| List of Accepted Posters | |
|
P001
|
Prediction of Debacle Parts for Robustness in a Cell by using Recurrent
Neural Networks |
| P002 |
Modeling and Simulation of Cyanobacterial Circadian Clock Mechanism
by Hybrid Functional Petri Net |
| P003 |
A New Regulatory Interactions Suggested by Simulations for Circadian
Genetic Control Mechanism in Mammals |
| P004 |
A New Petri Net Modeling Method for Signaling Pathways with a Focus
on Enzyme |
| P005 | CellDesigner2.0: A Process Diagram Editor for Gene-regulatory and Biochemical
Networks Akira Funahashi, Naoki Tanimura, Yukiko Matsuoka, Naritosi Yosinaga, Hiroaki Kitano |
| P006 | Optimization and System Analysis of the Heat Shock Response by CADLIVE
Kouji Mitsukiyo, Marie Kajiwara, Hiroyuki Kurata |
| P007 | A Large-Scale Dynamic Model of the Yeast Cell Cycle Shunsuke Yamamichi, Hiroyuki Kurata |
| P008 |
Control Aspect of Common Interactions Extracted from Inferred Network
Candidates of Gene Expression |
| P009 |
Simulation for detailed mathematical model of G1-to-S cell cycle phase
transition |
| P010 | BAAQ: A Grid-based Infrastructure for Integrating Bioinformatics Applications Xiujun Gong, Kei Yura, Nobuhiro Go |
| P011 | Simulation of Circadian Rhythms Using Grid Computing Takayuki Tanaka, Hiroyuki Kurata |
| P012 | Development of a computer simulation system for particle-level molecular
interactions Ryuzo Azuma, Yoshiki Yamaguchi, Tetsuji Kitagawa, Tomoyuki Yamamoto, Akihiko Konagaya |
| P013 |
The Molecular Dynamics Simulation of Prion Protein |
| P014 |
Symbolic-Numeric Optimization for Biological Kinetics by Quantifier
Elimination |
| P015 | Equilibrium Model of DNA Chip Hybridization Error John A. Rose, Masami Hagiya, Akira Suyama |
| P016 |
An Analysis Tool Library for Biochemical Modeling on E-Cell System
Version 3 |
| P017 | Development of Integrated Modeling Environment for E-Cell3 System Gabor Bereczki, Kouichi Takahashi, Takeshi Sakurada, Ng Yan Hong, Masaru Tomita |
| P018 | Development of E-Cell kinetic model interoperability environment Tatsuya Ishida, Takeshi Sakurada, Tomoya Kitayama, Masaru Tomita |
| P019 | 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 |
| P020 | Modeling Gene Networks Utilizing Evolutionary Information Using Bayesian
Network Models Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano |
| P021 | Estimating Regulatory Networks from DNA Microarrays and Protein-Protein
Interactions Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano |
| P022 |
Estimating Gene Networks from Expression Data and Binding Location
Data via Boolean Network |
| P023 | Multiscale Bootstrap Analysis of Gene Networks Based on Graphical Gaussian
Modeling Takeshi Kamimura, Hidetoshi Shimodaira |
| P024 |
Systematic Identification of Weak Connections between Clusters in
Biological Network |
| P025 | Genetic Network Reconstruction in Tryptophan Metabolism from Gene Expression
Profiles Akira Imaizumi, Hisashi Yasueda, Sachiyo Aburatani, Katsuhisa Horimoto |
| P026 | Selective Integration of Multiple Genomic Data for Biological Network
Inference Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai |
| P027 | Effective Procedures for the Estimation of Large-scale S-system Parameters Yukihiro Maki, Takanori Ueda, Masahiro Okamoto |
| P028 | Correlations Between Scale-free Genetic Regulatory Model Networks and
Dynamical Properties Chikoo Oosawa, Kazuhiro Takemoto, Genki Hanano |
| P029 | Periodic Oscillation in Gene Networks Modelled by Cyclic Feedback Systems Ruiqi Wang, Luonan Chen |
| P030 | A Gibbs Sampling Approach to Detection of Tree Motifs Lidio Marx Carvalho Meireles, Tatsuya Akutsu |
| P031 |
QSAR Analysis with Support Vector Machines and Graph Kernels |
| P032 | Stable Stochastic Dynamics in Yeast Cell Cycle Yurie Okabe, Masaki Sasai |
