System for Biological Pathways
Min Su Lee, Seung Soo Park, Hyun Seok Park
Genome Informatics 14: 681-682 (2003)
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Extraction of Biological Contexts and Ontological DAG Structures from Gene Groups Using GO Term Distribution
Sung Geun Lee, Jae Seong Yang, Wan Seon Lee, Miyoung Shin, Yang Seok Kim
Genome Informatics 14: 683-684 (2003)
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Ontology Using Role Concept Recognized on Biological Relationships and Its Application
Masaru Takeya, Hisataka Numa, Koji Doi
Genome Informatics 14: 685-686 (2003)
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Prediction of MHC Class I Binding Peptides Using an Ensemble Learning Approach
Nicolas Majeux, Keiko Udaka, Hiroshi Mamitsuka
Genome Informatics 14: 687-688 (2003)
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Development of Construction and Management Tools for Biological Named Entity Dictionary
Hyunchul Jang, Taehyun Kim, Hyunsook Lee, Soojun Park, Seonhee Park
Genome Informatics 14: 689-690 (2003)
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Language Resource and Rule Construction for Biological Named Entity System Using UMLS
Hyun-Sook Lee, Tae-Hyun Kim, Soo-Jun Park, Seon-Hee Park
Genome Informatics 14: 691-692 (2003)
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BIOSILICO: A Biochemical Database Retrieval System
Jin Sik Kim, Ji Hoon Jun, Yong Wook Kim, Sujin Chae, Mira Roh, Yong Ho In, Sang Yup Lee
Genome Informatics 14: 693-694 (2003)
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Development of Lossless Compression Techniques for Biology Information and Its Application for Bioinformatics Database Retrieval
Toshio Modegi
Genome Informatics 14: 695-696 (2003)
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An Algorithm to Identify Abbreviations from MEDLINE
Hiroko Ao, Toshihisa Takagi
Genome Informatics 14: 697-698 (2003)
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Extracting Information on Protein-Protein Interactions from Biological Literature Based on Machine Learning Approaches
Kazunari Sugiyama, Kenji Hatano, Masatoshi Yoshikawa, Shunsuke Uemura
Genome Informatics 14: 699-700 (2003)
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Evaluation System for Information Retrieval in Biomedical Field
Yasunori Yamamoto, Toshihisa Takagi
Genome Informatics 14: 701-702 (2003)
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Disease-Associated Genes Extraction from Literature Database
Takayuki Takahata, Yasuhiro Kouchi, Kaoru Asano, Toshihisa Takagi
Genome Informatics 14: 703-704 (2003)
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