Genome Informatics 2004

GIW04Poster.jpg

Genome Informatics 2004

Presented at the 15th International Conference on Genome Informatics
December 16-18, 2004, Yokohama Pacifico, Japan

Poster and Software Demonstrations

 


 

Software Demonstration Abstracts

MPSS: an integrated database system for surveying multitudinous proteins
Pei Hao, Wei-zhong He, Yi-Xue Li
GIW 2004 Poster Abstract: S01 [PDF file]

ASIAN on Personal Computer
Shigeru Saito, Kousuke Goto, Sachiyo Aburatani, Katsuhisa Horimoto
GIW 2004 Poster Abstract: S02 [PDF file]

Reflection of Knowledge Information in ProMode (A Database of Normal Mode Analyses on Proteins)
Hiroshi Wako, Motohiro Otsuka, Yuhki Tomizawa, Masaki Kato, Shigeru Endo
GIW 2004 Poster Abstract: S03 [PDF file]

MyGPS_client A Genome Browser Integrating Client-side Private Data and Server-side Large-scale Public Annotations
Katsura Hirosawa, Atsushi Moroda, Yoshikazu Hasegawa, Naohiko Heida, Yoshiki Mochizuki, Tetsuro Toyoda
GIW 2004 Poster Abstract: S04 [PDF file]

CADLIVE: New Modules for Domain Expansions and Topological Analysis
Hiroyuki Kurata, Yuki Shimokawa, Tomoko Noguchi, Natsumi Shimizu
GIW 2004 Poster Abstract: S05 [PDF file]

Visualization and Cluster Analysis using Spherical SOM
Daisuke Nakatsuka, Heizo Tokutaka
GIW 2004 Poster Abstract: S06 [PDF file]

MutationView: Addition of an enhanced search system for the clinical description in the OMIM based on a new algorithm
Masafumi Ohtsubo, Katsue Daicho, Kouichi Kawaguchi, Susumu Mitsuyama, Takashi Kawamura, Tomoyoshi Horisawa, Nobuyoshi Shimizu, Shinsei Minoshima
GIW 2004 Poster Abstract: S07 [PDF file]

Studying the molecular evolution of the SARS-coronavirus on the the DiscoveryNet Environment
Pei Hao, Yuan-Yuan Li, Wei-zhong He, Yi-Xue Li, Vasa Curcin, Moustafa Ghanem, Yike Guo
GIW 2004 Poster Abstract: S08 [PDF file]

GEDA-C: Gene Expression Data Analysis - Clustering based-on seed method
Ho-Youl Jung, Miyoung Shin, Seon-Hee Park
GIW 2004 Poster Abstract: S09 [PDF file]

Care-free Metabolic Map Editor - From Pathways to Maps -
Masanori Arita
GIW 2004 Poster Abstract: S10 [PDF file]

Bioinformatics Recipes with BioRuby
Mitsuteru Nakao, Naohisa Goto, Toshiaki Katayama
GIW 2004 Poster Abstract: S11 [PDF file]

“Piment” and “Macaroni”: Nervous System Protein Database
Takeshi Tomiki, Naruya Saitou
GIW 2004 Poster Abstract: S12 [PDF file]

HiGet: High Performance Database Entry Retrieval System
Kazutomo Ushijima, Chiharu Kawagoe, Kenta Nakai, Shuichi Kawashima, Hideo Bannai, Toshiaki Katayama
GIW 2004 Poster Abstract: S13 [PDF file]

Genomic Object Net 1.5: A Platform for Biopathway Modeling and Simulation
Masao Nagasaki, Atsushi Doi, Satoru Miyano
GIW 2004 Poster Abstract: S14 [PDF file]

Poster Abstracts

Prediction of Debacle Parts for Robustness in a Cell by using Recurrent Neural Networks
Hironori Kitakaze, Ryuhei Noda, Hiroshi Matsuno, Nobuhiko Ikeda, Satoru Miyano
GIW 2004 Poster Abstract: P001 [PDF file]

Modeling and Simulation of Cyanobacterial Circadian Clock Mechanism by Hybrid Functional Petri Net
Mao Yamaji, Hideo Iwasaki, Hiroshi Matsuno, Satoru Miyano
GIW 2004 Poster Abstract: P002 [PDF file]

A New Regulatory Interactions Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals
Yasushi Fujii, Yasuki Okitsu, Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye
GIW 2004 Poster Abstract: P003 [PDF file]

A New Petri Net Modeling Method for Signaling Pathways with a Focus on Enzyme
Chen Li, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano
GIW 2004 Poster Abstract: P004 [PDF file]

CellDesigner2.0: A Process Diagram Editor for Gene-regulatory and Biochemical Networks
Akira Funahashi, Naoki Tanimura, Yukiko Matsuoka, Naritosi Yosinaga, Hiroaki Kitano
GIW 2004 Poster Abstract: P005 [PDF file]

Optimization and System Analysis of the Heat Shock Response by CADLIVE
Kouji Mitsukiyo, Marie Kajiwara, Hiroyuki Kurata
GIW 2004 Poster Abstract: P006 [PDF file]

A Large-Scale Dynamic Model of the Yeast Cell Cycle
Shunsuke Yamamichi, Hiroyuki Kurata
GIW 2004 Poster Abstract: P007 [PDF file]

Control Aspect of Common Interactions Extracted from Inferred Network Candidates of Gene Expression
Masahiko Nakatsui, Takanori Ueda, Isao Ono, Masahiro Okamoto
GIW 2004 Poster Abstract: P008 [PDF file]

Simulation for detailed mathematical model of G1-to-S cell cycle phase transition
Yoshihiko Tashima, Taizo Hanai, Hiroyuki Hamada, Masahiro Okamoto
GIW 2004 Poster Abstract: P009 [PDF file]

BAAQ: A Grid-based Infrastructure for Integrating Bioinformatics Applications
Xiujun Gong, Kei Yura, Nobuhiro Go
GIW 2004 Poster Abstract: P010 [PDF file]