| P033 | Comparative Analysis of Conditional Regulation Across the Yeast Genomes Koji Ota, Susumu Goto, Minoru Kanehisa |
| P034 | An application of multiscale bootstrap resampling to hierarchical clustering
of microarray data:How accurate are these clusters? Ryota Suzuki, Hidetoshi Shimodaira |
| P035 | Mixed Factors Analysis for Identifying Transcriptional Modules and
Clusters on Microarray Experiments Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto |
| P036 |
Incorporating prior knowledge into clustering of gene expression profiles |
| P037 |
Mathematical Model Based Clustering of Gene Expression |
| P038 | Cleaning Microarray Expression Data with Markov Random Fields Based
on Profile Similarity Raymond Wan, Hiroshi Mamitsuka |
| P039 | 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 |
| P040 | Statistical Analysis of Gene Expression in Repair Mechanism under UV
Irradiation Sachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Katsuhisa Horimoto |
| P041 | 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 |
| P042 | Analysis for time-course profiles of transcription arrays Daisuke Tominaga, Paul Horton |
| P043 | A Step Towards Substructure Exploration from Gene Expression Patterns Masako Hoshino, Hiroshige Inazumi |
| P044 | Markov Property and Scale-free Organization of Gene Expression Tomoshiro Ochiai, Jose C. Nacher, Tatsuya Akutsu |
| P045 | Expression Analysis of Glycosyltransferase Genes in Human, Mouse, and
Rat Takashi Miyama, Shin Kawano, Minoru Kanehisa |
| P046 | 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 |
| P047 | 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 |
| P048 | On-chip selection of DNA ligands using a method for generating point
mutations Ryoichi Asai, Shin I. Nishimura, Takuyo Aita, Katsutoshi Takahashi |
| P049 | 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 |
| P050 | 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 |
| P051 | Gene-Transpositions on Functional Categories in Prokaryotic Genomes
Nobuyoshi Sugaya, Hiroo Murakami, Sachiyo Aburatani, Kunio Shimizu, Katsuhisa Horimoto |
| P052 | Prediction of DNA-binding sites in proteins using evolutionary profiles
Shandar Ahmad, Akinori Sarai |
| P053 |
Method for finding p53 binding sites using tiling array |
| P054 | Correlation between signal transduction domains and habitats in cyanobacteria Shinobu Okamoto, Shuichi Kawashima, Rei Narikawa, Minoru Kanehisa |
| P055 | Transmembrane regions prediction for G-protein-coupled receptors by
hidden Markov model Kayo Narukawa, Tadashi Kadowaki, Gozoh Tsujimoto |
| P056 |
GPCR and G-protein Coupling Selectivity Prediction Based on SVM with
Physico-Chemical Parameters |
| P057 | GLIDA : GPCR and Ligand Database Jiyoon Yang, Yasushi Okuno, Gozoh Tsujimoto |
| P058 | 3DMET: A Database of Three-Dimensional Structures of Natural Metabolites Miki Maeda |
| P059 | Graph Theoretic Analysis of Chemical Compounds in Biological Pathways Atsuko Yamaguchi, Yasushi Okuno, Hiroshi Mamitsuka |
| P060 | Prediction of Glycosyltransferases Synthesizing Glycoconjugates Using
Variable-length N-gram Model Yeon-Dae Kwon, Shougo Shimizu, Hisashi Narimatsu |
| P061 | An algorithm for graph isomorphism and its application to KEGG Compound
Search Nobuya Tanaka, Susumu Goto, Minoru Kanehisa |
| P062 | 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 |
| P063 | Glycan Linkage Substitution Matrix Rooted on Tree Alignments Kiyoko F. Aoki, Hiroshi Mamitsuka, Minoru Kanehisa |
| P064 | Classification and Motif Extraction of Glycans in Bloods Yoshiyuki Hizukuri, Yoshihiro Yamanishi, Osamu Nakamura, Fumio Yagi, Susumu Goto, Minoru Kanehisa |
| P065 | Integrated Quantification and Multivariate Analysis Workbench System
for Phospholipids Kaoru Mogushi, Katsutoshi Takahashi |
| P066 | Power-law Correlations of Connectivities in Biomolecular Networks Kazuhiro Takemoto, Chikoo Oosawa |
