Serial Regulation on Cell Cycle System in S.cerevisiae
Sachiyo Aburatani, Katsuhisa Horimoto

Efficient Inferring Method for Extracting Reliable Interactions from Time Series of Gene Expression Profile
Masahiko Nakatsui, Takanori Ueda, Maki Yukihiro, Isao Ono, Masahiro Okamoto

Emerging Needs for Restructuring Biomedical Knowledge and Education System
Tsuguchika Kaminuma, Masumi Yukawa, Yoshitomo Tanaka, Takako Takai-Igarashi, Yoshihiro Takemoto, Hiroshi Tanaka

Relation between Cell Division and Gene Expression by Using Single Cell Tracking System
Kazumi Hakamada, Satoshi Fujita, Jun Miyake

Identification of Apoptosis-Induced Gene Networks from Time Course Expression Profiles with Replicated Measurements
Osamu Hirose, Ryo Yoshida, Seiya Imoto, Satoru Miyano

p53 Pathways to Simulate the p53 Transcriptional Activity
Atsushi Doi, Masao Nagasaki, Kazuko Ueno, Hiroshi Matsuno, Satoru Miyano

An S-System Application for Mammalian Circadian Clock System
Daisuke Tominaga, Katsuhisa Horimoto

Noise-Induced Robust Synchronization in a Multicellular System
Ruiqi Wang, Luonan Chen, Kazuyuki Aihara

Mathematical Modeling of G1/S Phase in the Cell Cycle with Involving the p53/Mdm2 Network
Kazunari Iwamoto, Yoshihiko Tashima, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto

Sensitivity Analysis for the E.coli Nitrogen Assimilation System
Koichi Masaki, Hiroyuki Kurata

Analysis for the Conflict between G2/M Phase Arrest in the Cell Cycle and Apoptosis Induction
Yoshihiko Tashima, Yu Kisaka, Hiroyuki Hamada, Taizo Hanai, Yukihiro Eguchi, Masahiro Okamoto

Spatio-Temporal Dynamics of Molecules on the Cell Surface Studied by Particle Simulation
Ryuzo Azuma, Hiroshi Kobayashi, Tomoyuki Yamamoto, Akihiko Konagaya

Consistency of the Transition Theory in Computer Simulation of a Genetic Toggle Switch
Tomohiro Ushikubo, Masaki Sasai

Regulation of Metabolic Networks By Small Molecule Metabolites
Alex Gutteridge, Minoru Kanehisa, Susumu Goto

The Finitely Numerable Effect in the Coupled Molecular Motor Model
Kazunari Mouri, Tetsuya Shimokawa

A Steady-State Approximation-Based Solver for Stiff Biochemical Models
Emi Shiraishi, Hiroyuki Kurata

Genomic Data Assimilation for a Hybrid Functional Petri Net Model of Circadian Rhythm with Time Course Gene Expression Data
Masao Nagasaki, Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Atsushi Doi, Yoshinori Tamada, Hiroshi Matsuno, Satoru Miyano, Tomoyuki Higuchi

Cell Fate Simulation of ASE Cell in Caenorhabditis elegans Using Hybrid Functional Petri Net with Extension
Ayumu Saito, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano

A Cluster Identification Method without Using a Threshold of Correlation Coefficient in Hierarchical Cluster Analysis
Yuki Miyata, Yoichi Yamada, Ken-ichiro Muramoto

Cluster Analysis of Transcription Factor Binding Sites in the Promoter Regions of Cardiac Genes in Failing Hearts
Masaharu Nakayama, Hiroko Tada, Yasuhide Asaumi, Hiroaki Shimokawa

Module Discovery in Gene Expression Data Using Closed Itemset Mining Algorithm
Yoshifumi Okada, Wataru Fujibuchi, Paul Horton

A Gene Clustering Method Using Gene Expression Data and Gene Networks
Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka

Applying Gaussian Distribution-Dependent Criteria to Decision Trees for High-Dimensional Microarray Data
Raymond Wan, Ichigaku Takigawa, Hiroshi Mamitsuka

Computational Analysis of Global Expression Profiles in Mouse Natural Antisense Transcripts
Yuki Okada, Koji Numata, Rintaro Saito, Hidenori Kiyosawa, Akio Kanai, Masaru Tomita