Simulation of Circadian Rhythms Using Grid Computing
Takayuki Tanaka, Hiroyuki Kurata
GIW 2004 Poster Abstract: P011 [PDF file]

Development of a computer simulation system for particle-level molecular interactions
Ryuzo Azuma, Yoshiki Yamaguchi, Tetsuji Kitagawa, Tomoyuki Yamamoto, Akihiko Konagaya
GIW 2004 Poster Abstract: P012 [PDF file]

The Molecular Dynamics Simulation of Prion Protein
Masakazu Sekijima, Chie Motono, Tamotsu Noguchi, Tamotsu Noguchi, Kiyotoshi Kaneko, Yutaka Akiyama
GIW 2004 Poster Abstract: P013 [PDF file]

Symbolic-Numeric Optimization for Biological Kinetics by Quantifier Elimination
Shigeo Orii, Hirokazu Anai, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P014 [PDF file]

Equilibrium Model of DNA Chip Hybridization Error
John A. Rose, Masami Hagiya, Akira Suyama
GIW 2004 Poster Abstract: P015 [PDF file]

An Analysis Tool Library for Biochemical Modeling on E-Cell System Version 3
Kazunari Kaizu, Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita
GIW 2004 Poster Abstract: P016 [PDF file]

Development of Integrated Modeling Environment for E-Cell3 System
Gabor Bereczki, Kouichi Takahashi, Takeshi Sakurada, Ng Yan Hong, Masaru Tomita
GIW 2004 Poster Abstract: P017 [PDF file]

Development of E-Cell kinetic model interoperability environment
Tatsuya Ishida, Takeshi Sakurada, Tomoya Kitayama, Masaru Tomita
GIW 2004 Poster Abstract: P018 [PDF file]

Development of Distributed Cell Simulations Middleware with E-Cell System
Masahiro Sugimoto, Kouichi Takahashi, Daniel, Muhammad Nurazhar Bin Taher, Lu Yaomin, Novia Siswanto Be, Tracy Wong, Ng Yan Hong, Masaru Tomita
GIW 2004 Poster Abstract: P019 [PDF file]

Modeling Gene Networks Utilizing Evolutionary Information Using Bayesian Network Models
Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano
GIW 2004 Poster Abstract: P020 [PDF file]

Estimating Regulatory Networks from DNA Microarrays and Protein-Protein Interactions
Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano
GIW 2004 Poster Abstract: P021 [PDF file]

Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Network
Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano
GIW 2004 Poster Abstract: P022 [PDF file]

Multiscale Bootstrap Analysis of Gene Networks Based on Graphical Gaussian Modeling
Takeshi Kamimura, Hidetoshi Shimodaira
GIW 2004 Poster Abstract: P023 [PDF file]

Systematic Identification of Weak Connections between Clusters in Biological Network
Hiroki Sakai, Katsuhisa Horimoto, Minoru Kanehisa
GIW 2004 Poster Abstract: P024 [PDF file]

Genetic Network Reconstruction in Tryptophan Metabolism from Gene Expression Profiles
Akira Imaizumi, Hisashi Yasueda, Sachiyo Aburatani, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P025 [PDF file]

Selective Integration of Multiple Genomic Data for Biological Network Inference
Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
GIW 2004 Poster Abstract: P026 [PDF file]

Effective Procedures for the Estimation of Large-scale S-system Parameters
Yukihiro Maki, Takanori Ueda, Masahiro Okamoto
GIW 2004 Poster Abstract: P027 [PDF file]

Correlations Between Scale-free Genetic Regulatory Model Networks and Dynamical Properties
Chikoo Oosawa, Kazuhiro Takemoto, Genki Hanano
GIW 2004 Poster Abstract: P028 [PDF file]

Periodic Oscillation in Gene Networks Modelled by Cyclic Feedback Systems
Ruiqi Wang, Luonan Chen
GIW 2004 Poster Abstract: P029 [PDF file]

A Gibbs Sampling Approach to Detection of Tree Motifs
Lidio Marx Carvalho Meireles, Tatsuya Akutsu
GIW 2004 Poster Abstract: P030 [PDF file]

QSAR Analysis with Support Vector Machines and Graph Kernels
Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert
GIW 2004 Poster Abstract: P031 [PDF file]

Stable Stochastic Dynamics in Yeast Cell Cycle
Yurie Okabe, Masaki Sasai
GIW 2004 Poster Abstract: P032 [PDF file]

Comparative Analysis of Conditional Regulation Across the Yeast Genomes
Koji Ota, Susumu Goto, Minoru Kanehisa
GIW 2004 Poster Abstract: P033 [PDF file]

An application of multiscale bootstrap resampling to hierarchical clustering of microarray data: How accurate are these clusters?
Ryota Suzuki, Hidetoshi Shimodaira
GIW 2004 Poster Abstract: P034 [PDF file]

Mixed Factors Analysis for Identifying Transcriptional Modules and Clusters on Microarray Experiments
Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto
GIW 2004 Poster Abstract: P035 [PDF file]

Incorporating prior knowledge into clustering of gene expression profiles
Daisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara
GIW 2004 Poster Abstract: P036 [PDF file]

Mathematical Model Based Clustering of Gene Expression
Kazumi Hakamada, Taizo Hanai, Masahiro Okamoto
GIW 2004 Poster Abstract: P037 [PDF file]

Cleaning Microarray Expression Data with Markov Random Fields Based on Profile Similarity
Raymond Wan, Hiroshi Mamitsuka
GIW 2004 Poster Abstract: P038 [PDF file]

A practical system for the detection of chromosomal aberration in tumor cells by array CGH
Junya Futagawa, Tomohiro Isobe, Atsushi Moroda, Nobutaka Mitsuhashi, Ken Aoshima, Yasuhito Arai, Fumie Hosoda, Misao Ohki, Issei Imoto, Johji Inazawa, Tokuki Sakiyama
GIW 2004 Poster Abstract: P039 [PDF file]

