Systematic Analysis of Structure-Stability Relationship for Proteins and Mutants
Noboru Furukawa, Yuko Takeno, Goran Neshich, Akinori Sarai

Hierarchy of Metabolic Compounds Based on Their Synthesizing Capacity
Thomas Handorf, Oliver Ebenhöh, Daniel Kahn, Reinhart Heinrich

IBTS: An Extensible System for Integration of Bioinformatics Tools Allowing Cluster Computing
Youngmahn Hahn, Yongseong Cho, Sang Joo Lee

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

KAAS: KEGG Automatic Annotation Server
Yuki Moriya, Masumi Itoh, Sujiro Okuda, Minoru Kanehisa

Mining Implicit Biological Realted Entities from Literature Using a Probabilistic Model
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka

Constraints Based Dynamic Protein Interaction Network
Dong-Soo Han, Suk-Hoon Jung, Woo-Hyuk Jang, Choon-Ho Lee

New Features of MutationView: Implementation of Various Protein-Oriented Tools to Find out the Relation between Protein Function and Dseases
Masafumi Ohtsubo, Takashi Kawamura, Susumu Mitsuyama, Nobuyoshi Shimizu, Shinsei Minoshima

KEGG-Based Pathway Visualization Tool for Complex Omics Data
Nobuaki Kono, Kazuharu Arakawa, Yohei Yamada, Hirotada Mori, Masaru Tomita

Visualization of Gene Database on WEB Using Self Organizing Maps
Yasuhiko Miyazaki, Hiroshi Dozono, Hisao Tokushima, Yoshio Noguchi

Evolutionary Identifications of Functional Modules in Yeast Protein Interaction Network
Soichi Ogishima, Yasuhiro Suzuki, Takashi Hase, So Nakagawa, Hiroshi Tanaka

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

Structural Annotation Viewer and Database for Splice-Variant Human cDNA Sequence
Tetsuo Nishikawa, Kouichi Kimura, Jun-ichi Yamamoto, Ai Wakamatsu, Hiroshi Makita, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai

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

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

BioTextLinker: Dynamic Informative Link Annotation for Biological Text over Heterogeneous Databases
Hodong Lee, Jong C. Park

MiDB: Mitochondrial Proteomics Database in Human Heart
Hyun Joo, Taeho Kim, Jae Boum Youm, Nari Kim, Jin Han

FAMSBASE of Human, Rat and Mouse Genomes with Model Quality Estimation
Mitsuo Iwadate, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Hideaki Umeyama

Framework Approach for a Search Platform on Biological Data
Seok Jong Yu, Dan Bi Kim, Inae Hur, Sang Joo Lee

PSE: A Tool for Browsing a Large Amount of PubMed Abstracts with Gene Names and Common Words as the Keywords
Takashi Yoneya

RPAIR: A Database of Chemical Transformation Patterns in Enzymatic Reactions
Takuji Yamada, Masahiro Hattori, Min A Oh, Susumu Goto, Minoru Kanehisa

A Resource Discovery Service for Bioinformatics Applications in a Grid-Based Environment
Xiujun Gong, Jitender Jit Singh Cheema, Kensuke Nakamura, Kei Yura, Nobuhiro Go

Gene Annotation Using Proteomic Data
Yoko Ishino, Hisaaki Taniguchi

A Database for Comparative Analysis of Tunicate Promoter Sequences
Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

An Existence of Cooperative (Clustered) Genes in ColiphageΦk
Eisei Takushi, Miyako Kawachi

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

Finding Small and Resistance-Predictable Feature Sets for Bacterium Classification by Multi-Objective Optimization
Hiroshi Yamakawa, Yoshio Nakao, Takahisa Suzuki, Yumiko Sanbongi, Takashi Ida

Sensitizing GO Tools Using Multiple Ratio-Cutoffs for Gene Selection
Kenichi Hirotani, Yoichi Yamada, Miyuki Onda, Ken-ichiro Muramoto, Kenji Satou, Takashi Ito

Cell-Distance Networks: A Clue for Understanding of Cell Diversity
Larisa Kiseleva, Paul Horton, Wataru Fujibuchi

How Much We Know about Soluble Domains Existing in Loop Regions of Transmembrane Proteins ?
Syuuichi Yoshida, Masafumi Arai, Takuhiro Nishio, Toshio Shimizu

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

Inferring Protein Interaction Network by Boosting Algorithm
Yong Wang, Feng Bao, Jiadong Zhang, Luonan Chen

