G I W 2 0 0 3 - List of Accepted Posters -

List of Accepted Posters

T i t l e
A u t h o r (s)
FAMSBASE: Modeling Database of 161 GenomesMitsuo Iwadate, Kazuhiko Kanou, Daisuke Takaya, Katsuichiro Komatsu, Mayuko Takeda-Shitaka, Hideaki Umeyama
Pathways/Networks to Syndrome XTsuguchika Kaminuma, Masumi Yukawa, Naomi Komiyama, Kotoko Nakata, Hiroki Momose, Yoshitomo Tanaka, Hiroshi Tanaka
Detection of genes with tissue-specific patterns using Akaike's Information CriterionKoji Kadota, Katsutoshi Takahashi
Analysis of 3'/5' ratio of Actin and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)Yasuo Oshima, Akio Fujimura
Gclust: genome-wide clustering of protein sequences for identification of photosynthesis-related genes resulting from massive horizontal gene transferNaoki Sato
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
RiceBLAST: A Comprehensive Homology Search for Rice Specific SequencesYoshiaki Nagamura, Baltazar A. Antonio, Hisataka Numa, Ikuo Horiuchi, Manabu Akimoto, Shigehiro Honda, Koichi Sugioka, Nana Matoba, Yuji Shimizu, Katsuaki Watanabe, Takuji Sasaki, Kenichi Higo
Gene-Distribution Patterns on Cyanobacterial GenomesNobuyoshi Sugaya, Hiroo Murakami, Makihiko Satoh, Sachiyo Aburatani, Katsuhisa Horimoto
Computational models of calcium signaling in the pancreas - temporal and spatial regulationsKojiro Yano, Ole H. Petersen, Alexei V. Tepikin
Model Analysis of Helper T Cell DifferentiationSatoshi Yamada, Akihiko Yoshimura
Open Ontology Forge: A Tool for Ontology Creation and Text Annotation Applied to the Biomedical DomainAi Kawazoe, Tony Mullen, Koichi Takeuchi, Tuangthong Wattarujeekrit, Nigel Collier
Artificial Neural Network Model for Prediction of Childhood Allergic Asthma Using Single Nucleotide Polymorphism DataYasuyuki Tomita, Shuta Tomida, Yoichi Suzuki, Taro Shirakawa, Takeshi Kobayashi, Hiroyuki Honda
Gene Screening Method for Prognostic Prediction Using Projective ART ModelHiro Takahashi, Takeshi Kobayashi, Hiroyuki Honda
Improvements in ProMode (a database of normal mode analyses of proteins)Hiroshi Wako, Masaki Kato, Shigeru Endo
Inferring Strengths of Protein-Protein Interactions Using Linear ProgrammingMorihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu
Operon Prediction by DNA microarray: an Approach with a Bayesian Network ModelHitoshi SHIMIZU, Shigeyuki OBA, Shin ISHII
Heterogeneity in synonymous codon usage among genes of diverse bacterial genomesHaruo Suzuki, Rintaro Saito, Masaru Tomita
Comparative Analysis Workbench for Genetic NetworksPan-Gyu Kim, Kyung-Shin Lee, Hwan-Gue Cho, Seon Hee Park, Miyoung Shin, Eun Mi Kang
OBIYagns: A biochemical simulator in Grid environmentShuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya
CADLIVE Automatic Visualizing System for Large-Scale Biochemical MapsWeijiang Li, Hiroyuki Kurata
Identifying Obscure Periodic Patterns in Genomic DNA SequenceHiroo Murakami, Natsuhiro Ichinose, Tetsushi Yada, Sachiyo Abratani, Nobuyoshi Sugaya, Makihiko Sato, Katsuhisa Horimoto
Genome-Scale Detection of Tandemly-Duplicated Gene StructuresKeisuke Onishi, Hao Zhang, Takuro Tamura, Takashi Gojobori, Shintaroh Ueda
Conservation of DNA curvature signals in gene regulatory regionsRuy Jauregui, Enrique Merino
Prediction of Biochemical Reactions using Genetic ProgrammingMasahiro Sugimoto, Shinichi Kikuchi, Masaru Tomita
Genome-Wide Functional Classification/Identification of Prokaryotic Transmembrane Proteins Based on Transmembrane Topology SimilarityMasafumi Arai, Kosuke Okumura, Masanobu Satake, Toshio Shimizu