Statistical Analysis of Gene Expression in Repair Mechanism under UV Irradiation
Sachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P040 [PDF file]

Integrated Analysis of Gene Expression Profile and Metabolite Quantity Data of Arabidopsis thaliana Using BL-SOM
Yukiko Nakamura, Ryoko Morioka, Yoko Shinbo, Masami Yokota Hirai, Md. Altaf-Ul-Amin, Ken Kurokawa, Kotaro Minato, Kazuki Saito, Shigehiko Kanaya
GIW 2004 Poster Abstract: P041 [PDF file]

Analysis for time-course profiles of transcription arrays
Daisuke Tominaga, Paul Horton
GIW 2004 Poster Abstract: P042 [PDF file]

A Step Towards Substructure Exploration from Gene Expression Patterns
Masako Hoshino, Hiroshige Inazumi
GIW 2004 Poster Abstract: P043 [PDF file]

Markov Property and Scale-free Organization of Gene Expression
Tomoshiro Ochiai, Jose C. Nacher, Tatsuya Akutsu
GIW 2004 Poster Abstract: P044 [PDF file]

Expression Analysis of Glycosyltransferase Genes in Human, Mouse, and Rat
Takashi Miyama, Shin Kawano, Minoru Kanehisa
GIW 2004 Poster Abstract: P045 [PDF file]

Yeast Gene Classification based on Relevant Biological Functions for Gene Expression Data Analysis
Satoshi Kamegai, Takuya Oyama, Mikio Yoshida, Fumihito Miura, Kenji Satou, Takashi Ito
GIW 2004 Poster Abstract: P046 [PDF file]

Rational Design for Molecular Breeding of Industrially Useful Strains Based on Bioinformatic Data in Saccharomyces cerevisiae
Takashi Hirasawa, Katsunori Yoshikawa, Kengo Ashitani, Keisuke Nagahisa, Chikara Furusawa, Yoshio Katakura, Hiroshi Shimizu, Suteaki Shioya
GIW 2004 Poster Abstract: P047 [PDF file]

On-chip selection of DNA ligands using a method for generating point mutations
Ryoichi Asai, Shin I. Nishimura, Takuyo Aita, Katsutoshi Takahashi
GIW 2004 Poster Abstract: P048 [PDF file]

Automatic generation of KEGG OC (Ortholog Cluster) and its assignment to draft genomes
Yuki Moriya, Toshiaki Katayama, Akihiro Nakaya, Masumi Itoh, Akiyasu C. Yoshizawa, Shujiro Okuda, Minoru Kanehisa
GIW 2004 Poster Abstract: P049 [PDF file]

Functional Categorization of Multiple Genomes using KEGG OC in the Genome Indices
Shujiro Okuda, Akiyasu C. Yoshizawa, Yuki Moriya, Masumi Itoh, Toshiaki Katayama, Susumu Goto, Minoru Kanehisa
GIW 2004 Poster Abstract: P050 [PDF file]

Gene-Transpositions on Functional Categories in Prokaryotic Genomes
Nobuyoshi Sugaya, Hiroo Murakami, Sachiyo Aburatani, Kunio Shimizu, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P051 [PDF file]

Prediction of DNA-binding sites in proteins using evolutionary profiles
Shandar Ahmad, Akinori Sarai
GIW 2004 Poster Abstract: P052 [PDF file]

Method for finding p53 binding sites using tiling array
Shingo Tsuji, Kiyofumi Kaneshiro, Shuichi Tsutsumi, Sigeo Ihara, Hiroyuki Aburatani
GIW 2004 Poster Abstract: P053 [PDF file]

Correlation between signal transduction domains and habitats in cyanobacteria
Shinobu Okamoto, Shuichi Kawashima, Rei Narikawa, Minoru Kanehisa
GIW 2004 Poster Abstract: P054 [PDF file]

Transmembrane regions prediction for G-protein-coupled receptors by hidden Markov model
Kayo Narukawa, Tadashi Kadowaki, Gozoh Tsujimoto
GIW 2004 Poster Abstract: P055 [PDF file]

GPCR and G-protein Coupling Selectivity Prediction Based on SVM with Physico-Chemical Parameters
Makiko Suwa, Yukimitsu Yabuki, Takahiko Muramatsu, Takatsugu Hirokawa, Hidetoshi Mukai
GIW 2004 Poster Abstract: P056 [PDF file]

GLIDA : GPCR and Ligand Database
Jiyoon Yang, Yasushi Okuno, Gozoh Tsujimoto
GIW 2004 Poster Abstract: P057 [PDF file]

3DMET: A Database of Three-Dimensional Structures of Natural Metabolites
Miki Maeda
GIW 2004 Poster Abstract: P058 [PDF file]

Graph Theoretic Analysis of Chemical Compounds in Biological Pathways
Atsuko Yamaguchi, Yasushi Okuno, Hiroshi Mamitsuka
GIW 2004 Poster Abstract: P059 [PDF file]

Prediction of Glycosyltransferases Synthesizing Glycoconjugates Using Variable-length N-gram Model
Yeon-Dae Kwon, Shougo Shimizu, Hisashi Narimatsu
GIW 2004 Poster Abstract: P060 [PDF file]

An algorithm for graph isomorphism and its application to KEGG Compound Search
Nobuya Tanaka, Susumu Goto, Minoru Kanehisa
GIW 2004 Poster Abstract: P061 [PDF file]

RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions
Masaaki Kotera, Masahiro Hattori, Min-A Oh, Rumiko Yamamoto, Tomoko Komeno, Junko Yabuzaki, Koichiro Tonomura, Susumu Goto, Minoru Kanehisa
GIW 2004 Poster Abstract: P062 [PDF file]

Glycan Linkage Substitution Matrix Rooted on Tree Alignments
Kiyoko F. Aoki, Hiroshi Mamitsuka, Minoru Kanehisa
GIW 2004 Poster Abstract: P063 [PDF file]