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

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

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

Knowledge Discovery Using Cross Database Search
Asako Koike, Toshihisa Takagi

Ontology Based Petri Net Modeling of Signaling Networks
Takako Takai-Igarashi

Discovering Reliable Protein Interactions Using Bayesian Networks
Thanh Phuong Nguyen, Tu Bao Ho, Ngoc Binh Nguyen

Cluster Analysis of Neutrophilic Differentiation by Using Fuzzy K-Means
Akitsugu Suga, Kazumi Hakamada, Chinatsu Arima, Masahiro Okamoto, Hitoshi Ichikawa, Taizo Hanai

Validity Index for Fuzzy K-Means Clustering Using the Gap Statistic Method
Chinatsu Arima, Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai

Validation of Mathematical Model Based Clustering by Using Time-Course Data.
Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai

Improvement in the Accuracy of Gene Prediction in Rice cDNA Sequences
Fusano Todokoro, Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima, Tadashi Imanishi, Takashi Gojobori

Co-Expression Analysis Tool for Large Gene Expression Datasets
Hajime Harada, Natalia Polouliakh, Wataru Fujibuchi, Paul Horton

New Reliable Cancer Diagnosis Method Using Boosting and Projective Adaptive Resonance Theory
Hiro Takahashi, Yasuyuki Murase, Hiroyuki Honda

Classification Method for Prediction of Multifactorial Disease Development by Using Genetic and Environmental Factors
Yasuyuki Tomita, Mitsuhiro Yokota, Hiroyuki Honda

Ranking Metabolic Paths with Expression Similarities
Ichigaku Takigawa, Hiroshi Mamitsuka

Classifying Microarray Data Using Pairwise Similarity between Gene Profiles
Raymond Wan, Åsa M. Wheelock, Matthew J. Bartosiewicz, Hiroshi Mamitsuka

A Selection Criterion for Robust Classifier: Cancer Prognosis with Microarray Gene Expression
Ikumi Suzuki, Shigeyuki Oba, Shin Ishii

Memory-Efficient Clustering Algorithms for Microarray Gene Expression Data
Kazuyuki Numata, Hideo Bannai, Yoshinori Tamada, Michiel de Hoon, Seiya Imoto, Satoru Miyano

Clustering Gene Expression Data with Stepwise Data Envelopment Analysis
Masako Hoshino, Hiroshige Inazumi

Effective Nearest Neighbor Methods for Multiclass Cancer Classification Using Microarray Data
Satoshi Niijima, Satoru Kuhara

Algorithm for Predicting Co-Expression Genes by Improvement of Path Consistency Algorithm
Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto

A New Method for Analyzing Large-Scale Microarray Data Using Biological Knowledge
Shingo Tsuji, Kouji Nakayama, Masaru Sekijima, Shigeo Ihara, Hiroyuki Aburatani

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

Classification of Cancer Data with Genetic Programming
Topon Kumar Paul, Hitoshi Iba

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 Matuura, Heizo Tokutaka, Masaharu Seno

Detection of Cluster Boundary in Microarray Data by Reference to MIPS Functional Catalogue Database
Yoshifumi Okada, Takehiko Sahara, Satoru Ohgiya, Tomomasa Nagashima

Multiplicative Decomposition of Time- and Dose-Dependent Gene Expression Changes
Yukitaka Tani, Takeshi Kamimura, Takeshi Nagashima, Kaori Ide, Mariko Hatakeyama, Hidetoshi Shimodaira

Species-Specific Variation of Alternative Splicing and Transcriptional Initiation in Six Eukaryotes
Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh

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

Comparative Sequence Analysis of Human and Promoter Regions
Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

Comprehensive Analysis of Triplet Repeats in Vertebrate Genomes
Shigeo Okada, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

A Maximum Likelihood Method for Inference of Spliceosomal Intron Evolution
Hung Dinh Nguyen, Maki Yoshihama, Naoya Kenmochi

Comparative Genomic Analysis of Transcription Regulation Elements in Higher Eukaryotes
Natalia Polouliakh, Wataru Fujibuchi, Hajime Harada, Tohru Natsume, Paul Horton

Comparative Analysis of Autocorrelations of Electric Charges in Amino Acid Sequences of S.cerevisiae and E.coli
Runcong Ke, Shigeki Mitaku

Seeking Genomic Duplication in Prokaryotic Genomes by Equivalent Tandem Repeats Distributions
Satoshi Mizuta, Michimasa Koshino, Toshio Shimizu

Statistical Characterization of Transcription Start Sites in Plant Genomes
Shigeo Fijimori, Takanori Washio, Masaru Tomita

A Scale-Free Prior over Graph Structures for Bayesian Inference of Gene Networks
Takeshi Kamimura, Hidetoshi Shimodaira