| P067 | A method for estimation of enzyme kinetics in metabolic pathways using
GMA Tomoya Kitayama, Ayako Kinoshita, Yoichi Nakayama, Masaru Tomita |
| P068 | A method for customized cross-species metabolic pathway comparison Eric Lo, Takuji Yamada, Michihiro Tanaka, Masahiro Hattori, Susumu Goto, Chuan-Hsiung Chang, Minoru Kanehisa |
| P069 | Decomposition of kinetically feasible metabolic flux distributions
onto elementary modes Jean-Marc Schwartz, Minoru Kanehisa |
| P070 | Global Tree of Known Carbohydrate Structures to Analyze Biosynthetic
Pathways Kosuke Hashimoto, Shin Kawano, Yasushi Okuno, Minoru Kanehisa |
| P071 | Comparative analysis of enzymatic reactions reveals phylogenic evolution
of metabolic pathways Michihiro Tanaka, Naoki Nariai, Thomas Handorf, Oliver EbenhNoh, Satoru Miyano, Minoru Kanehisa, Reinhart Heinrich |
| P072 | 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 |
| P073 | Fold-Function Relationship of PLP-Dependent Enzymes Keiko Matsuda, Takaaki Nishioka, Kengo Kinoshita, Nobuhiro Go |
| P074 | A novel classification of enzyme catalytic reactions Nozomi Nagano |
| P075 | Phylogenetic Comparison of Human and Mouse Promoter Regions and Visualization
of a Variety of Conserved Elements Hirokazu Chiba, Kenta Nakai |
| P076 | Conservation of Physicochemical Properties during Protein Evolution
Masashi Fujita, Masumi Itoh, Minoru Kanehisa |
| P077 | A method for comparing microarray data of different species Kenji Hagimoto, Jun Miyazaki, Shigehiko Kanaya, Naotake Ogasawara, Toshiyuki Amagasa, Shunsuke Uemura |
| P078 | Chromosome Profiling: A Clue to Trace The Genome Evolution Ayumu Saito, Koichi Nishigaki |
| P079 | Searching for cis-elements in Mouse-Human Orthologous Promoter
Regions Natalia Polouliakh, Wataru Fujibuchi, Tohru Natsume, Paul Horton |
| P080 | Tandem Repeats in 44 Prokaryotic Genomes and Genome Evolution Satoshi Mizuta, Hikaru Munakata, Abulimiti Aimaiti, Kenji Oosawa, Toshio Shimizu |
| P081 | An approximate maximum likelihood method for phylogenetic tree analysis
based on high-temperature Markov Chain Monte Carlo Ryota Suzuki, Tomoya Taniguchi, Hidetoshi Shimodaira |
| P082 |
Extension of Prrn: implementation of a doubly nested randomized iterative
refinement strategy under a piecewise linear gap cost |
| P083 | Sequence Alignment Tool of Membrane Protein Takahiko Muramatsu, Makiko Suwa |
| P084 | A Rapid peptide based Alignment -free method to construct Genome trees
Independent of sequence annotation Vikash Kumar, Sunil Kumar |
| P085 |
Fast Homology Search using Categorisation Profiles |
| P086 | Measuring the Average Accuracy Performance of Homology Search XiaoLei Chen, Adam Cannane, Hugh E. Williams |
| P087 | Performance Comparison between Profiles from Hidden Markov Models and
from Pseudocount Method Makihiko Sato, Katsuhisa Horimoto |
| P088 | Development of Fast Tandem Repeat Analysis and Lossless Compression
Method for DNA Sequence Toshio Modegi |
| P089 | Inferring breakpoints from large-scale BAC-end sequences and a complete
genome sequence Katsuhiko Murakami, Yoshiyuki Sakaki |
| P090 | CATTAGAT - Web Server for Primer Specificity Scan Magnús M. Halldórsson, Haukur Thorgeirsson, Ýmir Vigfússon, Hans Thormar, Jón Jóhannes Jónsson |
| P091 |
Development of a Common Protocol for the Prediction of Microbial Genes |
| P092 | Diverse base composition skews in bacterial chromosomes Chi Chen, Carton W. Chen |
| P093 | 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 |
| P094 | Relationship between Chromosome Rearrangement and Repeat Sequences
in Human Chromosome 7 Hiroo Murakami, Nobuyoshi Sugaya, Sachiyo Aburatani, Katsuhisa Horimoto |
| P095 | Systematic Survey of Sequence Similarity between Sense and Anti-sense