Classification and Motif Extraction of Glycans in Bloods
Yoshiyuki Hizukuri, Yoshihiro Yamanishi, Osamu Nakamura, Fumio Yagi, Susumu Goto, Minoru Kanehisa
GIW 2004 Poster Abstract: P064 [PDF file]

Integrated Quantification and Multivariate Analysis Workbench System for Phospholipids
Kaoru Mogushi, Katsutoshi Takahashi
GIW 2004 Poster Abstract: P065 [PDF file]

Power-law Correlations of Connectivities in Biomolecular Networks
Kazuhiro Takemoto, Chikoo Oosawa
GIW 2004 Poster Abstract: P066 [PDF file]

A method for estimation of enzyme kinetics in metabolic pathways using GMA
Tomoya Kitayama, Ayako Kinoshita, Yoichi Nakayama, Masaru Tomita
GIW 2004 Poster Abstract: P067 [PDF file]

A method for customized cross-species metabolic pathway comparison
Eric Lo, Takuji Yamada, Michihiro Tanaka, Masahiro Hattori, Susumu Goto, Chuan-Hsiung Chang, Minoru Kanehisa
GIW 2004 Poster Abstract: P068 [PDF file]

Decomposition of kinetically feasible metabolic flux distributions onto elementary modes
Jean-Marc Schwartz, Minoru Kanehisa
GIW 2004 Poster Abstract: P069 [PDF file]

Global Tree of Known Carbohydrate Structures to Analyze Biosynthetic Pathways
Kosuke Hashimoto, Shin Kawano, Yasushi Okuno, Minoru Kanehisa
GIW 2004 Poster Abstract: P070 [PDF file]

Comparative analysis of enzymatic reactions reveals phylogenic evolution of metabolic pathways
Michihiro Tanaka, Naoki Nariai, Thomas Handorf, Oliver Ebenhöh, Satoru Miyano, Minoru Kanehisa, Reinhart Heinrich
GIW 2004 Poster Abstract: P071 [PDF file]

Functional Enzyme Exploration combining SIMPLEX screening assisted with Fuzzy Neural Network
Ryuji Kato, Hiroyuki Konishi, Yuichi Koga, Tsuneo Yamane, Takeshi Kobayashi, Hideo Nakano, Hiroyuki Honda
GIW 2004 Poster Abstract: P072 [PDF file]

Fold-Function Relationship of PLP-Dependent Enzymes
Keiko Matsuda, Takaaki Nishioka, Kengo Kinoshita, Nobuhiro Go
GIW 2004 Poster Abstract: P073 [PDF file]

A novel classification of enzyme catalytic reactions
Nozomi Nagano
GIW 2004 Poster Abstract: P074 [PDF file]

Phylogenetic Comparison of Human and Mouse Promoter Regions and Visualization of a Variety of Conserved Elements
Hirokazu Chiba, Kenta Nakai
GIW 2004 Poster Abstract: P075 [PDF file]

Conservation of Physicochemical Properties during Protein Evolution
Masashi Fujita, Masumi Itoh, Minoru Kanehisa
GIW 2004 Poster Abstract: P076 [PDF file]

A method for comparing microarray data of different species
Kenji Hagimoto, Jun Miyazaki, Shigehiko Kanaya, Naotake Ogasawara, Toshiyuki Amagasa, Shunsuke Uemura
GIW 2004 Poster Abstract: P077 [PDF file]

Chromosome Profiling: A Clue to Trace The Genome Evolution
Ayumu Saito, Koichi Nishigaki
GIW 2004 Poster Abstract: P078 [PDF file]

Searching for cis-elements in Mouse-Human Orthologous Promoter Regions
Natalia Polouliakh, Wataru Fujibuchi, Tohru Natsume, Paul Horton
GIW 2004 Poster Abstract: P079 [PDF file]

Tandem Repeats in 44 Prokaryotic Genomes and Genome Evolution
Satoshi Mizuta, Hikaru Munakata, Abulimiti Aimaiti, Kenji Oosawa, Toshio Shimizu
GIW 2004 Poster Abstract: P080 [PDF file]

An approximate maximum likelihood method for phylogenetic tree analysis based on high-temperature Markov Chain Monte Carlo
Ryota Suzuki, Tomoya Taniguchi, Hidetoshi Shimodaira
GIW 2004 Poster Abstract: P081 [PDF file]

Extension of Prrn: implementation of a doubly nested randomized iterative refinement strategy under a piecewise linear gap cost
Shinsuke Yamada, Osamu Gotoh, Hayato Yamana
GIW 2004 Poster Abstract: P082 [PDF file]

Sequence Alignment Tool of Membrane Protein
Takahiko Muramatsu, Makiko Suwa
GIW 2004 Poster Abstract: P083 [PDF file]

A Rapid peptide based Alignment -free method to construct Genome trees Independent of sequence annotation
Vikash Kumar, Sunil Kumar
GIW 2004 Poster Abstract: P084 [PDF file]

Fast Homology Search using Categorisation Profiles
Abhijit Chattaraj, Hugh E. Williams, Adam Cannane
GIW 2004 Poster Abstract: P085 [PDF file]

Measuring the Average Accuracy Performance of Homology Search
XiaoLei Chen, Adam Cannane, Hugh E. Williams
GIW 2004 Poster Abstract: P086 [PDF file]

Performance Comparison between Profiles from Hidden Markov Models and from Pseudocount Method
Makihiko Sato, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P087 [PDF file]

Development of Fast Tandem Repeat Analysis and Lossless Compression Method for DNA Sequence
Toshio Modegi
GIW 2004 Poster Abstract: P088 [PDF file]

Inferring breakpoints from large-scale BAC-end sequences and a complete genome sequence
Katsuhiko Murakami, Yoshiyuki Sakaki
GIW 2004 Poster Abstract: P089 [PDF file]