Analysis of Tandem Repeats Detected in Prokaryotic GenomesHikaru Munakata, Abulimiti Aimaiti, Akito Taneda, Kenji Oosawa, Toshio Shimizu
Prediction of Interfaces for GPCR OligomerWataru Nemoto, Hiroyuki Toh
Prediction of Protein Interaction Sites and Protein-Protein Interaction Pairs using Support Vector MachinesAsako Koike, Toshihisa Takagi
Correlated Mutation Analysis of C2H2 Zinc Finger DomainsTakafumi Nagano, Makiko Suwa, Kiyoshi Asai
Structure-Thermodynamic Relationship in Protein-DNA Binding: Heat Capacity ChangesHatsuho Uedaira, Hidetoshi Kono, Prabakaran Ponraj, Koji Kitajima, Akinori Sarai
Deterministic and Stochastic Models Analyze the Robustness of Circadian RhythmsYoshiyuki Sumida, Fumitaka Ohnishi, Hiroyuki Kurata
Integration of Postgenomic Data for GMA to Simulate a Metabolic CircuitTakayuki Tanaka, Hiroyuki Kurata
NAMIHEI: A Novel Algorithm for Genomic Polymorphism Detection from DNA SequenceGo Maeno, Tomohiro Isobe, Yuko Tokoro, Yuki Ejiri, Nobutaka Mitsuhashi, Tokuki Sakiyama, Ken Aoshima
Development of Lossless Compression Techniques for Biology Information and its Application for Bioinformatics Database RetrievalToshio Modegi
Estimation of the number of orphan genes in the genome sequencesSatoshi Fukuchi, Ken Nishikawa
Enhancement of the SOAP Server in DDBJ Web services to Process Tsunami of Biological DataYasumasa Shigemoto, Masahito Yamaguchi, Satoru Miyazaki, Hideaki Sugawara
Analysis of Horizontal Gene Transfer and Clustering of Microbial ORFs by use of a GRID environmentHideaki Sugawara, Yoji Nakamura, Kazuho Ikeo, Satoru Miyazaki, Takashi Gojobori, Kenji Satou, Akihiko Konagaya
Integrative Method for Identifying Combinatorial Regulation of Transcription FactorsMamoru Kato, Naoya Hata, Nila Banerjee, Michael Q. Zhang
Pedigree Analysis Programme GTree 1.2 and its ApplicationDaisuke Ogino, Shiro Mori, Masato Nose, Hideki Sawada
Statistical Analysis of the Relationship between Gene Expression and LocationSachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Katsuhisa Horimoto
Statistical analysis of symmetric exon sets in eukaryotic genesYiyu Jia, Chee Keong Kwoh, Meena K. Sakharkar, Pandjassarame Kangueane
Self-Organizing Clustering: A Novel Non-Hierarchical Method for Clustering Large Amount of DNA SequencesKou Amano, Hidemitsu Nakamura, Hiroaki Ichikawa
Development of HocDB (Homology-based Clustering DataBase), a sequence classification system for database searchingMotokazu Ishikawa, Yoshinori Sato, Hiroyuki Toh
IMPORT - Integrated Massive Probe's Optimal Recognition ToolsCheng Tao Wu, Chung Ya Liao, Hung Ju Su, Shiu Chieh Lan, Yu Yu Lin, Yu Ching Chang,
Simulation of Drosophila Boundary Cell Formation inForced-Expression of NotchΔERie Yamane, Junko Umezaki, Hiroshi Matsuno, Ryutaro Murakami, Naoyuki Yamasaki, Satoru Miyano
Xenopus Cell Cycle Pathway for Simulating Cell Division Processes by Genomic Object NetMika Matsui, Sachie Fujita, Shun-ichi Suzuki, Hiroshi Matsuno, Satoru Miyano
Extracting Information on Protein-Protein Interactions from Biological Literature Based on Machine Learning ApproachesKazunari Sugiyama, Kenji Hatano, Masatoshi Yoshikawa, Shunsuke Uemura
An algorithm to identify abbreviations from MEDLINEHiroko Ao, Toshihisa Takagi
Significance test of clusters in gene expression profile dataNatsuko Kawase, Shigeyuki Oba, Shin Ishii
Identifying Potential Regulatory Sequences of Alternative SplicingHitomi Itoh, Takanori Washio, Masaru Tomita
Bioinformatics Studies on Transmembrane Strand ProteinsM. Michael Gromiha, Shandar Ahmad, Makiko Suwa