Quantitative Control of Early Transcription by ERK and Akt Signal Transduction
Takashi Nakakuki, Kaori Ide, Takeshi Nagashima, Kaoru Takahashi, Noriko Yumoto, Mariko Hatakeyama

Prediction of Ligand- and ErbB Receptor-Specific Transcription Factors from Time-Course Gene Expression Data of Cancer Cells
Takeshi Nagashima, Jun Horiuchi, Kenji Nakano, Kaori Ide, Kaoru Takahashi, Mariko Hatakeyama

Modeling of Extracellular Matrix Degradation Processes in Cancer Metastasis Using Covariance Structure Analysis
Akiko Hatano, Kaoru Mogushi, Hiroshi Tanaka

Gene Expression Profiling of Hepatocellular Carcinoma Using Independent Component Analysis
Satoshi Nagaie, Kaoru Mogushi, Hiroshi Tanaka

ROKU: An Improved Method for the Detection of Tissue-Specific Expression Patterns
Koji Kadota, Jiazhen Ye, Yuji Nakai, Tohru Terada, Kentaro Shimizu

Identification of Tissue Specific Transcription Factors Using Microarray Gene Expression Data
Larisa Kiseleva, Ekaterina Shelest, Edgar Wingender, Paul Horton

Profiling Prostate Cancer Signatures by Statistical Analysis of mRNA Isoform Expression
T.Murlidharan Nair, Hai-Ri Li, Xiang-Dong Fu

A Comparative Study of Exploratory Analysis versus Statistical Analysis for Oligo-DNA Microarrays
Kenichiro Kanda, Kaoru Azumi, Nori Satoh, Sorin V. Sabau

Genome-Wide Detection of Human Copy Number Variations Using High-Density DNA Oligonucleotide Arrays
Daisuke Komura, Shumpei Ishikawa, Fan Shen, Kunihiro Nishimura, Sigeo Ihara, Hiroshi Nakamura, Keith W. Jones, Jing Huang, Hiroyuki Aburatani

Experimental Design for Time-Series Microarray Analysis
Ryosuke Ito, Hiroki Takahashi, Taku Oshima, Naotake Ogasawara, Md. Altaf-Ul-Amin, Ken Kurokawa, Shigehiko Kanaya

New Gene Filtering Method Using S2N' Based on the Concept of PART Filtering Method
Hiro Takahashi, Hiroyuki Honda

Gene Alignment for Cell Division Cycle Microarray Experiments without Sinusoidal Fittings
Y-h. Taguchi

Power Spectra of Bird-Influenza A Virus (BIV) ssRNA Base Sequences : Possibility of Cooperative Genes or Interferences
Eisei Takushi, Hiroyuki Sakamoto, Mitsuhiro Seino

Gene Finding for Microbial Metagenomics
Jungho Park, Hideki Noguchi, Toshihisa Takagi

Conservation of Regulation Systems in Firmicutes
Nicolas Sierro, Kenta Nakai

Comprehensive Detection of Terminal Oligo-Pyrimidine (TOP)Genes in the Human Genome
Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Sumio Sugano, Kenta Nakai

Autoimmune Diseases and Evolutionary Trace of the T-Cell Epitopes
Wataru Honda, Shuichi Kawashima, Minoru Kanehisa

Analysis of Tissue Specific Expression Patterns of Isozymes
Masataka Takarabe, Akira Tsuchida, Masashi Fujita, Shujiro Okuda, Akiyasu C. Yoshizawa, Takuji Yamada, Masumi Itoh, Susumu Goto, Minoru Kanehisa

A Web Application for Identification of Glycosaminoglycan (GAG) Binding Motifs in Plasmodium Falciparum
Nelson Hayes, Johan Normark, Daniel Nilsson, Craig Wheelock, Mats Wahlgren, Susumu Goto

Analysis of the Sub-Telomeric Region of the Malaria Parasite P. Falciparum Using aCGH Data
Diego Diez, Ulf Ribacke, Craig Wheelock, Mats Wahlgren, Susumu Goto