Strands in Escherichia coli Genome Kazuhiro Nakamura, Makihiko Sato, Katsuhisa Horimoto |
| P096 | Comprehensive promoter analyses using a database of transcription start
sites Riu Yamashita, Yutaka Suzuki, Katsuki Tsuritani, Sumio Sugano, Kenta Nakai |
| P097 | 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 |
| P098 |
Analysis of GC-compositional Strand Bias in the Transcription Start
Sites of Plant and Fungal Genes |
| P099 | Power Spectrum of DNA Base Sequence in Human Mitochondrial Genome Eisei Takushi, Yukinobu Chinen |
| P100 | A Possible Existence of Cooperative Gene and Transition in Bacteriophage
ΦX174 Genome Eisei Takushi |
| P101 | Quantitative analysis of synonymous codon usage bias Haruo Suzuki, Rintaro Saito, Masaru Tomita |
| P102 | 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 |
| P103 | Exhaustive analysis for screening of susceptible interactions between
genetic and environmental factors for multifactorial disease Yasuyuki Tomita, Mitsuhiro Yokota, Takeshi Kobayashi, Hiroyuki Honda |
| P104 | 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 |
| P105 | 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 |
| P106 | Logistic Regression Model of Binary Disease Trait for Case-Control
Study Considering Interactions between SNPs and Environments Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano |
| P107 | 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 |
| P108 | Clustering and Multiple Alignment for a Large Number of cDNA Sequences
Including Splicing Variants Tomohiro Yasuda |
| P109 | 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 |
| P110 | Development of ASTRA: database of human alternative splicing patterns Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh |
| P111 | Alternative splicing of transmembrane regions in human gene Masateru Yamamoto, Chie Motono, Hideki Nagasaki, Makiko Suwa |
| P112 | Non-coding RNA finding based on probabilistic secondary structure information Taishin Kin, Koji Tsuda, Kiyoshi Asai |
| P113 | Detection of tRNA genes from DNA sequences of Eukaryotes Makoto Kinouchi, Yoshihiro Kudo |
| P114 | Scarna: Stem Candidate Aligner for RNA Kiyoshi Asai, Taishin Kin |
| P115 | Detection of non-coding RNAs by properties of stems Hiroki Ueda, Jun-Ichi Sagara, Minoru Nakazawa, Shimmi Hattori |
| P116 | A genetic algorithm approach for finding the common structure of two
homologous RNAs Akito Taneda |
| P117 | Hierarchical Alignment of RNA Secondary Structures Including Pseudoknots Shinnosuke Seki, Atsushi Kijima, Satoshi Kobayashi, Gen-ichi Sanpei |
| P118 | Integrated Reliability-Assessment for Protein-Protein Interaction Data Akihito Tokuda, Asako Koike, Toshihisa Takagi |
| P119 | 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 |
| P120 | Validation and prediction of protein-protein interactions by pairwise
analysis of functional protein families Sarah Mohseni-Zadeh, Jacques Camonis, Jérôme Wojcik, Emmanuel Barillot |
| P121 | Using Sequence Homology to Filter High-throughput Protein-protein Interaction
Data Ashwini Patil, Haruki Nakamura |
| P122 | Prediction of Protein-Protein Interactions Based on Real-Valued Phylogenetic
Profiles Using Partial Correlation Coefficient Tetsuya Sato, Yoshihiro Yamanishi, Minoru Kanehisa, Hiroyuki Toh |
| P123 | A Function Prediction of Unknown Proteins in Protein-Protein Interaction
Data Jae-Young Jung, Jae-Hun Choi, Jong-Min Park, Seon-Hee Park |
| P124 | Prediction of uncharacterized protein functions by integrating protein-protein
interaction data and domain information Kinya Okada, Kiyoshi Asai |
| P125 | Analysis of protein interaction networks in neurodegenerative disorders Vachiranee Limviphuvadh, Seigo Tanaka, Susumu Goto, Kunihiro Ueda, Minoru Kanehisa |
| P126 | A Fast Method for Inferring Strengths of Protein-Protein Interactions