Features of Gene Extraction by Nonlinear Support Vector Machines in Gene Expression AnalysisDaisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara
Towards Splicing Pattern Detection Based on cDNA SequencesTomohiro Yasuda, Koichi Kimura, Tetsuo Nishikawa
Computer simulation system for modeling of reaction-diffusion of biochemical pathways Ryuzo Azuma, Yoshiki Yamaguchi, Tetsuji Kitagawa, Akihiko Konagaya
A Prototype of PubMed Central JapanHideaki Sugawara, Takashi Gojobori, Takeshi Konno, Yasumasa Shigemoto, Masahito Yamaguchi
Refinement of Comparative-Modeling Structures by Multicanonical Molecular DynamicsWei Cao, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
SNPAnalyzer: web-based workbench for the SNPs analysisJihho Yoo, Bonghee Seo, Yangseok Kim
Support Vector Machines for Predicting Protein-Protein InteractionsShinsuke Dohkan, Asako Koike, Toshihisa Takagi
Omic Space and TotalomicsTetsuro Toyoda, Akiyoshi Wada
Space-Gene : Microbial Gene Prediction System based on Linux ClusteringJong-won Chang, Chungoo Park, Dong Soo Jung, Mi-hwa Kim, Jae-woo Kim, Seung-sik Yoo, Hong Gil Nam
Predict Functionally Important Residues Responsible for Estrogen Receptor Subtype DivergenceFeng Wang, Hirohisa Kishino, Yasuhiko Wada
Development of a New Gene-Network Estimation SystemShigeyuki Mitsui, Hiroya Nobori, Tuyoshi Takada, Kunihiro Kishida, Yoshiki Miura, Hiroshi Ikawa
Language Resource and Rule Construction for Biological Named Entity System using UMLSHyun-Sook Lee, Tae-Hyun Kim, Soo-Jun Park, Seon-Hee Park
The Translated Region Inspector for cDNA SequencesKouichi Kimura, Tetsuo Nisikawa, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
Mapping the Genome Sequences on Self Organizing MapsHiroshi Dozono, Hisao Tokushima, Yoshio Noguchi
Disease-associated Genes Extraction from Literature DatabaseTakayuki Takahata, Yasuhiro Kouchi, Kaoru Asano, Toshihisa Takagi
In Silico Prediction of Peroxisomal Proteins in MouseIgor V. Kurochkin, Christian Schonbach, Akihiko Konagaya
Drug Screening of GPCR using Active LearningYukiko 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
Development of Construction and Management Tools for Biological Named Entity DictionaryHyunchul Jang, Taehyun Kim, Hyunsook Lee, Soojun Park, Seonhee Park
Developing Genome-Scale Prediction System for Transcription Factors and Their TargetsAkinori Sarai, Shandar Ahmad, Michael M. Gromiha, M. D. Shaji Kumar, Abdulla Bava, Hidetoshi Kono
Protein-Ligand Interactions: ProLINT database and QSAR AnalysisShandar Ahmad, Kouji Kitajima, Samuel Selvaraj, Hideo Kubodera, Shinji Sunada, Jianghong An, Akinori Sarai
Development of Residue look-up tables and Graphical Representation of Solvent Accessibility in ProteinsShandar Ahmad, Jung-Ying Wang, M. Michael Gromiha, Hamed Fawareh, Akinori Sarai
Automatic Extraction of Expression-related Features Shared by a Given Group of GenesTakuya Oyama, Mikio Yoshida, Satoshi Kamegai, Kagehiko Kitano, Fumihito Miura, Noriko Kawaguchi, Miyuki Onda, Kenji Satou, Takashi Ito
SIMDEB-ECS : E-CELL static model debuggerNaota Ishikawa, Iriko Kaneko, Toshikazu Ebisuzaki
Current Status of ProNIT: Thermodynamic Database for Protein-Nucleic Acid InteractionsM.D. Shaji Kumar, Ponraj Prabakaran, M. Michael Gromiha, Hatsuho Uedaira, Kouji Kitajima, Akinori Sarai
Automatically Finding Good Clusters with Seed K-meansMiyoung Shin, Eun Mi Kang, Seon Hee Park
Newly identified motifs within PAS domains of filamentous cyanobacteriaRei Narikawa, Shinobu Okamoto, Masahiko Ikeuchi, Masayuki Ohmori