Physicochemical and Structural Characterization of Nonapeptides Targeted in Autoimmune Diseases
Wataru Honda, Shuichi Kawashima, Minoru Kanehisa

Genome-Wide Protein-Protein Interaction Network Prediction for Oryza Sativa
Chen-Yu Chen, Chen-hsiung Chan, Sheng-An Lee, Cheng-Yan Kao

Dependence of the Accuracy of Protein Secondary Structure Prediction on Long-Range Interactions
Daisuke Kihara

Fast Protein-Protein Docking Algorithm Using Pre-Identified Binding Site Patches
Daisuke Kihara, Sael Lee, Karthik Ramani, Srinivasan Turuvekere, Manish Agrawal, Bin Li

Ligand Binding Sites Prediction with the Visibility Criteria
Bin Li, Srinivasan Turuvekere, Manish Agrawal, Karthik Ramani, Daisuke Kihara

A Weighting Profile Method for Protein-RNA Interaction Prediction
Euna Jeong, Satoru Miyano

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

A Software for a New Methodology of Kinetics Analyses of Protein-Ligand Interaction
Masaki Yamamura, Takuma Shiraki, Takashi Kodama, Tatsuo Nakagawa, Natsuhiro Ichinose, Osasmu Gotoh

Identifying Cooperative Transcriptional Regulations Using Protein-Protein Interactions
Nobuyoshi Nagamine, Yuji Kawada, Yasubumi Sakakibara

WoLF PSORT: Protein Localization Prediction Software
Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai

Online Discrimination of β-Barrel Membrane Proteins from Amino Acid Sequence
Michael Gromiha, Makiko Suwa

Comparison of Prediction Methods for Protein-Protein Interactions Using Co-Evolutionary Information
Tetsuya Sato, Yoshihiro Yamanishi, Hisako Ichihara, Minoru Kanehisa, Hiroyuki Toh

Characterization of Secondary Structure Elements in Riboswitches
Ai Muto, Masahiro Hattori, Minoru Kanehisa

Identification of Clinical Data Effect on Aplastic Anemia Treatment Using Multilayer Fuzzy Neural Network
Hironori Mutoh, Seiji Kojima, Hiroyuki Honda

Reliability Index for 2-class Classification in Diagnosis of Disease: Ribin
Masahiro Nakatochi, Hiro Takahashi, Hiroyuki Honda

Automatic Assignment of Full EC Numbers Based on Structural Changes of Chemical Compounds
Nobuya Tanaka, Tadashi Kadowaki, Susumu Goto, Minoru Kanehisa

Chemical Genomic Sutdy of Endocrine Disrupting Chemicals in Metabolic Pathways
Tadashi Kadowaki, Tetsuya Adachi, Shinobu Okamoto, Nobuya Tanaka, Koichiro Tonomura, Gozoh Tsujimoto, Minoru Kanehisa

Development of a Method for Predicting Biological Functions of Compounds Using Support Vector Machine
Tomohiro Sato, Yo Matsuo, Shigeyuki Yokoyama

Modeling Tertiary Structure of Complementarity Determining Region of Antibodies
Toru Hosokawa, Kenta Nakai, Kengo Kinoshita

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

AR(n) Models Applied in Estimation of Genetic Covariance Functions for QTL Mapping
Yini Cui, Runqing Yang, Shaoqing Huang

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, Toshio Ohtani, Kimiko Yamamoto

Comprehensive Promoter Analyses Using a Database of Transcription Start Sites
Riu Yamashita, Katsuki Tsuritani, Yutaka Suzuki, Hiroyuki Wakaguri, Sumio Sugano, Kenta Nakai

A Genome-Wide Analysis of p53 Binding Sites Using Tiling Arrays
Shuichi Tsutsumi, Kiyofumi Kaneshiro, Shingo Tsuji, Hiroyuki Aburatani

Discriminative Detection of Transcription Factor Binding Sites from Location Data
Yuji Kawada, Yasubumi Sakakibara

PPMuSA: PROSITE-Pattern Matcher Using Suffix Array
Aki Hasegawa, Akihiko Konagaya

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

Machine Learning Prediction of Amino Acid Sequence Characterization in Protein N-Myristoylation
Ryo Okada, Chigusa Miyakawa, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano

Prediction of Long Disorder Region Using Two-Step SVM
Shuichi Hirose, Kana Shimizu, Satoru Kanai, Tamotsu Noguchi

Large-Scale Analysis of Expressed Pseudogenes in Higher Eucaryotes
Hayataro Kochi, Rintaro Saito, Masaru Tomita

