Software Demonstration Abstracts
Poster Abstracts
Using the Approach of Comparative Proteomics and Systems Biology to Decipher the Human Protein Network
Chung-Yen Lin, Fan-Kai Lin, Chi-Shyang Cho, Chieh-Hwa Lin, Li-Wei Lai, Chao A. Hsiung
GIW 2005 Poster Abstract: S01 [PDF file]
b-Src: A Source-Code Search Engine for Bioinformatics Open-Source Packages
Mitsuteru Nakao, Paul Horton
GIW 2005 Poster Abstract: S02 [PDF file]
INOH: Pathways and Ontologies
Noriko Sakai, Tatsuya Kushida, Satoko Yamamoto, Emi Hattori, Hiromi Nakamura, Yuki Yamagata, Yukiko Nakanishi, Toshihisa Takagi, Ken Ichiro Fukuda
GIW 2005 Poster Abstract: S03 [PDF file]
Fast Retrieval of Useful Information from Literature Database
Hiroko Matsui, Shigeki Tanishima, Norihiro Akasaka, Takafumi Hayashi, Keiko Oketa, Keizoh Uehara
GIW 2005 Poster Abstract: S04 [PDF file]
VECT: The Visual Extraction and Conversion Tool
Hui-Hsien Chou
GIW 2005 Poster Abstract: S05 [PDF file]
Toxicogenomics: Novel Computational Strategies for Prediction of Long Term Carcinogenicity
Jochen Koenig, Claire Pallez, Hans Gmuender, Reinhard Doelz, Deepak Thakkar, Frank Staubli
GIW 2005 Poster Abstract: S06 [PDF file]
AlignScope : A System for Visualization and Analysis of Whole Genome Alignments
Hee-Jeong Jin, Hye-Jung Kim, Hwan-Gue Cho
GIW 2005 Poster Abstract: S07 [PDF file]
KeyMolnet: An Integrated Platform for Analysis of Molecular Networks
Atsushi Nogi, Hiromi Sato, Miki Fukuda, Makoto Shigetaka, Yohei Ozeki, Misa Ogura, Kyoko Nakanishi, Rie Taniguchi, Hisako Kuriki, Nakako Iwasaki, Yoko Inoue, Yoko Wakamatsu, Shizuka Homma, Mikiko Izumi, Yoshinobu Mizoguchi, Yuichi Kikushima, Takeshi Namba, Keiichi Ayabe, Nobuo Tomioka, Akiko Itai
GIW 2005 Poster Abstract: S08 [PDF file]
BioRuby+ChemRuby: An Exploratory Software Project
Toshiaki Katayama, Mitsuteru C. Nakao, Naohisa Goto, Nobuya Tanaka
GIW 2005 Poster Abstract: S09 [PDF file]
Cell Illustrator 2.0: A Platform for Biopathway Modeling and Simulation
Masao Nagasaki, Atsushi Doi, Satoru Miyano
GIW 2005 Poster Abstract: S10 [PDF file]
Tools for Supporting Computational Experiments on Genomic Object Net
Toshinori Tanaka, Katsuyuki Harada, Hironori Kitakaze, Junkichi Yamanaka, Hiroshi Matsuno, Satoru Miyano
GIW 2005 Poster Abstract: S11 [PDF file]
Systematic Analysis of Structure-Stability Relationship for Proteins and Mutants
Noboru Furukawa, Yuko Takeno, Goran Neshich, Akinori Sarai
GIW 2005 Poster Abstract: P001 [PDF file]
Hierarchy of Metabolic Compounds Based on Their Synthesizing Capacity
Thomas Handorf, Oliver Ebenhöh, Daniel Kahn, Reinhart Heinrich
GIW 2005 Poster Abstract: P002 [PDF file]
IBTS: An Extensible System for Integration of Bioinformatics Tools Allowing Cluster Computing
Youngmahn Hahn, Yongseong Cho, Sang Joo Lee
GIW 2005 Poster Abstract: P003 [PDF file]
Virtual Drug Screening of Endothelin Receptor Ligands Using Active Learning
Yukiko Fujiwara, Yoshiko Yamashita, Minoru Asogawa, Chiaki Fukushima, Masaaki Asao, Hideshi Shimadzu, Kazuya Nakao, Ryo Shimizu
GIW 2005 Poster Abstract: P004 [PDF file]
KAAS: KEGG Automatic Annotation Server
Yuki Moriya, Masumi Itoh, Sujiro Okuda, Minoru Kanehisa
GIW 2005 Poster Abstract: P005 [PDF file]
Mining Implicit Biological Realted Entities from Literature Using a Probabilistic Model
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
GIW 2005 Poster Abstract: P006 [PDF file]
Constraints Based Dynamic Protein Interaction Network
Dong-Soo Han, Suk-Hoon Jung, Woo-Hyuk Jang, Choon-Ho Lee
GIW 2005 Poster Abstract: P007 [PDF file]
New Features of MutationView : Implementation of Various Protein-Oriented Tools to Find out the Relation between Protein Function and Diseases
Masafumi Ohtsubo, Takashi Kawamura, Susumu Mitsuyama, Nobuyoshi Shimizu, Shinsei Minoshima
GIW 2005 Poster Abstract: P008 [PDF file]
KEGG-Based Pathway Visualization Tool for Complex Omics Data
Nobuaki Kono, Kazuharu Arakawa, Yohei Yamada, Hirotada Mori, Masaru Tomita
GIW 2005 Poster Abstract: P009 [PDF file]