Proteins with Charge Periodicity of 28 Residues in Amino Acid Sequences from Total Genomes
Runcong Ke, Shigeki Mitaku

Characteristic Distribution of GC Contents for Proteins with Charge Periodicity of 28 Residues
Ryusuke Sawada, Runcong Ke, Noriyuki Sakiyama, Shigeki Mitaku

Analysis and Estimation for the Substituted Sequences of DNA Sequences for Saccharomyces Cerevisiae with a Kind of Marcov Model
Mitsuhiro Seino, Hiroyuki Sakamoto

Stochastic Local Genome Alignment and Comprehensive Search for Conserved Gene Clusters
Tsuyoshi Hachiya, Yasubumi Sakakibara

Computational Analysis of Human mRNAs Regulated by GRSF-1, a Positive Regulator of Influenza Virus
Hikaru Taniguchi, Kosuke Fujishima, Yuka Watanabe, Yuko Osada, Masaru Tomita, Rintaro Saito, Akio Kanai

Significant Deviation in the Configuration of Tandem Repeats in Prokaryotic Genomes
Shintaro Hirayama, Satoshi Mizuta

RNA Base Pairing Probability Alignment by Genetic Algorithm
Akito Taneda

Detailed Analysis of Reentrant Loops and Neighboring Sites in Alpha-Helical Transmembrane Proteins
Kinya Matsushiro, Wataru Nakahata, Satoshi Mizuta

Distribution of Relative Mutation Frequency
Hyunchul Kim, Masaru Tomita

MotifCombinator: A Web Tool to Search for Combinations of Cis-Regulatory Motifs
Mamoru Kato, Tatsuhiko Tsunoda

Frame-Cluster Mapping: Genomewide Analysis for Detection of Localized Signal Regions
Kou Amano, Hidemitsu Nakamura, Hisataka Numa, Yosiaki Nagamura, Hiroaki Ichikawa, Kaoru Fukami-Kobayashi

Analysis of Aspergillus oryzae tRNA Genes Using Multivariate Analysis
Jun-Ichi Sagara

Analysis of Amino Acid Sequence by Self Organization Maps
Takeshi Takahashi, Hiroshi Dozono

Prediction of Transcription Factor Binding Sites in Saccharomyces cerevisiae
Takuya Ueno, Hidetoshi Kono, Sarai Akinori

Structural Breakpoint Prediction and its Application Based on Dimers in Amino Acid Sequence
Yoshihide Makino, Nobuya Itoh

Ab-initio Identification of Promoter Elements in Antimicrobial Peptide-Coding Genes
Manisha Brahmachary, Christian Schönbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S.P.T Krishnan, Chin-Yo Lin, David A Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B Bajic

Structural Analysis on Functional Epitope
Jian Huang, Minoru Kanehisa

A GP Based Algorithm for HP-Model Problem
Takahiro Yabuki, Hitoshi Iba

Combining Molecular Dynamics Simulation with a Graph Theoretical Approach to Study Protein Complex Flexibility
AbdulRajjak Shaikh, Mohamed Ismael, Pei Qiang, Hideyuki Tsuboi,Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba,Momoji Kubo, Eiichiro Ichiishi, Carlos A. Del Carpio, Akira Miyamoto

Inferring Domain Combination Pattern and Its Biological Meaning via Association Rules
Suk-hoon Jung, Dong-soo Han, Sung-doke Lee

A Novel Method to Determine the Assembling Space between Two Protein Subunits
Miki Maeda, Hiroya Nobori

Biomolecular Computations toward Enzyme-Catalyzed Transformations of Non-Natural Organic Compounds: Ab initio Fragment Molecular Orbital Calculations
Takahisa Tanaka, Takatomo Kimura, Yoichiro Yagi, Yoshinobu Naoshima

Can Brownian Dynamics be a Useful Tool for Structure-Based Drug Design?
Akifumi Oda, Hisao Matsuzaki, Noriyuki Yamaotsu, Shuichi Hirono

A Benchmark Study of the ``Soft Docking" Module of MIAX,Using a Set of Unbound Proteins
Pei Qiang, Mohamed Ismael, Abdul Rajjak Shaikh, Hideyuki Tsuboi, Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Momoji Kubo, Eiichiro Ichiishi, Carlos A. Del Carpio, Akira Miyamoto