and A Hardness Result Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu |
| P127 | Improving Prediction of MHC Class I Binding Peptides with Additional
Binding Data Shanfeng Zhu, Kiyoko F. Aoki, Keiko Udaka, Hiroshi Mamitsuka |
| P128 | GreenPepper: The docking prediction software of protein complex Toshiharu Kondo, Hirokazu Ishida, Ryo Yamauchi, Eijiro Watanabe, Chizuru Hirose, Mitiko Go |
| P129 | Computer Modeling of Enzyme Protein-Chiral Ligand Interactions: Enantioselectivity
of Lipase Enzyme Yoshinobu Naoshima, Yoshihiro Mori, Yoichiro Yagi |
| P130 | Selection of Proper Template Complex for Modeling Protein-Protein Complex Naoshi Fukuhara, Takeshi Kawabata, Nobuhiro Go |
| P131 | The analysis between functions and densities in yeast intercomplex
protein-protein interactions So Nakagawa, Soichi Ogishima, Takeshi Hase, Yashuhiro Suzuki, Hiroshi Tanaka |
| P132 | 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 |
| P133 | Hierarchical Structure of the Protein-protein Interaction Networks Ka-Lok Ng, Po-Han Lee, Chien-Hung Huang |
| P134 |
InteractionViewer: A Visualization Tool for Protein-Protein Interaction
Networks |
| P135 | Design and Implementation of Navigation System for Protein Interaction
Networks Jong-Min Park, Jae-Hun Choi, Jae-Young Jung, Seon-Hee Park |
| P136 | In Silico Search for Nuclear Receptor Target Genes Yoshitomo Tanaka, Tsuguchika Kaminuma, Kotoko Nakata, Hiroshi Tanaka |
| P137 | 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 |
| P138 | WoLF PSORT: Protein Localization Prediction Program Paul Horton, Koon-Jeun Park |
| P139 | Identification of novel chloroplast proteins of endosymbiotic origin
by phylogenetic profiling using homolog groups Naoki Sato, Masayuki Ishikawa |
| P140 | Translational Polymorphism as an Important Source of Eukaryotic Proteins
Variety Alex V. Kochetov, Nikolay A. Kolchanov, Akinori Sarai |
| P141 | Extended proteins with negative net charges in total proteomes Nobuyuki Uchikoga, Runcong Ke, Fumitsugu Akazawa, Masashi Sonoyama, Shigeki Mitaku |
| P142 | Analysis of Amino Acid Conservation in Transmembrane Helices Satoshi Hamada, Sukenobu Konishi, Takuhiro Nishio, Toshio Shimizu |
| P143 | A Transmembrane Topology Prediction Procedure for Identifying GPCR
Sequences Yasuhito Inoue, Takao Kimura, Toshio Shimizu |
| P144 | Domain Architecture of Prokaryotic Single-Spanning Transmembrane Proteins Masafumi Arai, Takafumi Fukushi, Satoshi Mizuta, Masanobu Satake, Toshio Shimizu |
| P145 | Detection of conformational changes in the membrane proteins by using
PDB-REPRDB Tamotsu Noguchi |
| P146 | Simulation of electric charge distribution of all proteins in Saccharomyces
cerevisiae proteome Runcong Ke, Shigeki Mitaku |
| P147 | De novo peptide sequencing using ion-peak intensity and amino
acid cleavage intensity ratio Mitsuhiro Kanazawa, Atsushi Ogiwara, Hisae Anyoji, Umpei Nagashima |
| P148 | Quantitative Proteomics Analysis System i-OPAL Atsushi Ogiwara, Hsiao-kun Tu, Mitsuhiro Kanazawa, Hisae Anyoji, Takao Kawakami, Toshihide Nishimura |
| P149 | Mutation effect on number distribution of transmembrane helices in
total proteome of Drosophila melanogaster Ryusuke Sawada, Masashi Sonoyama, Shigeki Mitaku |
| P150 | Predicting the protein disordered region using modified position specific
scoring matrix Kana Shimizu, Shuichi Hirose, Tamotsu Noguchi, Yoichi Muraoka |
| P151 | Sequence and Structural Analysis of Outer Membrane Proteins: Applications
to Discrimination and Prediction M. Michael Gromiha, Shandar Ahmad, Makiko Suwa |
| P152 | Conservation of Domain Geometry in Proteins Jung-Hoon Han, Nicola Kerrison, Cyrus Chothia, Sarah Teichmann |
| P153 | A Structural Sequence Representation of Protein: Secondary Structure
Element Sequence(SSES) Sung-Hee Park, Chan-Yong Park, Dae-Hee Kim, Seon-Hee Park |