Visualization of Gene Database on WEB Using Self Organizing Maps
Yasuhiko Miyazaki, Hiroshi Dozono, Hisao Tokushima, Yoshio Noguchi
GIW 2005 Poster Abstract: P010 [PDF file]
Evolutionary Identifications of Functional Modules in Yeast Protein Interaction Network
Soichi Ogishima, Yasuhiro Suzuki, Takashi Hase, So Nakagawa, Hiroshi Tanaka
GIW 2005 Poster Abstract: P011 [PDF file]
An Integrated Database and Knowledge-Base of Interaction between Human Proteins and Commonly Used Drugs
Hiroyasu Shimada, Masashi Nemoto, Ken Horiuchi, Atsuko Yamaguchi, Motoi Tobita, Kenji Araki, Tetsuo Nishikawa
GIW 2005 Poster Abstract: P012 [PDF file]
Structural Annotation Viewer and Database for Splice-Variant Human cDNA Sequences
Tetsuo Nishikawa, Kouichi Kimura, Jun-ichi Yamamoto, Ai Wakamatsu, Hiroshi Makita, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
GIW 2005 Poster Abstract: P013 [PDF file]
PRIME: Platform for RIKEN Metabolomics
Atsushi Fukushima, Miyako Kusano, Kenji Akiyama, Takeshi Obayashi, Takayuki Tohge, Masami Yokota Hirai, Shigehiko Kanaya, Masanori Arita, Yoko Shinbo, Kazuo Shinozaki, Tetsuya Sakurai, Kazuki Saito
GIW 2005 Poster Abstract: P014 [PDF file]
Construction of Reference Cis-Regulatory Module Database as a Tool for the Pattern Analysis of Cis-Regulatory Regions on Human Genome Sequence
Eri Kibukawa, Yoshiaki Tanaka, Satoru Miyazaki
GIW 2005 Poster Abstract: P015 [PDF file]
BioTextLinker: Dynamic Informative Link Annotation for Biological Text over Heterogeneous Databases
Hodong Lee, Jong C. Park
GIW 2005 Poster Abstract: P016 [PDF file]
MiDB: Mitochondrial Proteomics Database in Human Heart
Hyun Joo, Taeho Kim, Jae Boum Youm, Nari Kim, Jin Han
GIW 2005 Poster Abstract: P017 [PDF file]
FAMSBASE of Human, Rat and Mouse Genomes with Model Quality Estimation
Mitsuo Iwadate, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Hideaki Umeyama
GIW 2005 Poster Abstract: P018 [PDF file]
Framework Approach for a Search Platform on Biological Data
Seok Jong Yu, Dan Bi Kim, Inae Hur, Sang Joo Lee
GIW 2005 Poster Abstract: P019 [PDF file]
PSE: A Tool for Browsing a Large Amount of PubMed Abstracts with Gene Names and Common Words as the Keywords
Takashi Yoneya
GIW 2005 Poster Abstract: P020 [PDF file]
RPAIR: A Database of Chemical Transformation Patterns in Enzymatic Reactions
Takuji Yamada, Masahiro Hattori, Min A. Oh, Susumu Goto, Minoru Kanehisa
GIW 2005 Poster Abstract: P021 [PDF file]
A Resource Discovery Service for Bioinformatics Applications in a Grid-Based Environment
Xiujun Gong, Jitender Jit Singh Cheema, Kensuke Nakamura, Kei Yura, Nobuhiro Go
GIW 2005 Poster Abstract: P022 [PDF file]
Gene Annotation Using Proteomic Data
Yoko Ishino, Hisaaki Taniguchi
GIW 2005 Poster Abstract: P023 [PDF file]
A Database for Comparative Analysis of Tunicate Promoter Sequences
Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
GIW 2005 Poster Abstract: P024 [PDF file]
An Existence of Cooperative (Clustered) Genes in Coliphageφk
Eisei Takushi, Miyako Kawachi
GIW 2005 Poster Abstract: P025 [PDF file]
Evaluation Measures of `Marker Selection' and `Genotype Membership' in Large-Scale SNP Genotyping
Eli Kaminuma, Hiroshi Masuya, Hiromi Motegi, K. Ryo Takahasi, Miki Nakazawa, Minami Matsui, Yoichi Gondo, Tetsuo Noda, Toshihiko Shiroishi, Shigeharu Wakana, Tetsuro Toyoda
GIW 2005 Poster Abstract: P026 [PDF file]
Finding Small and Resistance-Predictable Feature Sets for Bacterium Classification by Multi-Objective Optimization
Hiroshi Yamakawa, Yoshio Nakao, Takahisa Suzuki, Yumiko Sanbongi, Takashi Ida
GIW 2005 Poster Abstract: P027 [PDF file]
Sensitizing GO Tools Using Multiple Ratio-Cutoffs for Gene Selection
Kenichi Hirotani, Yoichi Yamada, Miyuki Onda, Ken-ichiro Muramoto, Kenji Satou, Takashi Ito
GIW 2005 Poster Abstract: P028 [PDF file]
Cell-Distance Networks: A Clue for Understanding of Cell Diversity
Larisa Kiseleva, Paul Horton, Wataru Fujibuchi
GIW 2005 Poster Abstract: P029 [PDF file]
How Much We Know about Soluble Domains Existing in Loop Regions of Transmembrane Proteins?