Supervised Consensus Scoring Methods for Structure-Based Drug Design
Reiji Teramoto, Hiroaki Fukunishi

Scoring Analysis of DNA Binding Sites of DNA Binding Proteins
Reika Okihara, Yukako Sakatsuji, Ayumi Suzuki, Ichiro Yamato, Satoru Miyazaki

Classification of Protein-DNA Complexes Based on Structural Descriptiors
Ponraj Prabakaran, Shandar Ahmad, M.Michael Gromiha, Maria G. Singarayan, Akinori Sarai

Comparative Analysis of Amino Acid Residues and Structures between RNase HII and Argonaute Proteins from Pyrococcus furiosus
Sayaka Kitamura, Kosuke Fujishima, Asako Sato, Arun Krishnan, Masaru Tomita, Akio Kanai

Murlet: A Practical Multiple Alignment Tool for Structural RNA Sequences
Hisanori Kiryu, Yasuo Tabei, Taishin Kin, Kiyoshi Asai

fRNAdb: A Platform for Mining/Annotating Functional RNA Candidates from Non-Coding RNA Sequences
Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Takashi Komori, Kiyoshi Asai

RNAmine: Frequent Stem Pattern Miner from RNAs
Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai

An Evolving Zipper Automaton for RNA Secondary Structure Prediction: Improvement by Sequence Homology Inclusion
Carlos A. Del Carpio M., Mohamed Ismael, Eiichiro Ichiishi, Hideyuki Tsuboi, Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Momoji Kubo, Akira Miyamoto

Comprehensive Analysis of miRNA Effect to the Transcripts
Keishin Nishida, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

Multiple Alignment of RNAs by Maximizing the Sum of the Matching Probability of Stem Fragments
Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai

Phylogenetic Analysis of Essential Genes by Using ORI-GENE
Hirotoshi Kawano, Hideaki Mizuno, Akinori Sarai

Evidence for ‘Introns-Late’ from Intron Phase Distribution
Hung Dinh Nguyen, Maki Yoshihama, Naoya Kenmochi

Algebraic Evolution of the Genetic Code
Takashi Kawamura

Distance Structure of Homologous Gene Cluster in Cyanobacteria
Naobumi Sasaki, Naoki Sato

Tracing Back Xenobiotic Responsive and NR Mediated Pathways/Networks
Yoshitomo Tanaka, Masumi Yukawa, Hiroshi Tanaka, Tsuguchika Kaminuma

Analyses of the Nutrient Dependency of Parasites to Hosts Using KEGG Database
Ai Muto, Masahiro Hattori, Wataru Honda, Minoru Kanehisa

Identification of Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture
Kenji K. Kojima, Minoru Kanehisa

Comprehensive Analysis of Domain Architectures of Transmembrane Proteins
Syuuichi Yoshida, Yoshihiro Yamazaki, Takuhiro Nishio, Sunao Kaneko, Toshio Shimizu

Gene Expression Profile Analysis for Circadian Promoter Activities of Cyanobacterial Bioluminescent Reporter Strains Using Non-Metric Multidimensional Scaling
Tokitaka Oyama, Hiroshi Ito, Takao Kondo, Y-h. Taguchi

Comparative Sequence Analysis between Human and Mouse: Promoter Conservation and Protein Conservation
Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

Whole-Genome Functional Linkage Network Construction in the Domain Level by Probabilistic Model
Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen

Systematic Analysis of Functional SNP with Type 2 Diabetes Mellitus (T2DM) in the Korean Population
Hyo-Jeong Ban, Keun-Joon Park, Ji-Hong Kim, Hyun-Woo Han

Analysis of Disease-Associated Mutations and SNP in Relationship with Protein Structure
Taku Ashikari, Hidetoshi Kono, Akinori Sarai

Adaptive Threshold for Detecting Significant Fold Changes in Microarray Data
Hidenori Inaoka, Yutaka Fukuoka

Precise Correlation between MLV Integration Sites and Transcription Start Sites in the Human Genome
Yoshiaki Tanaka, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