CATTAGAT - Web Server for Primer Specificity Scan
Magnús M. Halldórsson, Haukur Thorgeirsson, Ýmir Vigfússon, Hans Thormar, Jón Jóhannes Jónsson
GIW 2004 Poster Abstract: P090 [PDF file]

Development of a Common Protocol for the Prediction of Microbial Genes
Takehide Kosuge, Toshihisa Okido, Masaki Hirahata, Yasumasa Shigemoto, Satoru Miyazaki, Takashi Abe, Takashi Gojobori, Hideaki Sugawara
GIW 2004 Poster Abstract: P091 [PDF file]

Diverse base composition skews in bacterial chromosomes
Chi Chen, Carton W. Chen
GIW 2004 Poster Abstract: P092 [PDF file]

Analysis of the bacterial sequences recognized by RNA-binding proteins and compounds
Ai Muto, Akiyasu C. Yoshizawa, Shujiro Okuda, Masumi Itoh, Masahiro Hattori, Minoru Kanehisa
GIW 2004 Poster Abstract: P093 [PDF file]

Relationship between Chromosome Rearrangement and Repeat Sequences in Human Chromosome 7
Hiroo Murakami, Nobuyoshi Sugaya, Sachiyo Aburatani, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P094 [PDF file]

Systematic Survey of Sequence Similarity between Sense and Anti-sense Strands in Escherichia coli Genome
Kazuhiro Nakamura, Makihiko Sato, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P095 [PDF file]

Comprehensive promoter analyses using a database of transcription start sites
Riu Yamashita, Yutaka Suzuki, Katsuki Tsuritani, Sumio Sugano, Kenta Nakai
GIW 2004 Poster Abstract: P096 [PDF file]

Variation Analysis of Transcription Start Sites and ORFs in Splicing Variant cDNAs and Integrated Database System of the Results
Tetsuo Nishikawa, Kouichi Kimura, Ai Wakamatsu, Jun-ichi Uechi, Hiroshi Makita, Jun-ichi Yamamoto, Tomohiro Yasuda, Masashi Nemoto, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
GIW 2004 Poster Abstract: P097 [PDF file]

Analysis of GC-compositional Strand Bias in the Transcription Start Sites of Plant and Fungal Genes
Shigeo Fujimori, Takanori Washio, Masaru Tomita
GIW 2004 Poster Abstract: P098 [PDF file]

Power Spectrum of DNA Base Sequence in Human Mitochondrial Genome
Eisei Takushi, Yukinobu Chinen
GIW 2004 Poster Abstract: P099 [PDF file]

A Possible Existence of Cooperative Gene and Transition in Bacteriophage φX174 Genome
Eisei Takushi
GIW 2004 Poster Abstract: P100 [PDF file]

Quantitative analysis of synonymous codon usage bias
Haruo Suzuki, Rintaro Saito, Masaru Tomita
GIW 2004 Poster Abstract: P101 [PDF file]

The kingdom of Plantae EST Indices: a resource for plant genomics community
Ali Masoudi-Nejad, Ruy Jauregui, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa, Takashi R. Endo
GIW 2004 Poster Abstract: P102 [PDF file]

Exhaustive analysis for screening of susceptible interactions between genetic and environmental factors for multifactorial disease
Yasuyuki Tomita, Mitsuhiro Yokota, Takeshi Kobayashi, Hiroyuki Honda
GIW 2004 Poster Abstract: P103 [PDF file]

Exhaustive combination search method for SNPs combination Related to Helicobacter pylori infection susceptibility Using Artificial Neural Network
Hironori Mutoh, Nobuyuki Hamajima, Takeshi Kobayashi, Hiroyuki Honda
GIW 2004 Poster Abstract: P104 [PDF file]

Investigating the Optimal Dataset Size for SNP Hunting
Toshiko Matsumoto, Yasuyuki Nozaki, Ryo Nakashige, Minori Shinya, Yoko Yoshikawa, Shuhei Mano, Tadashi Imanishi, Hidetoshi Inoko, Gen Tamiya, Takashi Gojobori
GIW 2004 Poster Abstract: P105 [PDF file]

Logistic Regression Model of Binary Disease Trait for Case-Control Study Considering Interactions between SNPs and Environments
Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano
GIW 2004 Poster Abstract: P106 [PDF file]

Prediction of regulatory SNPs influencing Gene expression on Chromosome 5q31-33
Gil-Mi Ryu, Jee Yeon Heo, Sangbae Kim, Ka Kyung Kim, Chan Park, Kuchan Kimm, InSong Koh
GIW 2004 Poster Abstract: P107 [PDF file]

Clustering and Multiple Alignment for a Large Number of cDNA Sequences Including Splicing Variants
Tomohiro Yasuda
GIW 2004 Poster Abstract: P108 [PDF file]

Analysis of splicing variants of human full-length cDNAs
Ai Wakamatsu, Jun-ichi Yamamoto, Kouichi Kimura, Tetsuo Nishikawa, Yutaka Suzuki, Sumio Sugano, Keiichi Nagai, Nobuo Nomura, Takao Isogai
GIW 2004 Poster Abstract: P109 [PDF file]

Development of ASTRA: database of human alternative splicing patterns
Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh
GIW 2004 Poster Abstract: P110 [PDF file]

Alternative splicing of transmembrane regions in human gene
Masateru Yamamoto, Chie Motono, Hideki Nagasaki, Makiko Suwa
GIW 2004 Poster Abstract: P111 [PDF file]

Non-coding RNA finding based on probabilistic secondary structure information
Taishin Kin, Koji Tsuda, Kiyoshi Asai
GIW 2004 Poster Abstract: P112 [PDF file]

Detection of tRNA genes from DNA sequences of Eukaryotes
Makoto Kinouchi, Yoshihiro Kudo
GIW 2004 Poster Abstract: P113 [PDF file]

Scarna: Stem Candidate Aligner for RNA
Kiyoshi Asai, Taishin Kin
GIW 2004 Poster Abstract: P114 [PDF file]