Syuuichi Yoshida, Masafumi Arai, Takuhiro Nishio, Toshio Shimizu
GIW 2005 Poster Abstract: P030 [PDF file]
Discovering Novel MicroRNAs from Small RNA Component of the Mouse Embryo Transcriptome
Tatsuya Ando, Sachiko Okamoto, Masahiro Sato, Hiroyuki Izu, Masanori Takayama, Masanari Kitagawa, Junichi Mineno, Kiyozo Asada, Ikunoshin Kato
GIW 2005 Poster Abstract: P031 [PDF file]
Inferring Protein Interaction Network by Boosting Algorithm
Yong Wang, Feng Bao, Jiadong Zhang, Luonan Chen
GIW 2005 Poster Abstract: P032 [PDF file]
Construction of Human Gene Catalogue by mRNA Using 1.4 Million of Full-Length cDNAs by Oligo-Capping Method
Ai Wakamatsu, Jun-ichi Yamamoto, Kouichi Kimura, Keisuke Tsuchiya, Tetsuo Nishikawa, Sumio Sugano, Takao Isogai
GIW 2005 Poster Abstract: P033 [PDF file]
Genome Mapping Analysis of Splice Variant One-Pass Sequences of Human Full-Length cDNAs
Kouichi Kimura, Tetsuo Nishikawa, Ai Wakamatsu, Jun'ichi Yamamoto, Keiichi Nagai, Nobuo Nomura, Sumio Sugano, Takao Isogai
GIW 2005 Poster Abstract: P034 [PDF file]
State Space Model with Markov Switching for Estimating Time-Dependent Gene Regulatory Networks from Time Series Microarray Experiments
Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
GIW 2005 Poster Abstract: P035 [PDF file]
Knowledge Discovery Using Cross Database Search
Asako Koike, Toshihisa Takagi
GIW 2005 Poster Abstract: P036 [PDF file]
Ontology Based Petri Net Modeling of Signaling Networks
Takako Takai-Igarashi
GIW 2005 Poster Abstract: P037 [PDF file]
Discovering Reliable Protein Interactions Using Bayesian Networks
Thanh Phuong Nguyen, Tu Bao Ho, Ngoc Binh Nguyen
GIW 2005 Poster Abstract: P038 [PDF file]
Cluster Analysis of Neutrophilic Differentiation by Using Fuzzy K-Means
Akitsugu Suga, Kazumi Hakamada, Chinatsu Arima, Masahiro Okamoto, Hitoshi Ichikawa, Taizo Hanai
GIW 2005 Poster Abstract: P039 [PDF file]
Validity Index for Fuzzy K-Means Clustering Using the Gap Statistic Method
Chinatsu Arima, Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai
GIW 2005 Poster Abstract: P040 [PDF file]
Validation of Mathematical Model Based Clustering by Using Time-Course Data
Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai
GIW 2005 Poster Abstract: P041 [PDF file]
Improvement in the Accuracy of Gene Prediction in Rice cDNA Sequences
Fusano Todokoro, Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima, Tadashi Imanishi, Takashi Gojobori
GIW 2005 Poster Abstract: P042 [PDF file]
Co-Expression Analysis Tool for Large Gene Expression Datasets
Hajime Harada, Natalia Polouliakh, Wataru Fujibuchi, Paul Horton
GIW 2005 Poster Abstract: P043 [PDF file]
New Reliable Cancer Diagnosis Method Using Boosting and Projective Adaptive Resonance Theory
Hiro Takahashi, Yasuyuki Murase, Hiroyuki Honda
GIW 2005 Poster Abstract: P044 [PDF file]
Classification Method for Prediction of Multifactorial Disease Development by Using Genetic and Environmental Factors
Yasuyuki Tomita, Mitsuhiro Yokota, Hiroyuki Honda
GIW 2005 Poster Abstract: P045 [PDF file]
Ranking Metabolic Paths with Expression Similarities
Ichigaku Takigawa, Hiroshi Mamitsuka
GIW 2005 Poster Abstract: P046 [PDF file]
Classifying Microarray Data Using Pairwise Similarity between Gene Profiles
Raymond Wan, Åsa M. Wheelock, Matthew J. Bartosiewicz, Hiroshi Mamitsuka
GIW 2005 Poster Abstract: P047 [PDF file]
A Selection Criterion for Robust Classifiers: Cancer Prognosis with Microarray Gene Expression
Ikumi Suzuki, Shigeyuki Oba, Shin Ishii
GIW 2005 Poster Abstract: P048 [PDF file]
Memory-Efficient Clustering Algorithms for Microarray Gene Expression Data
Kazuyuki Numata, Hideo Bannai, Yoshinori Tamada, Michiel de Hoon, Seiya Imoto, Satoru Miyano
GIW 2005 Poster Abstract: P049 [PDF file]
Clustering Gene Expression Data with Stepwise Data Envelopment Analysis
Masako Hoshino, Hiroshige Inazumi
GIW 2005 Poster Abstract: P050 [PDF file]
Effective Nearest Neighbor Methods for Multiclass Cancer Classification Using Microarray Data
Satoshi Niijima, Satoru Kuhara
GIW 2005 Poster Abstract: P051 [PDF file]
Algorithm for Predicting Co-Expression Genes by Improvement of Path Consistency Algorithm
Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto
GIW 2005 Poster Abstract: P052 [PDF file]
A New Method for Analyzing Large-Scale Microarray Data Using Biological Knowledge
Shingo Tsuji, Kouji Nakayama, Masaru Sekijima, Shigeo Ihara, Hiroyuki Aburatani
GIW 2005 Poster Abstract: P053 [PDF file]
Non-Negative Matrix Factorization of Lung Adenocarcinoma Expression Profiles
Takeshi Fujiwara, Shumpei Ishikawa, Yujin Hoshida, Kentaro Inamura, Takayuki Isagawa, Miyuki Shimane, Hiroyuki Aburatani, Yuichi Ishikawa, Hitoshi Nomura
GIW 2005 Poster Abstract: P054 [PDF file]
Classification of Cancer Data with Genetic Programming
Topon Kumar Paul, Hitoshi Iba
GIW 2005 Poster Abstract: P055 [PDF file]
The Application of Cell Surface Marker DNA Microarray in the Search for Molecular Targets
Tuoya, Koichi Hirayama, Yuh Sugii, Tadahiro Nagaoka, Takayuki Fukuda, Hiroko Tada, Hidenori Yamada, Yasaburo Matsuura, Heizo Tokutaka, Masaharu Seno
GIW 2005 Poster Abstract: P056 [PDF file]
Detection of Cluster Boundary in Microarray Data by Reference to MIPS Functional Catalogue Database
Yoshifumi Okada, Takehiko Sahara, Satoru Ohgiya, Tomomasa Nagashima
GIW 2005 Poster Abstract: P057 [PDF file]
Multiplicative Decomposition of Time- and Dose-Dependent Gene Expression Changes
Yukitaka Tani, Takeshi Kamimura, Takeshi Nagashima, Kaori Ide, Mariko Hatakeyama, Hidetoshi Shimodaira
GIW 2005 Poster Abstract: P058 [PDF file]
Species-Specific Variation of Alternative Splicing and Transcriptional Initiation in Six Eukaryotes
Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh
GIW 2005 Poster Abstract: P059 [PDF file]
The Requirements and Problems to Use Draft Sequencing Results in Comparative Genomics of Bacteria
Hidetoshi Yamashita, Yuki Maruyama, Ryuta Komatsu, Toru Suzuki, Seiki Kuramitsu, Kiyozo Asada, Ikunoshin Kato, Masanari Kitagawa
GIW 2005 Poster Abstract: P060 [PDF file]
Comparative Sequence Analysis of Human and Promoter Regions
Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
GIW 2005 Poster Abstract: P061 [PDF file]
Comprehensive Analysis of Triplet Repeats in Vertebrate Genomes
Shigeo Okada, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
GIW 2005 Poster Abstract: P062 [PDF file]
A Maximum Likelihood Method for Inference of Spliceosomal Intron Evolution
Hung Dinh Nguyen, Maki Yoshihama, Naoya Kenmochi
GIW 2005 Poster Abstract: P063 [PDF file]
Comparative Genomic Analysis of Transcription Regulation Elements in Higher Eukaryotes
Natalia Polouliakh, Wataru Fujibuchi, Hajime Harada, Tohru Natsume, Paul Horton
GIW 2005 Poster Abstract: P064 [PDF file]
Comparative Analysis of Autocorrelations of Electric Charges in Amino Acid Sequences of S. cerevisiae and E. coli
Runcong Ke, Shigeki Mitaku
GIW 2005 Poster Abstract: P065 [PDF file]
Seeking Genomic Duplication in Prokaryotic Genomes by Equivalent Tandem Repeats Distributions
Satoshi Mizuta, Michimasa Koshino, Toshio Shimizu
GIW 2005 Poster Abstract: P066 [PDF file]
Statistical Characterization of Transcription Start Sites in Plant Genomes
Shigeo Fujimori, Takanori Washio, Masaru Tomita
GIW 2005 Poster Abstract: P067 [PDF file]
A Scale-Free Prior over Graph Structures for Bayesian Inference of Gene Networks
Takeshi Kamimura, Hidetoshi Shimodaira
GIW 2005 Poster Abstract: P068 [PDF file]
Physicochemical and Structural Characterization of Nonapeptides Targeted in Autoimmune Diseases
Wataru Honda, Shuichi Kawashima, Minoru Kanehisa
GIW 2005 Poster Abstract: P069 [PDF file]
Genome-Wide Protein-Protein Interaction Network Prediction for Oryza sativa
Chen-Yu Chen, Chen-hsiung Chan, Sheng-An Lee, Cheng-Yan Kao
GIW 2005 Poster Abstract: P070 [PDF file]
Dependence of the Accuracy of Protein Secondary Structure Prediction on Long-Range Interactions
Daisuke Kihara
GIW 2005 Poster Abstract: P071 [PDF file]
Fast Protein-Protein Docking Algorithm Using Pre-Identified Binding Site Patches
Daisuke Kihara, Sael Lee, Karthik Ramani, Srinivasan Turuvekere, Manish Agrawal, Bin Li
GIW 2005 Poster Abstract: P072 [PDF file]
Ligand Binding Sites Prediction with the Visibility Criteria
Bin Li, Srinivasan Turuvekere, Manish Agrawal, Karthik Ramani, Daisuke Kihara
GIW 2005 Poster Abstract: P073 [PDF file]
A Weighting Profile Method for Protein-RNA Interaction Prediction
Euna Jeong, Satoru Miyano