Development of Translational Signal Database and Analysis of Sequence-Activity Relationship
Hayato Nishida, Alex Kochetov, Akinori Sarai

Genome Wide Analysis of the Alternative Splicing Based on Full-Length cDNA Data
Hiroki Sakai, Yutaka Suzuki, Katsuhisa Horimoto, Sumio Sugano, Minoru Kanehisa

An Unsupervised Diplotype Clustering Method to Improve Race-Based Medicine
Junji Tanaka, Masato Inoue, Naoyuki Kamatani

Toward Full-Automatic Derivation of P450 Gene Database --Performance of Familywise Applied to Plant Genomes--
Makoto Hirosawa, Daisuke Shibata, Osamu Gotoh

Discovery of Protein Coding Genes Through Chromosome-to-Chromosome Sequence Comparison
Osamu Gotoh, Masao Morita, Nobuyuki Ichiyoshi, Tetsushi Yada

Development of a Primer Design Program for Multiplex PCR
Seok Jong Yu, Yong Seong Cho, Byeong-Jin Jeong, Hyeon S. Son, Sang Joo Lee

Watermark Embedding Techniques for DNA Sequences Using Codon Usage Bias Features
Toshio Modegi

Genome Analize by Using Spherical SOM
Yasaburo Matsuura, Toshimichi Ikemura, Takashi Abe, Heizo Tokutaka, Masaaki Ohkita

The Identification of a Cancer Cell Gene by Using SOM
Yasaburo Matsuura, Tuoya, Masaharu Seno, Heizo Tokutaka, Masaaki Ohkita

Bioprocess Optimal Control Simulator Design and Development
Youssef Jebrou, Masahiro Okamoto

A System-Biological Approach to Interferon-Based Therapies
Kazunori Miyazaki, Satoshi Itoh

BAAQ: A Platform for Integrating Bioinformatics Tools and Sharing Knowledge
Jitender Jit Singh Cheema, Xiujun Gong, Kensuke Nakamura, Kei Yura, Nobuhiro Go

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 Inouye

Expanding Large Scale Signal Transduction Networks
Kosuke Hashimoto, Bernd Binder, Minoru Kanehisa, Oliver Ebenhöh, Reinhart Heinrich

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

CADLIVE: Computer-Aided Design of Living Systems
Hiroyuki Kurata, Marie Kajiwara, Yuki Shimokawa

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

Interlocked Feedback is not the Best Choice for PER Oscillators
Fumitaka Ohnishi, Hiroyuki Kurata

Symbolic-Numeric Estimation of Kinetic Parameters in Biochemical Pathways by Quantifier Elimination
Shigeo Orii, Hirokazu Anai, Katsuhisa Horimoto

Developing Cardiac Cell Models (Kyoto model) on simBio
Nobuaki Sarai, Satoshi Matsuoka, Akinori Noma

A Modeling Tool for E-CELL System: Power-Law Model Generator Based on Time-Course Data
Shigeru Sato, Yasuhiro Naito, Masaru Tomita

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

Theoretical Research on Dynamics of the Genetic Toggle Switch
Tomohiro Ushikubo, Wataru Inoue, Mitsumasa Yoda, Masaki Sasai

Optimization of a Large-Scale Dynamic Model of the Cell Cycle Network Using Multi Objective GA
Shunsuke Yamamichi, Hiroyuki Kurata

Module Decomposition and Integration Optimizes Gene Regulatory and Metabolic Networks
Keisuke Yoshida, Hiroyuki Kurata

Structure-Based Analysis of Cooperativity in Protain-DNA Recognition
Akinori Sarai, Satoshi Fujii, Marcos J. Araúzo-Bravo, Hidetoshi Kono

Indirect Readout in Drug-DNA Complexes
Marcos J. Araúzo-Bravo, Akinori Sarai

Prediction of Pseudoknotted RNA Structure by a Structural Alignment Using Genetic Algorithm
Akito Taneda

A New Method of Computing Ligand-Based Pharmacophore Models for Flexible Chemical Compounds
Atsuko Yamaguchi, Hiroyasu Shimada, Ken Horiuchi, Tetsuo Nishikawa

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

Thermal Adaptations of DNA-Binding Proteins
Masashi Fujita, Minoru Kanehisa

CCG-Based RNA Secondary Structure Prediction
Hee-Jin Lee, Jong C. Park

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

Genome-Wide Protein Structure Characterization of Mycoplasma Genitalium
Jun-Wei Hsu, Chen-hsiung Chan, Cheng-Yan Kao