Detection of non-coding RNAs by properties of stems
Hiroki Ueda, Jun-Ichi Sagara, Minoru Nakazawa, Shimmi Hattori
GIW 2004 Poster Abstract: P115 [PDF file]

A genetic algorithm approach for finding the common structure of two homologous RNAs
Akito Taneda
GIW 2004 Poster Abstract: P116 [PDF file]

Hierarchical Alignment of RNA Secondary Structures Including Pseudoknots
Shinnosuke Seki, Atsushi Kijima, Satoshi Kobayashi, Gen-ichi Sanpei
GIW 2004 Poster Abstract: P117 [PDF file]

Integrated Reliability-Assessment for Protein-Protein Interaction Data
Akihito Tokuda, Asako Koike, Toshihisa Takagi
GIW 2004 Poster Abstract: P118 [PDF file]

Conserved Protein-Protein Interactions in Different Species
Yoko Shinbo, Toshihiro Koma, Md. Altaf-Ul-Amin, Ken Kurokawa, Hirotada Mori, Naotake Ogasawara, Yukiko Nakamura, Shigehiko Kanaya
GIW 2004 Poster Abstract: P119 [PDF file]

Validation and prediction of protein-protein interactions by pairwise analysis of functional protein families
Sarah Mohseni-Zadeh, Jacques Camonis, Jérôme Wojcik, Emmanuel Barillot
GIW 2004 Poster Abstract: P120 [PDF file]

Using Sequence Homology to Filter High-throughput Protein-protein Interaction Data
Ashwini Patil, Haruki Nakamura
GIW 2004 Poster Abstract: P121 [PDF file]

Prediction of Protein-Protein Interactions Based on Real-Valued Phylogenetic Profiles Using Partial Correlation Coefficient
Tetsuya Sato, Yoshihiro Yamanishi, Minoru Kanehisa, Hiroyuki Toh
GIW 2004 Poster Abstract: P122 [PDF file]

A Function Prediction of Unknown Proteins in Protein-Protein Interaction Data
Jae-Young Jung, Jae-Hun Choi, Jong-Min Park, Seon-Hee Park
GIW 2004 Poster Abstract: P123 [PDF file]

Prediction of uncharacterized protein functions by integrating protein-protein interaction data and domain information
Kinya Okada, Kiyoshi Asai
GIW 2004 Poster Abstract: P124 [PDF file]

Analysis of protein interaction networks in neurodegenerative disorders
Vachiranee Limviphuvadh, Seigo Tanaka, Susumu Goto, Kunihiro Ueda, Minoru Kanehisa
GIW 2004 Poster Abstract: P125 [PDF file]

A Fast Method for Inferring Strengths of Protein-Protein Interactions and A Hardness Result
Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu
GIW 2004 Poster Abstract: P126 [PDF file]

Improving Prediction of MHC Class I Binding Peptides with Additional Binding Data
Shanfeng Zhu, Kiyoko F. Aoki, Keiko Udaka, Hiroshi Mamitsuka
GIW 2004 Poster Abstract: P127 [PDF file]

GreenPepper: The docking prediction software of protein complex
Toshiharu Kondo, Hirokazu Ishida, Ryo Yamauchi, Eijiro Watanabe, Chizuru Hirose, Mitiko Go
GIW 2004 Poster Abstract: P128 [PDF file]

Computer Modeling of Enzyme Protein-Chiral Ligand Interactions: Enantioselectivity of Lipase Enzyme
Yoshinobu Naoshima, Yoshihiro Mori, Yoichiro Yagi
GIW 2004 Poster Abstract: P129 [PDF file]

Selection of Proper Template Complex for Modeling Protein-Protein Complex
Naoshi Fukuhara, Takeshi Kawabata, Nobuhiro Go
GIW 2004 Poster Abstract: P130 [PDF file]

The analysis between functions and densities in yeast intercomplex protein-protein interactions
So Nakagawa, Soichi Ogishima, Takeshi Hase, Yashuhiro Suzuki, Hiroshi Tanaka
GIW 2004 Poster Abstract: P131 [PDF file]

Deciphering the Protein Network of Caenorhabditis elegans in the Approach of Systems Biology
Chung-Yen Lin, Chi-Shiang Cho, Chia-Ming Chang, Chia-Ling Chen, Fan-Kai Lin, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung
GIW 2004 Poster Abstract: P132 [PDF file]

Hierarchical Structure of the Protein-protein Interaction Networks
Ka-Lok Ng, Po-Han Lee, Chien-Hung Huang
GIW 2004 Poster Abstract: P133 [PDF file]

InteractionViewer: A Visualization Tool for Protein-Protein Interaction Networks
Jun-Wei Hsu, Tao-Wei Huang, Yao-Lin Chang, Cheng-Yen Kao
GIW 2004 Poster Abstract: P134 [PDF file]

Design and Implementation of Navigation System for Protein Interaction Networks
Jong-Min Park, Jae-Hun Choi, Jae-Young Jung, Seon-Hee Park
GIW 2004 Poster Abstract: P135 [PDF file]

In Silico Search for Nuclear Receptor Target Genes
Yoshitomo Tanaka, Tsuguchika Kaminuma, Kotoko Nakata, Hiroshi Tanaka
GIW 2004 Poster Abstract: P136 [PDF file]

Universal Proteomics tools for Protein Quantitation and Data Management - Xome & Mass Navigator
Koji Yanagisawa, Yasuto Yokoi, Ken Aoshima, Yuji Miura, Yoshiya Oda, Yasushi Ishihama, Tsuyoshi Tabata, Takatoshi Kawai, Takeshi Nagasu
GIW 2004 Poster Abstract: P137 [PDF file]

WoLF PSORT: Protein Localization Prediction Program
Paul Horton, Koon-Jeun Park
GIW 2004 Poster Abstract: P138 [PDF file]

Identification of novel chloroplast proteins of endosymbiotic origin by phylogenetic profiling using homolog groups
Naoki Sato, Masayuki Ishikawa
GIW 2004 Poster Abstract: P139 [PDF file]