GIW 2005 Poster Abstract: P074 [PDF file]
Protein-Protein Docking by the Benzene Clusters Fitting, Grid Scoring and the Pairwise Interaction Potential in CAPRI Rounds 3-5
Genki Terashi, Mayuko Takeda-Shitaka, Daisuke Takaya, Katsuichiro Komatsu, Hideaki Umeyama
GIW 2005 Poster Abstract: P075 [PDF file]
A Software for a New Methodology of Kinetics Analyses of Protein-Ligand Interaction
Masaki Yamamura, Takuma Shiraki, Takashi S.Kodama, Tatsuo Nakagawa, Natsuhiro Ichinose, Osamu Gotoh
GIW 2005 Poster Abstract: P076 [PDF file]
Identifying Cooperative Transcriptional Regulations Using Protein-Protein Interactions
Nobuyoshi Nagamine, Yuji Kawada, Yasubumi Sakakibara
GIW 2005 Poster Abstract: P077 [PDF file]
WoLF PSORT: Protein Localization Prediction Software
Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai
GIW 2005 Poster Abstract: P078 [PDF file]
Online Discrimination of β-Barrel Membrane Proteins from Amino Acid Sequence
M. Michael Gromiha, Makiko Suwa
GIW 2005 Poster Abstract: P079 [PDF file]
Comparison of Prediction Methods for Protein-Protein Interactions Using Co-Evolutionary Information
Tetsuya Sato, Yoshihiro Yamanishi, Hisako Ichihara, Minoru Kanehisa, Hiroyuki Toh
GIW 2005 Poster Abstract: P080 [PDF file]
Characterization of Secondary Structure Elements in Riboswitches
Ai Muto, Masahiro Hattori, Minoru Kanehisa
GIW 2005 Poster Abstract: P081 [PDF file]
Identification of Clinical Data Effect on Aplastic Anemia Treatment Using Multilayer Fuzzy Neural Network
Hironori Mutoh, Seiji Kojima, Hiroyuki Honda
GIW 2005 Poster Abstract: P082 [PDF file]
Reliability Index for 2-class Classification in Diagnosis of Disease: RIbin
Masahiro Nakatochi, Hiro Takahashi, Hiroyuki Honda
GIW 2005 Poster Abstract: P083 [PDF file]
Automatic Assignment of Full EC Numbers Based on Structural Changes of Chemical Compounds
Nobuya Tanaka, Tadashi Kadowaki, Susumu Goto, Minoru Kanehisa
GIW 2005 Poster Abstract: P084 [PDF file]
Chemical Genomic Sutdy of Endocrine Disrupting Chemicals in Metabolic Pathways
Tadashi Kadowaki, Tetsuya Adachi, Shinobu Okamoto, Nobuya Tanaka, Koichiro Tonomura, Gozoh Tsujimoto, Minoru Kanehisa
GIW 2005 Poster Abstract: P085 [PDF file]
Development of a Method for Predicting Biological Functions of Compounds Using Support Vector Machine
Tomohiro Sato, Yo Matsuo, Shigeyuki Yokoyama
GIW 2005 Poster Abstract: P086 [PDF file]
Modeling Tertiary Structure of Complementarity Determining Region of Antibodies
Toru Hosokawa, Kenta Nakai, Kengo Kinoshita
GIW 2005 Poster Abstract: P087 [PDF file]
A New Perspective on an Old Tool: Extending the Coverage of Sequence Similarity-Based Function Prediction with PFP
Troy Bartholomew Hawkins, Stanislav Luban, Daisuke Kihara
GIW 2005 Poster Abstract: P088 [PDF file]
AR(n) Models Applied in Estimation of Genetic Covariance Functions for QTL Mapping
Yini Cui, Runqing Yang, Shaoqing Huang
GIW 2005 Poster Abstract: P089 [PDF file]
Direct Physical Mapping Method Based on Scanning Probe Microscope
Yoshitaka Suetsugu, Kazumi Tsukamoto, Seigo Kuwazaki, Takeshi Yamauchi, Tomoyuki Yoshino, Motoharu Shichiri, Hirokazu Takahashi, Junko Narukawa, Shigeru Sugiyama, Kazuei Mita, Toshio Ohtani, Kimiko Yamamoto
GIW 2005 Poster Abstract: P090 [PDF file]
Comprehensive Promoter Analyses Using a Database of Transcription Start Sites
Riu Yamashita, Katsuki Tsuritani, Yutaka Suzuki, Hiroyuki Wakaguri, Sumio Sugano, Kenta Nakai
GIW 2005 Poster Abstract: P091 [PDF file]
A Genome-Wide Analysis of p53 Binding Sites Using Tiling Arrays
Shuichi Tsutsumi, Kiyofumi Kaneshiro, Shingo Tsuji, Hiroyuki Aburatani
GIW 2005 Poster Abstract: P092 [PDF file]
Discriminative Detection of Transcription Factor Binding Sites from Location Data
Yuji Kawada, Yasubumi Sakakibara
GIW 2005 Poster Abstract: P093 [PDF file]
PPMuSA: PROSITE-Pattern Matcher Using Suffix Array
Aki Hasegawa, Akihiko Konagaya
GIW 2005 Poster Abstract: P094 [PDF file]
Sequence-Based Analyses of Biosynthesis Rate Limiting Factors in Wheat Germ Cell-Free System
Naoya Fujita, Motoaki Seki, Kazuo Shinozaki, Kengo Kinoshita, Tatsuya Sawasaki, Yaeta Endo, Kenta Nakai
GIW 2005 Poster Abstract: P095 [PDF file]
Machine Learning Prediction of Amino Acid Sequence Characterization in Protein N-Myristoylation