| P154 | Computational Method for Determining Global Protein Topology from Distance
Restraints by Chemical Cross-Linking Akira R. Kinjo, Ken Nishikawa, Tatsuya Akutsu, Katsuhisa Horimoto |
| P155 | GATS: Grid Aided Target Selection for molecular simulation Yuichi Hirata, Said Mirza Pahlevi, Masaaki Kawata, Isao Kojima, Nagashima Unpei, Mitsuo Yokokawa, Satoshi Sekiguchi |
| P156 | A new protein classification method using dynamic classifier Chan-Yong Park, Sung-Hee Park, Dae-Hee Kim, Seon-Hee Park, Chi-Jung Hwang |
| P157 | 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 |
| P158 | Structural diversity as a source of quasispeciation in human immunodeficiency
virus type 1 Teruaki Watabe, Hirohisa Kishino, Yasuhiro Kitazoe |
| P159 | FAMSBASE: Modeling Database of 277 Genomes Mitsuo Iwadate, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Eiichiro Suzuki, Hideaki Umeyama |
| P160 | Question Answering System in Biomedical Domain Kouji Takahashi, Asako Koike, Toshihisa Takagi |
| P161 | New cancer diagnosis method on the basis of fuzzy theory and boosting Hiro Takahashi, Hiroyuki Honda |
| P162 | Model Analysis of Foam Cell Formation in Atherosclerosis Satoshi Yamada, Nobuhiro Yamada |
| P163 | Building Patterns for Biomedical Event Extraction Hong-Woo Chun, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii |
| P164 | A Generic Pipeline Architecture for Bioinformatics System Hsiao-Kun Tu, Mitsuhiro Kanazawa, Hisae Anyoji, Atsushi Ogiwara |
| P165 | A Support System for Creating the Minimum Yeast Genom by Searching
Non-Essential Area Takahiro Sumiya, Masafumi Nishizawa, Yukinori Kitadai, Tatsuo Tomita, Atsushi Nakamura |
| P166 | Construction of Subcellular Locations prediction tool for Three Kingdoms:
Fungi, Animal and Plant Keun-Joon Park, Paul Horton |
| P167 | Moleview : A program for molecular visualization Chan-Yong Park, Sung-Hee Park, Dae-Hee Kim, Seon-Hee Park, Chi-Jung Hwang |
| P168 | 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 |
| P169 | Three-dimensional visualization of allelic copy number data Kunihiro Nishimura, Shumpei Ishikawa, Koichi Hirota, Hiroyuki Aburatani, Michitaka Hirose |
| P170 | 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 |
| P171 | MFAML: an XML-based standard format for metabolic flux analysis
Hongseok Yun, Dong-Yup Lee, Seunghyun Lee, Joonwoo Jeong, Sang Yup Lee |
| P172 | 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 |
| P173 | 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 |
| P174 | 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 |
| P175 | Extraction of the cooccurrence sentences of gene names and keywords
from Pubmed abstracts Takashi Yoneya |
| P176 | Evaluation of the Article Collecting System Based on Rough Reading
Strategy Ryo Okada, Manabu Sugii, Miyako Tanaka, Hiroshi Matsuno, Satoru Miyano |
| P177 | Knowledge discovery based on conceptual network Asako Koike, Toshihisa Takagi |
| P178 | Domain Independent Named Entity Recognition from Biological Literature Hyun-Sook Lee, Soo-Jun Park, Hyunchul Jang, Jaesoo Lim, Seon-Hee Park |
| P179 | INOH: A Pathway Database of Biological Events Takao Asanuma, Tatsuya Kushida, Satoko Yamamoto, Yuki Yamagata, Azumi Sekiguchi, Toshihisa Takagi, Ken Ichiro Fukuda |
| P180 | Ontology of Experiments for Bioinformatics Larissa N. Soldatova, Ross D. King |
| P181 | KAIKOGAAS: An Automated Annotation System for Silkworm Genome Michihiko Shimomura, Yuji Shimizu, Shun-ichi Sasanuma, Baltazar A. Antonio, Yoshiaki Nagamura, Kazuei Mita, Takuji Sasaki |
| P182 | 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 |
| P183 | 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 |
| P184 | 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 |
| P185 | 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 |
E-mail: giw2004@ims.u-tokyo.ac.jp