Translational Polymorphism as an Important Source of Eukaryotic Proteins Variety
Alex V. Kochetov, Nikolay A. Kolchanov, Akinori Sarai
GIW 2004 Poster Abstract: P140 [PDF file]

Extended proteins with negative net charges in total proteomes
Nobuyuki Uchikoga, Runcong Ke, Fumitsugu Akazawa, Masashi Sonoyama, Shigeki Mitaku
GIW 2004 Poster Abstract: P141 [PDF file]

Analysis of Amino Acid Conservation in Transmembrane Helices
Satoshi Hamada, Sukenobu Konishi, Takuhiro Nishio, Toshio Shimizu
GIW 2004 Poster Abstract: P142 [PDF file]

A Transmembrane Topology Prediction Procedure for Identifying GPCR Sequences
Yasuhito Inoue, Takao Kimura, Toshio Shimizu
GIW 2004 Poster Abstract: P143 [PDF file]

Domain Architecture of Prokaryotic Single-Spanning Transmembrane Proteins
Masafumi Arai, Takafumi Fukushi, Satoshi Mizuta, Masanobu Satake, Toshio Shimizu
GIW 2004 Poster Abstract: P144 [PDF file]

Detection of conformational changes in the membrane proteins by using PDB-REPRDB
Tamotsu Noguchi
GIW 2004 Poster Abstract: P145 [PDF file]

Simulation of electric charge distribution of all proteins in Saccharomyces cerevisiae proteome
Runcong Ke, Shigeki Mitaku
GIW 2004 Poster Abstract: P146 [PDF file]

De novo peptide sequencing using ion-peak intensity and amino acid cleavage intensity ratio
Mitsuhiro Kanazawa, Atsushi Ogiwara, Hisae Anyoji, Umpei Nagashima
GIW 2004 Poster Abstract: P147 [PDF file]

Quantitative Proteomics Analysis System i-OPAL
Atsushi Ogiwara, Hsiao-kun Tu, Mitsuhiro Kanazawa, Hisae Anyoji, Takao Kawakami, Toshihide Nishimura
GIW 2004 Poster Abstract: P148 [PDF file]

Mutation effect on number distribution of transmembrane helices in total proteome of Drosophila melanogaster
Ryusuke Sawada, Masashi Sonoyama, Shigeki Mitaku
GIW 2004 Poster Abstract: P149 [PDF file]

Predicting the protein disordered region using modified position specific scoring matrix
Kana Shimizu, Shuichi Hirose, Tamotsu Noguchi, Yoichi Muraoka
GIW 2004 Poster Abstract: P150 [PDF file]

Sequence and Structural Analysis of Outer Membrane Proteins: Applications to Discrimination and Prediction
M. Michael Gromiha, Shandar Ahmad, Makiko Suwa
GIW 2004 Poster Abstract: P151 [PDF file]

Conservation of Domain Geometry in Proteins
Jung-Hoon Han, Nicola Kerrison, Cyrus Chothia, Sarah Teichmann
GIW 2004 Poster Abstract: P152 [PDF file]

A Structural Sequence Representation of Protein: Secondary Structure Element Sequence(SSES)
Sung-Hee Park, Chan-Yong Park, Dae-Hee Kim, Seon-Hee Park
GIW 2004 Poster Abstract: P153 [PDF file]

Computational Method for Determining Global Protein Topology from Distance Restraints by Chemical Cross-Linking
Akira R. Kinjo, Ken Nishikawa, Tatsuya Akutsu, Katsuhisa Horimoto
GIW 2004 Poster Abstract: P154 [PDF file]

GATS: Grid Aided Target Selection for molecular simulation
Yuichi Hirata, Said Mirza Pahlevi, Masaaki Kawata, Isao Kojima, Nagashima Unpei, Mitsuo Yokokawa, Satoshi Sekiguchi
GIW 2004 Poster Abstract: P155 [PDF file]

A new protein classification method using dynamic classifier
Chan-Yong Park, Sung-Hee Park, Dae-Hee Kim, Seon-Hee Park, Chi-Jung Hwang
GIW 2004 Poster Abstract: P156 [PDF file]

Functional Classification of Coiled-Coil Proteins in Multiple Genomes
Akiyasu C. Yoshizawa, Shujiro Okuda, Yuki Moriya, Masumi Itoh, Toshiaki Katayama, Shin Kawano, Shinobu Okamoto, Shuichi Kawashima, Minoru Kanehisa
GIW 2004 Poster Abstract: P157 [PDF file]

Structural diversity as a source of quasispeciation in human immunodeficiency virus type 1
Teruaki Watabe, Hirohisa Kishino, Yasuhiro Kitazoe
GIW 2004 Poster Abstract: P158 [PDF file]

FAMSBASE: Modeling Database of 277 Genomes
Mitsuo Iwadate, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Eiichiro Suzuki, Hideaki Umeyama
GIW 2004 Poster Abstract: P159 [PDF file]

Question Answering System in Biomedical Domain
Kouji Takahashi, Asako Koike, Toshihisa Takagi
GIW 2004 Poster Abstract: P160 [PDF file]

New cancer diagnosis method on the basis of fuzzy theory and boosting
Hiro Takahashi, Hiroyuki Honda
GIW 2004 Poster Abstract: P161 [PDF file]

Model Analysis of Foam Cell Formation in Atherosclerosis
Satoshi Yamada, Nobuhiro Yamada
GIW 2004 Poster Abstract: P162 [PDF file]

Building Patterns for Biomedical Event Extraction
Hong-Woo Chun, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii
GIW 2004 Poster Abstract: P163 [PDF file]

A Generic Pipeline Architecture for Bioinformatics System
Hsiao-Kun Tu, Mitsuhiro Kanazawa, Hisae Anyoji, Atsushi Ogiwara
GIW 2004 Poster Abstract: P164 [PDF file]