Ryo Okada, Chigusa Miyakawa, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano
GIW 2005 Poster Abstract: P096 [PDF file]
Prediction of Long Disorder Region Using Two-Step SVM
Shuichi Hirose, Kana Shimizu, Satoru Kanai, Tamotsu Noguchi
GIW 2005 Poster Abstract: P097 [PDF file]
Large-Scale Analysis of Expressed Pseudogenes in Higher Eucaryotes
Hayataro Kochi, Rintaro Saito, Masaru Tomita
GIW 2005 Poster Abstract: P098 [PDF file]
Development of Translational Signal Database and Analysis of Sequence-Activity Relationship
Hayato Nishida, Alex. Kochetov, Akinori Sarai
GIW 2005 Poster Abstract: P099 [PDF file]
Genome Wide Analysis of the Alternative Splicing Based on Full-Length cDNA Data
Hiroki Sakai, Yutaka Suzuki, Katsuhisa Horimoto, Sumio Sugano, Minoru Kanehisa
GIW 2005 Poster Abstract: P100 [PDF file]
An Unsupervised Diplotype Clustering Method to Improve Race-Based Medicine
Junji Tanaka, Masato Inoue, Naoyuki Kamatani
GIW 2005 Poster Abstract: P101 [PDF file]
Toward Full-Automatic Derivation of P450 Gene Database --Performance of Familywise Applied to Plant Genomes--
Makoto Hirosawa, Daisuke Shibata, Osamu Gotoh
GIW 2005 Poster Abstract: P102 [PDF file]
Discovery of Protein Coding Genes Through Chromosome-to-Chromosome Sequence Comparison
Osamu Gotoh, Masao Morita, Nobuyuki Ichiyoshi, Tetsushi Yada
GIW 2005 Poster Abstract: P103 [PDF file]
Development of a Primer Design Program for Multiplex PCR
Seok Jong Yu, Yong Seong Cho, Byeong-Jin Jeong, Hyeon S. Son, Sang Joo Lee
GIW 2005 Poster Abstract: P104 [PDF file]
Watermark Embedding Techniques for DNA Sequences Using Codon Usage Bias Features
Toshio Modegi
GIW 2005 Poster Abstract: P105 [PDF file]
Genome Analize by Using Spherical SOM
Yasaburo Matsuura, Toshimichi Ikemura, Takashi Abe, Heizo Tokutaka, Masaaki Ohkita
GIW 2005 Poster Abstract: P106 [PDF file]
The Identification of a Cancer Cell Gene by Using SOM
Yasaburo Matsuura, Tuoya, Masaharu Seno, Heizo Tokutaka, Masaaki Ohkita
GIW 2005 Poster Abstract: P107 [PDF file]
Bioprocess Optimal Control Simulator Design and Development
Jebrou Youssef, Masahiro Okamoto
GIW 2005 Poster Abstract: P108 [PDF file]
A System-Biological Approach to Interferon-Based Therapies
Kazunori Miyazaki, Satoshi Itoh
GIW 2005 Poster Abstract: P109 [PDF file]
BAAQ: A Platform for Integrating Bioinformatics Tools and Sharing Knowledge
Jitender Jit Singh Cheema, Xiujun Gong, Kensuke Nakamura, Kei Yura, Nobuhiro Go
GIW 2005 Poster Abstract: P110 [PDF file]
Simulation of Light-Induced Phase Response in Mammals with Hybrid Function Petri Net
Yumi Harada, Natsumi Mito, Yasushi Fujii, Hiroshi Matsuno, Satoru Miyano, Sin-Ichi T. Inouye
GIW 2005 Poster Abstract: P111 [PDF file]
Expanding Large Scale Signal Transduction Networks
Kosuke Hashimoto, Bernd Binder, Minoru Kanehisa, Oliver Ebenhoeh, Reinhart Heinrich
GIW 2005 Poster Abstract: P112 [PDF file]
Comprehensive Detection of TM Protein Genes which might be Associated with Febrile Seizure
Yasuhito Inoue, Kazuaki Kanai, Satoshi Mizuta, Motohiro Okada, Sunao Kaneko, Toshio Shimizu
GIW 2005 Poster Abstract: P113 [PDF file]
CADLIVE: Computer-Aided Design of Living Systems
Hiroyuki Kurata, Marie Kajiwara, Yuki Shimokawa,
GIW 2005 Poster Abstract: P114 [PDF file]
Petri Net Based Modeling of Signaling Pathways Including Inhibitory Function
Chen Li, Shunichi Suzuki, Yoko Takeuchi, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano
GIW 2005 Poster Abstract: P115 [PDF file]
Interlocked Feedback Is Not the Best Choice for PER Oscillators
Fumitaka Ohnishi, Hiroyuki Kurata
GIW 2005 Poster Abstract: P116 [PDF file]
Symbolic-Numeric Estimation of Kinetic Parameters in Biochemical Pathways by Quantifier Elimination
Shigeo Orii, Hirokazu Anai, Katsuhisa Horimoto
GIW 2005 Poster Abstract: P117 [PDF file]
Developing Cardiac Cell Models (Kyoto model) on em simBio
Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma
GIW 2005 Poster Abstract: P118 [PDF file]
A Modeling Tool for E-CELL System: Power-Law Model Generator Based on Time-Course Data
Shigeru Sato, Yasuhiro Naito, Masaru Tomita
GIW 2005 Poster Abstract: P119 [PDF file]
Kinetic Modeling of Metabolic Pathways in Acetone-Butanol-Ethanol (ABE) Fermentation Using Novel Simulator