M3 : Merging module model for a network with scale-free properties and modularityKazuhiro Takemoto, Chikoo Oosawa
Latest developments in ProTherm: Thermodynamic Database for Proteins and MutantsK. Abdulla Bava, M. Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, Akinori Sarai
Crosstalk between metabolic and regulatory pathwaysMin Kyung Kim, Hyun Seok Park, Seong Joon Yoo
Prediction of MHC Class I Binding Peptides Using an Ensemble Learning ApproachNicolas Majeux, Keiko Udaka, Hiroshi Mamitsuka
Prediction of Residues in Protein-RNA Interaction Sites by Neural NetworksEuna Jeong, I-Fang Chung, Satoru Miyano
Distribution of chromophore-binding GAF domains in genome sequenceShinobu Okamoto, Masayuki Ohomori
Protein Classification via Kernel Matrix CompletionTaishin Kin, Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
A System for Visualizing Gene Expressions using Metabolic NetworksRyoko Tamaru, Toshiyuki Amagasa, Shigehiko Kanaya, Shunsuke Uemura
UniPath: A Knowledge Representation System for Biological PathwaysMin Su Lee, Seung Soo Park, Hyun Seok Park
Detect of Novel Alternative Form at Development Stages in BrainSungHun Lee, MyungGuen Chung, SungHee Park, SooJun Park, SeonHee Park
Finding Signiffcant Patterns Characterizing Types of Alternative SplicingHiroki Sakai, Osamu Maruyama
An integrated database of interaction between human proteins and commonly used drugsMasashi Nemoto, Kenji Araki, Ken Horiuchi, Motoi Tobita, Tetsuo Nishikawa
Image Preprocessing For cDNA microarray Using Deconvolution MethodHyo Jung Ban, Myungguen Chung, Yong Sung Lee, Jin Hyuk Kim, Young Seek Lee
A Comparative Study on Formal Grammars for PseudoknotsYuki Kato, Hiroyuki Seki, Tadao Kasami
PFcDNA: Prediction of a full length gene from partial sequenceSooYoung Cho, Myungguen Chung, Seung-baek Han, Hyun Kim, YoungSeek Lee
Prediction of transcription factor binding site by extracting common sequencesMyung Eun Lim, Jeong Seop Sim, Myung Geun Chung, Sun Hee Park
Translational Efficiency Prediction Using Structural Learning MethodKoya Mori, Rintaro Saito, Shinichi Kikuchi, Masaru Tomita
Parallelized Simulation of Molecular Dynamics with a Special-Purpose Computer: MDGRAPE-2Naoki Takada, Noriyuki Futatsugi, Atsushi Suenaga, Tetsu Narumi, Noriaki Okimoto, Hidenori Hirano, Atsushi Kawai, Kenji Yasuoka, Toshikazu Ebisuzaki, Makoto Taiji, Akihiko Konagaya
Microarray Visualization System on the G-language GAEYohei Yamada, Kazuharu Arakawa, Hirotada Mori, Masaru Tomita
BIOSILICO: A Biochemical Database Retrieval SystemJin Sik Kim, Ji Hoon Jun, Yong Wook Kim, Sujin Chae, Mira Roh, Yong Ho In, Sang Yup Lee
On the Accuracy of Transmembrane Segment Prediction of Helical Integral Membrane ProteinsShin Tanimoto, Gautam Basu, Takeshi Kawabata, Nobuhiro Go
An Efficient Pathway Search using an Indexing Scheme for RDFAkiyoshi MATONO, Toshiyuki AMAGASA, Masatoshi YOSHIKAWA, Shunsuke UEMURA
Statistical Significance of Tree Similarity ScoresKiyoko F. Aoki, Atsuko Yamaguchi, Yasushi Okuno, Tatsuya Akutsu, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka
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
A Consensus Transmembrane Topology Prediction Method of High-ReliabilityJun-Xiong Xia, Toshio Shimizu
Comprehensive Functional Identification of Transmembrane Proteins Using the BTP MethodYasuhito Inoue, Toshio Shimizu
A cDNA Evaluation System for Highly Efficient Sequencing of Splicing Variant cDNAsJun-ichi Yamamoto, Naoto Hatano, Kenji Araki, Hiroshi Makita, Kouichi Kimura, Ai Wakamatsu, Shizuko Ishii, Tetsuo Nishikawa, Takao Isogai