High Quality Protein Structure Prediction Server, SKE-FAMSD
Kazuhiko Kanou, Mitsuo Iwadate, Genki Terashi, Daisuke Takaya, Mayuko Takeda-Shitaka, Hideaki Umeyama

Computational Analysis of microRNA Recognition Sites
Keishin Nishida, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

RNA Structural Alignment with Conditional Random Fields
Kengo Sato, Yasubumi Sakakibara

Predicting Non-Coding RNAs Based on Free Energy Minimization by Means of Genetic Algorithms
Kouichi Okada, Hitoshi Iba

Sequence and Structural Analysis of Ligand Bindig Sites in Membrane Proteins
M.Xavier Suresh, M.Michael Gromiha, M. Suwa

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

Pareto-Optimal Motif for Predicting Peptide Binders
Menaka Rajapakse, Bertil Schmidt, Vladimir Brusic

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

An Alignment Algorithm by Matching Fixed-Length Stem Fragments for Comparing RNA Sequences
Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai

Non-Arbitrary Judgment for Periodicity of Time-Series Data by an Information Criterion and Discrete Fourier Transform
Daisuke Tominaga, Paul Horton

Searching for Similar Gene Expression Profiles Across Platforms
Wataru Fujibuchi, Larisa Kiseleva, Paul Horton

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

Inference Engine for Gene Expression by Bayesian Network
Hirofumi Suzaki, Akinori Sarai

A Hypothesis of Intrinsic Vital Volatility in Gene Expression
Hiroto Yoshii, Hideki Takayasu

Gene Duplication Models and Reconstruction of Network Evolution
Juris Viksna, David Gilbert, Dace Ruklisa

Efficient Method for Extracting Common Core Binomial Genetic Interactions
Masahiko Nakatsui, Takanori Ueda, Isao Ono, Masahiro Okamoto

Structural and Functional Analysis of Transiently Expressed Metabolic Networks
Mina Oh, Wolfram Liebermeister, Minoru Kanehisa, Reinhart Heinrich, Oliver Ebenhöh

Estimation of Gene Regulatory Network Using Stochastic Differential Equation Model
Shinya Nabatame, Hitoshi Iba

Comparative Study of State Space Models for Time-Course Gene Expression Data of Yeast
Rui Yamaguchi, Tomoyuki Higuchi

On Conditions for Morphogenetic Diversity of Multicellular Organisms
Hiroshi Yoshida, Hirokazu Anai, Shigeo Orii, Katsuhisa Horimoto

Orchestration of Gene Systems Inferred from Expression Profiles in Hepatocellular Carcinoma
Katsuhisa Horimoto, Sachiyo Aburatani, Shigeru Saito, Masao Honda, Shu-ichi Kaneko

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

Evaluation of Inference Performance by ASIAN in Transcriptional Regulatory Relationships
Ritsuko Onuki, Sachiyo Aburatani, Katsuhisa Horimoto, Minoru Kanehisa

Inference of Cell Cycle-Regulatory Systems Network in Saccharomyces cerevisiae
Sachiyo Aburatani, Shigeru Saito, Katsuhisa Horimoto

Inferring Module-Based Gene Networks from Time Course Microarray Data by State Space Models
Osamu Hirose, Ryo Yoshida, Seiya Imoto, Satoru Miyano

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

Scaling-Law and Fluctuation in Gene Expression
Jose C. Nacher, Tomoshiro Ochiai, Tatsuya Akutsu

Stochastic Fluctuation and Relaxation in a Genetic Feedback Loop
Yurie Okabe, Yu Yagi, Masaki Sasai

Effects of Disease-Associated Mutations and SNP on Protein Structures
Akiyuki Koga, Hidetoshi Kono, Akinori Sarai

Particle Simulation Approach for Cellular Level Spatio-Temporal Properties
Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Ryo Umetsu, Tomoyuki Yamamoto, Akihiko Konagaya

Theoretical Analysis of Metabolic Networks: Attempt to Express Topological Position of Individual Atoms in a Given Network
Jun Ohta

Objective Distances for Transcriptome Analyses According to the Thermodynamic Model
Tomokazu Konishi

Elucidation of Xenobiotic Responsive and NR Mediated Pathways/Networks
Tsuguchika Kaminuma, Masumi Yukawa, Naomi Komiyama, Tatsuya Nakano, Kotoko Nakata, Yoshitomo Tanaka, Hiroshi Tanaka

Improvement of ASIAN Web Site
Kousuke Goto, Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto

Characteristic Chemical Transformation Patterns in Biodegradation Pathways
Mina Oh, Masahiro Hattori, Susumu Goto, Minoru Kanehisa