A Support System for Creating the Minimum Yeast Genom by Searching Non-Essential Area
Takahiro Sumiya, Masafumi Nishizawa, Yukinori Kitadai, Tatsuo Tomita, Atsushi Nakamura
GIW 2004 Poster Abstract: P165 [PDF file]

Construction of Subcellular Locations prediction tool for Three Kingdoms: Fungi, Animal and Plant
Keun-Joon Park, Paul Horton
GIW 2004 Poster Abstract: P166 [PDF file]

Moleview : A program for molecular visualization
Chan-Yong Park, Sung-Hee Park, Dae-Hee Kim, Seon-Hee Park, Chi-Jung Hwang
GIW 2004 Poster Abstract: P167 [PDF file]

Intris: A Viewer for Splice Variants and their Expression Profiles --- Summarization into Variant Types
Kouichi Kimura, Tetsuo Nishikawa, Ai Wakamatsu, Jun-ichi Yamamoto, Ken'ichi Nagai, Nobuo Nomura, Takao Isogai
GIW 2004 Poster Abstract: P168 [PDF file]

Three-dimensional visualization of allelic copy number data
Kunihiro Nishimura, Shumpei Ishikawa, Koichi Hirota, Hiroyuki Aburatani, Michitaka Hirose
GIW 2004 Poster Abstract: P169 [PDF file]

Polymorphism Markup Language (PML) for the interoperability of data on SNPs and other sequence variations
Hideaki Sugawara, Hiroshi Mizushima, Tokio Kano, Yasumasa Shigemoto, Yoichi Hashimoto, Isao Tomabechi, Masayuki Ikawa, Naoki Sakagami, Toshiyuki Katagiri, Takashige Oroguchi
GIW 2004 Poster Abstract: P170 [PDF file]

MFAML: an XML-based standard format for metabolic flux analysis
Hongseok Yun, Dong-Yup Lee, Seunghyun Lee, Joonwoo Jeong, Sang Yup Lee
GIW 2004 Poster Abstract: P171 [PDF file]

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures
Norihiro Kikuchi, Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Takashi Sato, Toshihide Shikanai, Yoriko Takahashi, Hisashi Narimatsu
GIW 2004 Poster Abstract: P172 [PDF file]

Improving Parsing Precision of an Existing Parser for Extracting Biological Relation Events
Hyunchul Jang, Jaesoo Lim, Hyun-Sook Lee, Soo-Jun Park, Seon-Hee Park, Kyu-Chul Lee
GIW 2004 Poster Abstract: P173 [PDF file]

Corpus Tagging Tool for Tagging Biological Named Entities and Their Relation Events
Hyunchul Jang, Hyun-Sook Lee, Jaesoo Lim, Soo-Jun Park, Seon-Hee Park, Kyu-Chul Lee
GIW 2004 Poster Abstract: P174 [PDF file]

Extraction of the cooccurrence sentences of gene names and keywords from Pubmed abstracts
Takashi Yoneya
GIW 2004 Poster Abstract: P175 [PDF file]

Evaluation of the Article Collecting System Based on Rough Reading Strategy
Ryo Okada, Manabu Sugii, Miyako Tanaka, Hiroshi Matsuno, Satoru Miyano
GIW 2004 Poster Abstract: P176 [PDF file]

Knowledge discovery based on conceptual network
Asako Koike, Toshihisa Takagi
GIW 2004 Poster Abstract: P177 [PDF file]

Domain Independent Named Entity Recognition from Biological Literature
Hyun-Sook Lee, Soo-Jun Park, Hyunchul Jang, Jaesoo Lim, Seon-Hee Park
GIW 2004 Poster Abstract: P178 [PDF file]

INOH: A Pathway Database of Biological Events
Takao Asanuma, Tatsuya Kushida, Satoko Yamamoto, Yuki Yamagata, Azumi Sekiguchi, Toshihisa Takagi, Ken Ichiro Fukuda
GIW 2004 Poster Abstract: P179 [PDF file]

Ontology of Experiments for Bioinformatics
Larissa N. Soldatova, Ross D. King
GIW 2004 Poster Abstract: P180 [PDF file]

KAIKOGAAS: An Automated Annotation System for Silkworm Genome
Michihiko Shimomura, Yuji Shimizu, Shun-ichi Sasanuma, Baltazar A. Antonio, Yoshiaki Nagamura, Kazuei Mita, Takuji Sasaki
GIW 2004 Poster Abstract: P181 [PDF file]

Construction of H-Invitational Database CIB-DDBJ Flat File Server
Toshihisa Okido, Yasumasa Shigemoto, Masashi Matsuo, Tadashi Koike, Satoshi Fukuchi, Tadashi Imanishi, Satoru Miyazaki, Yoshio Tateno, Takashi Gojobori
GIW 2004 Poster Abstract: P182 [PDF file]

DNA conformational energy from molecular dynamics simulations: Toward the understanding of the indirect readout mechanism in protein-DNA recognition
Marcos J. Araúzo-Bravo, Shandar Ahmad, Satoshi Fujii, Shigeori Takenaka, Hidetoshi Kono, Nobuhiro Go, Akinori Sarai
GIW 2004 Poster Abstract: P183 [PDF file]

Algorithms for Direct Clone-mapping Technology using Scanning Near-field Optical/Atomic Force Microscopy
Yoshitaka Suetsugu, Tomoyuki Yoshino, Seigo Kuwazaki, Hirokazu Takahashi, Junko Narukawa, Motoharu Shichiri, Daisuke Fukushi, Kazuei Mita, Shigeru Sugiyama, Toshio Ohtani, Kimiko Yamamoto
GIW 2004 Poster Abstract: P184 [PDF file]

A Novel Method for Screening Arabidopsis Mutants in silico based on Statistical Modeling
Eli Kaminuma, Naohiko Heida, Takeshi Yoshizumi, Miki Nakazawa, Minami Matsui, Tetsuro Toyoda
GIW 2004 Poster Abstract: P185 [PDF file]