Hideaki Shinto, Yukihiro Tashiro, Mayu Yamashita, Genta Kobayashi, Tatsuya Sekiguchi, Taizo Hanai, Masahiro Okamoto, Kenji Sonomoto
GIW 2005 Poster Abstract: P120 [PDF file]
Theoretical Research on Dynamics of the Genetic Toggle Switch
Tomohiro Ushikubo, Wataru Inoue, Mitsumasa Yoda, Masaki Sasai
GIW 2005 Poster Abstract: P121 [PDF file]
Optimization of a Large-Scale Dynamic Model of the Cell Cycle Network Using Multi Objective GA
Shunsuke Yamamichi, Hiroyuki Kurata
GIW 2005 Poster Abstract: P122 [PDF file]
Module Decomposition and Integration Optimizes Gene Regulatory and Metabolic Networks
Keisuke Yoshida, Hiroyuki Kurata
GIW 2005 Poster Abstract: P123 [PDF file]
Structure-Based Analysis of Cooperativity in Protain-DNA Recognition
Akinori Sarai, Satoshi Fujii, Marcos J. Araúzo-Bravo, Hidetoshi Kono
GIW 2005 Poster Abstract: P124 [PDF file]
Indirect Readout in Drug-DNA Complexes
Marcos J. Araúzo-Bravo, Akinori Sarai
GIW 2005 Poster Abstract: P125 [PDF file]
Prediction of Pseudoknotted RNA Structure by a Structural Alignment Using Genetic Algorithm
Akito Taneda
GIW 2005 Poster Abstract: P126 [PDF file]
A New Method of Computing Ligand-Based Pharmacophore Models for Flexible Chemical Compounds
Atsuko Yamaguchi, Hiroyasu Shimada, Ken Horiuchi, Tetsuo Nishikawa
GIW 2005 Poster Abstract: P127 [PDF file]
Large Scale Protein Side-Chain Packing Based on Maximum Edge-Weight Clique Finding Algorithms
Dukka Bahadur K. C., J. B. Brown, Etsuji Tomita, Jun'ichi Suzuki, Tatsuya Akutsu
GIW 2005 Poster Abstract: P128 [PDF file]
Thermal Adaptations of DNA-Binding Proteins
Masashi Fujita, Minoru Kanehisa
GIW 2005 Poster Abstract: P129 [PDF file]
CCG-Based RNA Secondary Structure Prediction
Hee-Jin Lee, Jong C. Park
GIW 2005 Poster Abstract: P130 [PDF file]
Comparisons between Dynamic Properties of Homologous Protein Structure in ProMode (Database of Normal Mode Analyses on Proteins)
Hiroshi Wako, Motohiro Otsuka, Yuhki Tomizawa, Masaki Kato, Shigeru Endo
GIW 2005 Poster Abstract: P131 [PDF file]
Genome-Wide Protein Structure Characterization of Mycoplasma genitalium
Jun-Wei Hsu, Chen-hsiung Chan, Cheng-Yan Kao
GIW 2005 Poster Abstract: P132 [PDF file]
High Quality Protein Structure Prediction Server, SKE-FAMSD
Kazuhiko Kanou, Mitsuo Iwadate, Genki Terashi, Daisuke Takaya, Mayuko Takeda-Shitaka, Hideaki Umeyama
GIW 2005 Poster Abstract: P133 [PDF file]
Computational Analysis of microRNA Recognition Site
Keishin Nishida, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
GIW 2005 Poster Abstract: P134 [PDF file]
RNA Structural Alignment with Conditional Random Fields
Kengo Sato, Yasubumi Sakakibara
GIW 2005 Poster Abstract: P135 [PDF file]
Predicting Non-Coding RNAs Based on Free Energy Minimization by Means of Genetic Algorithms
Kouichi Okada, Hitoshi Iba
GIW 2005 Poster Abstract: P136 [PDF file]
Sequence and Structural Analysis of Ligand Bindig Sites in Membrane Proteins
M. Xavier Suresh, M. Michael Gromiha, M. Suwa
GIW 2005 Poster Abstract: P137 [PDF file]
Homology Modeling in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction) Using CHIMERA and FAMS
Mayuko Takeda-Shitaka, Genki Terashi, Daisuke Takaya, Kazuhiko Kanou, Mitsuo Iwadate, Hideaki Umeyama
GIW 2005 Poster Abstract: P138 [PDF file]
Pareto-Optimal Motif for Predicting Peptide Binders
Menaka Rajapakse, Bertil Schmidt, Vladimir Brusic
GIW 2005 Poster Abstract: P139 [PDF file]
Fold Recognition and Flexibility of the HIV-1 V3-Loop Crown Structure During the Course of Adaptation to a Host
Teruaki Watabe, Hirohisa Kishino, Yasuhiro Kitazoe
GIW 2005 Poster Abstract: P140 [PDF file]
An Alignment Algorithm by Matching Fixed-Length Stem Fragments for Comparing RNA Sequences
Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai
GIW 2005 Poster Abstract: P141 [PDF file]
Non-Arbitrary Judgment for Periodicity of Time-Series Data by an Information Criterion and Discrete Fourier Transform
Daisuke Tominaga, Paul Horton
GIW 2005 Poster Abstract: P142 [PDF file]
Searching for Similar Gene Expression Profiles Across Platforms
Wataru Fujibuchi, Larisa Kiseleva, Paul Horton
GIW 2005 Poster Abstract: P143 [PDF file]
Phenotype MicroArray Analysis of Escherichia coli K-12: An in silico Approach