CADLIVE-Based Analysis for the Budding Yeast Cell CycleNatsumi Shimizu, Shunsuke Yamamichi, Hiroyuki Kurata
Large Scale Analysis of Transcriptional and TranslationalControl Mechanism in Human Ribosomal ProteinsKyota Ishii, Tamayo Uechi, Takanori Washio, Maki Yoshihama, Naoya Kenmochi, Masaru Tomita
Extraction of Biological Contexts and Ontological DAG Structures from Gene Groups using GO Term DistributionSung Geun Lee, Jae Seong Yang, Wan Seon Lee, Miyoung Shin, Yang Seok Kim
An algorithm for classification of alternative splicing and transcriptional initiation and its genome-wide applicationHideki Nagasaki, Makiko Suwa, Osamu Gotoh
Maximum Likelihood Superposition of Protein StructuresTsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai
Real-Time Mapping System of cDNAs and Genomes using Grid ComputingYusuke Saito, Manabu Gomi, Hideo Matsuda, Naohisa Goto, Ken Kurokawa, Teruo Yasunaga
A new method for characterizing functionally-unknown proteins using specific amino acid frequency and periodicity at the proteome levelKosuke Fujishima, Jun Imoto, Akio Kanai, Masaru Tomita
Automatic generation of cell-wide pathway model from complete genomeKazuharu Arakawa, Yohei Yamada, Hiromi Komai, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
Profile-Profile Comparison based on Hidden Markov Model ProfilesMakihiko Sato, Nobuyoshi Sugaya, Hiroo Murakami, Sachiyo Aburatani, Katsuhisa Horimoto
Analysis of Gene Regulation Network by Nuclear Receptor PPARHiroki Momose, Tsuguchika Kaminuma, Yoshitomo Tanaka, Kotoko Nakata, Hiroshi Tanaka
Novel types of two-domain multi-copper oxidases: Possible missing links in the evolutionKensuke Nakamura, Takeshi Kawabata, Kei Yura, Nobuhiro Go
Identification of Regulation Networks of Lipid Metabolism by Nuclear ReceptorsYoshitomo Tanaka, Tsuguchika Kaminuma, Hiroki Momose, Kotoko Nakata, Hiroshi Tanaka
TTOP : a system for evolutionary annotation of phylogenic treesSrinesh Kundu, Masato Hagiwara, Kanako O. Koyanagi, Tadashi Imanishi, Takeshi Itoh
Algorithms for Computing an Optimal Protein Threading with Profiles and Distance RestraintsTatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun’ichi Suzuki, Katsuhisa Horimoto
Characterization of one-pass and full-length sequences of oligo-capping cDNA clones by genome mappingTetsuo Nishikawa, Kouichi Kimura, Tomohiro Yasuda, Jun-ichi Yamamot, Ai Wakamatsu, Shizuko Ishii, Masashi Nemoto, Jun-ichi Uechi, Yutaka Suzuki, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
Clustering Method Based on Onset and Cessation of Gene ExpressionKazumi Hakamada, Taizo Hanai, Masahiro Okamoto
3-D Visualization Software of a Gene Regulatory NetworkKouichi Okada, Nasimul Noman, Naoki Hosoyama, Hitoshi Iba
PLOC: Prediction of Subcellular Location of ProteinsKeun-Joon Park, Minoru Kanehisa, Yutaka Akiyama
Prediction from sequence to structure at oligonucleotide level by MD simulationsManish Biyani, Koichi Nishigaki
Ontology Using Role Concept Recognized on Biological Relationships and Its ApplicationMasaru Takeya, Hisataka Numa, Koji Doi
Human Full-length Pre-mRNA Sequence Dataset for Computational Gene Prediction and Alternative Splicing AnalysisMasahiko Mizuno, Osamu Gotoh, Makiko Suwa
Quantifying the Spiral Leaf Trait of Arabidopsis from the 3D Shape Model towards Computational PhenomicsEli Kaminuma, Naohiko Heida, Yuko Tsumoto, Minami Matsui, Tetsuro Toyoda, Akihiko Konagaya
GOODIES: GO based Data Mining Tool for Characteristic Attribute Interpretation on a Group of Biological EntitiesSung Geun Lee, Wan Seon Lee, Yang Seok Kim
Evaluation System for Information Retrieval in Biomedical FieldYasunori Yamamoto, Toshihisa Takagi
Molecular Modeling for Generation of Structural and Molecular Electronic Descriptors for QSAR using Quantum Mechanical Semiempirical and ab initio methodsMohd. Shahid Khan, Zahid H. Khan
On improving protein functional identification in pattern recognition based on continuous density HMMDooil Kim, Dae-Sil Lee
G-language Genome Analysis Environment Version 2Hayataro Kouchi, Kazuharu Arakawa, Ryo Hattori, Yohei Yamada, Yusuke Kobayashi, Atsuko Kishi, Kosaku Shinoda, Masaru Tomita
Inner Residues in the Transmembrane Helix Bundle are More ConservativeSukenobu Konishi, Takuhiro Nishio, Toshio Shimizu
Development of Bacteria Analysis System v.2 on the G-language Genome Analysis EnvironmentDaisuke Kyuma, Kazuharu Arakawa, Koya Mori, Masaru Tomita
Dynamics of Reprssilator: From Noise to Coherent OscillationTomohiro Ushikubo, Wataru Inoue, Masaki Sasai
Regulator identification by expression profiles of transcriptional factor mutants and promoter sequence in Bacillus subtilisNobuyuki Fujii, Joe Akitomi, Kazuo Kobayashi, Naotake Ogasawara, Shigehiko Kanaya
Improvement in accuracy of gene prediction of human cDNA sequencesFusano Todokoro, Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima, Tadashi Imanishi, Takashi Gojobori
Scalable BLAST service in OBIGrid environmentFumikazu Konishi, Yukimasa Shiroto, Ryo Umetsu, Akihiko Konagaya
Systematic analyses of P-loop containing nucleotide triphosphate hydrolase superfamily based on sequence, structure and functionYoichi Kawamura, Kiyoshi Asai, Shin Ishii, Nozomi Nagano
Detection of tissue specific genes by putative regulatory motifs in Human promoter sequencesKatsuhiko Murakami, Toshio Kojima, Yoshiyuki Sakaki
Graph Complexity of Chemical Compounds in Biological PathwaysAtsuko Yamaguchi, Kiyoko F. Aoki, Hiroshi Mamitsuka
Prognosis prediction by microarray gene expression using Support Vector MachineChihoko Tago, Taizo Hanai, Masahiro Okamoto
On Visualization, Screening, and Classification ofCell Cycle-Regulated Genes in YeastHenry Horng-Shing Lu, Han-Ming Wu
Detection of processed pseudogenes based on cDNA mapping to the human genomeHiroaki Sakai, Kanako O. Koyanagi, Takeshi Itoh, Tadashi Imanishi, Takashi Gojobori
Mapping of Artificial Nucleosome Positioning Sequences to the Saccharomyces cerevisiae GenomeVorathaya Tantoolvesm, Yoichi Takenaka, Satoshi Harashima, Hideo Matsuda
Splice Variant Search with Gene Expression DataTadashi Kadowaki, Satoshi Shiojima, Gozoh Tsujimoto
A Method for Normalization of Gene Expression DataMakoto Kano, Hisashi Kashima, Tetsuo Shibuya, Kaori Ide, Aiko Kashihara, Noriko Nakagawa, Seiki Kuramitsu, Mariko Hatakeyama, Akihiko Konagaya
Transcriptome profiling and deciphering the regulatory role of global transcription factor fadRByung Hun Kim, Si Jae Park, Sang Yup Lee
Detection of the Splicing Sites with Kernel Method Approaches Dealing with Nucleotide DoubletsMasaki Yamamura, Osamu Gotoh
Gene Expression Analysis Using Fuzzy K-means ClusteringChinatsu Arima, Taizo Hanai, Masahiro Okamoto
Kinetics behavior of G1-to-S cell cycle phase transition modelYoshihiko Tashima, Taizo Hanai, Hiroyuki Hamada, Masahiro Okamoto
CAPIES: DNA Microarray-based Class Prediction System for Computational DiagnosticsSung Geun Lee, Bonghee Seo, Yang Seok Kim
A Protein Structure Retrieval System using Atom-Atom Bond-Line HistogramSung-hee Park, Soo-jun Park, Sung-hoon Lee, Sun-hee Park