Hiroaki Gobara, Tomoya Baba, Md. Altaf-Ul-Amin, Masanori Arita, Ken Kurokawa, Shigehiko Kanaya, Hirotada Mori
GIW 2005 Poster Abstract: P144 [PDF file]
Inference Engine for Gene Expression by Bayesian Network
Hirofumi Suzaki, Akinori Sarai
GIW 2005 Poster Abstract: P145 [PDF file]
A Hypothesis of Intrinsic Vital Volatility in Gene Expression
Hiroto Yoshii, Hideki Takayasu
GIW 2005 Poster Abstract: P146 [PDF file]
Gene Duplication Models and Reconstruction of Network Evolution
Juris Viksna, David Gilbert, Dace Ruklisa
GIW 2005 Poster Abstract: P147 [PDF file]
Efficient Method for Extracting Common Core Binomial Genetic Interactions
Masahiko Nakatsui, Takanori Ueda, Isao Ono, Masahiro Okamoto
GIW 2005 Poster Abstract: P148 [PDF file]
Structural and Functional Analysis of Transiently Expressed Metabolic Networks
Mina Oh, Wolfram Liebermeister, Minoru Kanehisa, Reinhart Heinrich, Oliver Ebenhöh
GIW 2005 Poster Abstract: P149 [PDF file]
Estimation of Gene Regulatory Network Using Stochastic Differential Equation Model
Shinya Nabatame, Hitoshi Iba
GIW 2005 Poster Abstract: P150 [PDF file]
Comparative Study of State Space Models for Time-Course Gene Expression Data of Yeast
Rui Yamaguchi, Tomoyuki Higuchi
GIW 2005 Poster Abstract: P151 [PDF file]
On Conditions for Morphogenetic Diversity of Multicellular Organisms
Hiroshi Yoshida, Hirokazu Anai, Shigeo Orii, Katsuhisa Horimoto
GIW 2005 Poster Abstract: P152 [PDF file]
Orchestration of Gene Systems Inferred from Expression Profiles in Hepatocellular Carcinoma
Katsuhisa Horimoto, Sachiyo Aburatani, Shigeru Saito, Masao Honda, Shu-ichi Kaneko
GIW 2005 Poster Abstract: P153 [PDF file]
Causal Inference of Gene Systems Network in Hepatocellular Carcinoma Progression by Graphical Chain Model
Masao Honda, Shu-ichi Kaneko, Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto
GIW 2005 Poster Abstract: P154 [PDF file]
Evaluation of Inference Performance by ASIAN in Transcriptional Regulatory Relationships
Ritsuko Onuki, Sachiyo Aburatani, Katsuhisa Horimoto, Minoru Kanehisa
GIW 2005 Poster Abstract: P155 [PDF file]
Inference of Cell Cycle-Regulatory Systems Network in Saccharomyces cerevisiae
Sachiyo Aburatani, Shigeru Saito, Katsuhisa Horimoto
GIW 2005 Poster Abstract: P156 [PDF file]
Inferring Module-Based Gene Networks from Time Course Microarray Data by State Space Models
Osamu Hirose, Ryo Yoshida, Seiya Imoto, Satoru Miyano
GIW 2005 Poster Abstract: P157 [PDF file]
Identification of Drug Active Pathways Based on Gene Networks Estimated by Bayesian Networks and Gene Expression Data
Yoshinori Tamada, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
GIW 2005 Poster Abstract: P158 [PDF file]
Scaling-Law and Fluctuation in Gene Expression
Jose C. Nacher, Tomoshiro Ochiai, Tatsuya Akutsu
GIW 2005 Poster Abstract: P159 [PDF file]
Stochastic Fluctuation and Relaxation in a Genetic Feedback Loop
Yurie Okabe, Yu Yagi, Masaki Sasai
GIW 2005 Poster Abstract: P160 [PDF file]
Effects of Disease-Associated Mutations and SNP on Protein Structures
Akiyuki Koga, Hidetoshi Kono, Akinori Sarai
GIW 2005 Poster Abstract: P161 [PDF file]
Particle Simulation Approach for Cellular Level Spatio-Temporal Properties
Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Ryo Umetsu, Tomoyuki Yamamoto, Akihiko Konagaya
GIW 2005 Poster Abstract: P162 [PDF file]
Theoretical Analysis of Metabolic Networks: Attempt to Express Topological Position of Individual Atoms in a Given Network
Jun Ohta
GIW 2005 Poster Abstract: P163 [PDF file]
Objective Distances for Transcriptome Analyses According to the Thermodynamic Model
Tomokazu Konishi
GIW 2005 Poster Abstract: P164 [PDF file]
Elucidation of Xenobiotic Responsive and NR Mediated Pathways/Networks
Tsuguchika Kaminuma, Masumi Yukawa, Naomi Komiyama, Tatsuya Nakano, Kotoko Nakata, Yoshitomo Tanaka, Hiroshi Tanaka
GIW 2005 Poster Abstract: P165 [PDF file]
Improvement of ASIAN Web Site
Kousuke Goto, Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto
GIW 2005 Poster Abstract: P166 [PDF file]
Characteristic Chemical Transformation Patterns in Biodegradation Pathways
Mina Oh, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
GIW 2005 Poster Abstract: P167 [PDF file]