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
in silico Simulation Represents Adenoviral Gene Knockdown of Myocardial Ventricular CellYasuhiro Naito, Motohiro Yoneda, Sayaka Ishinabe, Shoko Miyamoto, Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma, Masaru Tomita
Mapping Database of cDNA and Genome Designed to Use for Various ApplicationsAkifumi Yamashita, Ken Kurokawa, Teruo Yasunaga
Prediction of Protein Functions Based on K-cores of Protein-Protein Interaction Networks and Amino Acid SequencesMd. Altaf-Ul-Amin, Kensaku Nishikata, Toshihiro Koma, Teppei Miyasato, Yoko Shinbo, Md. Arifuzzaman, Chieko Wada, Maki Maeda, Taku Oshima, Hirotada Mori, Shigehiko Kanaya
Classification of protein sequences into paralog and ortholog clusters using sequence similarity profiles of KEGG/SSDBYohsuke Minowa, Toshiaki Katayama, Akihiro Nakaya, Susumu Goto, Minoru Kanehisa
Model Construction of the Energy Metabolism Pathway in Myocardial CellMotohiro Yoneda, Shoko Miyamoto, Yasuhiro Naito, Sayaka Ishinabe, Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma, Masaru Tomita
Positive charge cores in DNA-binding proteinsKimiko Horibe, Shigeki Mitaku
Prediction of Glycan Structures from Glycosyltransferase Expression ProfilesShin Kawano, Yasushi Okuno, Kosuke Hashimoto, Harumi Yamamoto, Hiromu Takematsu, Yasunori Kozutsumi, Susumu Goto, Minoru Kanehisa
Analysis of DNA microarray data by using Self-Organizing MapsTomoyuki Kato, Kikuo Fujimura, Heizo Tokutaka, Yasushi Kawata, Masaaki Ohkita
Prediction of Protein - Protein Interactions from Phylogenetic Trees Using Partial Correlation CoefficientTetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Hiroyuki Toh, Minoru Kanehisa
GLYCAN: The Database of Carbohydrate StructuresKosuke Hashimoto, Masami Hamajima, Susumu Goto, Shigekazu Masumoto, Masayuki Kawasima, Minoru Kanehisa
Extraction of Organism Groups from Whole Genome ComparisonsYoshihiro Yamanishi, Akiyasu C. Yoshizawa, Masumi Itoh, Toshiaki Katayama, Minoru Kanehisa
Analysis of Reactive Modules in the Metabolic PathwaysMasaaki Kotera, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
Transmembrane Protein Evolution by Internal Gene DuplicationHironori Mitsuke, Keisuke Noto, Masafumi Arai, Toshio Shimizu
Common Features in Substrates of Multidrug Resistance TransportersYoshinobu Igarashi, Yasushi Okuno, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
Extraction of a Thermodynamic Property for Biochemical Reactions in the Metabolic PathwayMichihiro Tanaka, Yasushi Okuno, Takuji Yamada, Susumu Goto, Shunsuke Uemura, Minoru Kanehisa
Self-nonself discrimination based on incompatibility of amino acid sequences of human and virusesWataru Honda, Shuichi Kawashima, Minoru Kanehisa
KEGG API: A web service using SOAP/WSDL to access the KEGG systemShuichi Kawashima, Toshiaki Katayama, Yoko Sato, Minoru Kanehisa
Metabolic pathway reconstruction for malaria parasite Plasmodium falciparumVachiranee Limviphuvadh, Yasushi Okuno, Toshiaki Katayama, Susumu Goto, Akiyasu C. Yoshizawa, Minoru Kanehisa
Development of Community Annotation Databases for Linking Genomes to Cellular FunctionsMiho Furumichi, Yoko Sato, Toshiaki Katayama, Shuichi Kawashima, Minoru Kanehisa
The Construction of a Database for Ubiquitin Signaling CascadeTadahiko Sakiyama, Shuichi Kawashima, Akiyasu C. Yoshizawa, Minoru Kanehisa
Comprehensive Analysis of Delay in Transcriptional Regulation using Expression ProfilesKoji Ota, Takuji Yamada, Yoshihiro Yamanishi, Susumu Goto, Minoru Kanehisa
Combining Gene Expression Data with DNA Sequence Information for Estimating Gene Networks using Bayesian Network ModelYoshinori Tamada, SunYong Kim, Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
A Combined Experimental and Inferring InteractomesChung-Yen Lin, Chi-Shang Cho, Li-Ming Wang, Chia-Ling Chen, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung
HAPPY: Hypothetical And Putative Protein Database SystemTakuya Murakami, Masatomo Najima, Michihiro Ogawa, Ken Kurokawa, Teruo Yasunaga
Genome Scale Classification of Extended Proteins by a predictor SOSUIdumbbellNobuyuki Uchikoga, Ke Rungcong, Fumitsugu Akazawa, Masashi Sonoyama, Shigeki Mitaku
KAREIDMAP: A System for Predicting and Mining Gene Regulatory NetworksHironori Mizuguchi, Dai Kusui, Taku Oshima, Shigehiko Kanaya, Hirotada Mori
Analysis of Domain Combinations in Eukaryotic GenomesMasumi Itoh, Akiyasu C. Yoshizawa, Shujiro Okuda, Susumu Goto, Minoru Kanehisa
Multiscale Bootstrap Analysis of Gene Networks Based on Bayesian Networks and Nonparametric RegressionTakeshi Kamimura, Hidetoshi, Shimodaira, Seiya Imoto, SunYong Kim, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
Comprehensive Survey of Intracellular Transport System-Related Proteins in Complete Genomes and Draft GenomesAkiyasu C. Yoshizawa, Masumi Itoh, Shujiro Okuda, Vachiranee Limviphuvadh, Tadahiko Sakiyama, Shuichi Kawashima, Minoru Kanehisa
Normalization of Target Flourescent using Reference Flourescent for cDNA Microarray MethodYu Suzuki, Kenji Hatano, Shigehiko Kanaya, Shunsuke Uemura
The Clusters of Transmembrane Protein genes in Prokaryotic GenomesIchitaro Oya, Satoshi Mizuta, Toshio Shimizu
Detection of remote homologue using predicted structural informationDaisuke Ishibe, Katsunori Uehara, Takeshi Kawabata, Nobuhiro Go
Genome wide analysis reveals strong correlation between CpG islands and tissue-specificityRiu Yamashita, Yutaka Suzuki, Toshihisa Takagi, Sumio Sugano, Kenta Nakai
Bioinformatics for Oncogenomic Target IdentificationMasaru Katoh
Comparative Genomics between Drosophila and HumanMasuko Katoh, Masaru Katoh
BioRuby: Open-source Bioinformatics LibraryNaohisa Goto, Mitsuteru C. Nakao, Shiuichi Kawashima, Toshiaki Katayama, Minoru Kanehisa
Phylogenetic analysis of eubacterial transcriptional systems based on the DBTBS database of B. subtilis transcription factors and promotersYuko Makita, Naotake Ogasawara, Kenta Nakai
Protein Family Classiffication Using Second-Order Recurrent Neural NetworksJinmiao Chen, Narendra S. Chaudhari
A PCA based method of gene expression visual analysisKunihiro Nishimura, Koji Abe, Shumpei Ishikawa, Shuichi Tsutsumi, Koichi Hirota, Hiroyuki Aburatani, Michitaka Hirose
Genetic Networks with Stochastic FluctuationsLuonan Chen, Ruiqi Wang, Kazuyuki Aihara
INOH: A Textual Knowledge based Pathway DatabaseSatoko Yamamoto, Tatsuya Kushida, Naotaka Ono, Yuki Yamagata, Toshihisa Takagi, Ken-ichiro Fukuda
Gene List of Sphingomonas chungbukensis DJ77Kwon Hae-Ryong, Hyun-Ju Um, Jeong-Su Oh, Wan-Sup Cho, Young-Chang Kim
Extraction of Biological Motifs by Gibbs Sampler from the promoters of Homo Sapiens, Saccharomyces cerevisiae and Bacillus subtilisNatalia Poluliakh, Kenta Nakai
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
Enumeration of Likely Gene Networks and Network Motif Extraction for Large Gene NetworksSascha Ott, Satoru Miyano
Development of Efficient Designing Method for Target Specific Probe Sets So Young Yoo, Hyeong Jun An, Doheon Lee, Sang Yup Lee


E-mail: giw2004@ims.u-tokyo.ac.jp