Hierarchical Bayes Approach to Array CGH Data Normalization
Shigeyuki Oba, Shin Ishii

Development of a Platform for Functional Genomics under the Generation Challenge Programme (GCP)
Masaru Takeya, Kohji Suzuki, Koji Doi, Shoshi Kikuchi, Richard Bruskiewich

Annotating Genes with Labelled and Unlabelled Data
Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara

Developing SVM Classifier for GPI-(Like)-Anchored Proteins Prediction
Wei Cao, Shugo Nakamura, Kentaro Shimizu

Enrichment of Protein Utilization in Protein-Protein Interaction Prediction by Adjusting e-value of InterProScan and Using Gene Ontology
Woo-Hyuk Jang, Hee-Young Hur, Dong-Soo Han

An Approach to Identify Unknown Gene Function through Higher Order Correlations for Gene Clusters
Akira Funae, Daisuke Komura, Hiroshi Nakamura, Sigeo Ihara

Proposal of Graphic Assessment Method of Attribute Significance for Comprehensive Combination Analysis
Masahiro Nakatochi, Hiroyuki Honda

Predicting Types of Protein-Protein Interactions Using Various Multiple-Instance Learning Algorithms
Hiroshi Yamakawa, Koji Maruhashi, Yoshio Nakao

Relationship between Data Size and Accuracy of Prediction of Protein-Protein Interactions by Co-Evolutionary Information
Tetsuya Sato, Yoshihiro Yamanishi, Hisako Ichihara, Kei-ichi Kuma, Minoru Kanehisa, Hiroyuki Toh

Prediction Accuracy Evaluation of Domain and Domain Combination Based Prediction Methods for Protein-Protein Interaction
Dong-Soo Han, Woo-Hyuk Jang

Protein Feature Prediction Using Chi-Square in PPI Networks
YongHo Lee, JaeHun Choi, JongMin Park, SunLee Bang, SooJun Park

Predicting Ligand Binding Sites of Uncharacterized Protein
Mizuki Morita, Shugo Nakamura, Kentaro Shimizu

Explore MicroRNA Precursors through a High-Throughput Computational Prediction
Yu-Ching Chang, Shih-Je Lan, Yu-Yu Lin, Cheng-Tao Wu

Comparison of the Prediction Abilities of FBA, MOMA and ROOM for a pykF Mutant of E. coli
Quanyu Zhao, Hiroyuki Kurata

DNA Repair Recognition via Support Vector Machines
J.B. Brown, Tatsuya Akutsu

Discrimination of β-Barrel Membrane Proteins Using Machine Learning Techniques
M.Michael Gromiha, Makiko Suwa

Prediction of Protein-Protein Interaction Sites with Two-Stage Support Vector Machine
Masanori Kakuta, Kentaro Shimizu

Prediction of Mucin-Type O-Glycosylation by Layered Neural Networks and Support Vector Machines
Ikue Nouno, Hirotaka Sakamoto, Takeshi Iritani, Kazutoshi Sakakibara, Ikuko Nishikawa, Masahiro Ito

Computational Prediction of Drosophila MicroRNA Targets and Analysis of their Negative Feedback Control
Yuka Watanabe, Nozomu Yachie, Masaru Tomita, Akio Kanai

Detection of Transcription Units Based on Integration of Non-Targeted Analyses
Hirokazu Kobayashi, Yoshiaki Kiura, Kazuo Kobayashi, Md. Altaf-Ul-Amin, Naotake Ogasawara, Shigehiko Kanaya, Ken Kurokawa

Prediction of Glycosphingolipid Chemical Structure from MALDI-TOF MS Data
Yuki Matsumuro, Saki Itonori, Mutsumi Sugita, Masahiro Ito

An Expectation-Maximization Algorithm for Reconstructing Heterogeneous Gene-Content Evolution
Wataru Iwasaki, Toshihisa Takagi

From Function Prediction to Pathway Prediction: A New Pipeline Based on KAAS and GENIES
Yuki Moriya, Yoshihiro Yamanishi, Masumi Itoh, Shinobu Okamoto, Minoru Kanehisa

Proposal of BagPART (Bagging Projective Adaptive Resonance Theory) for Analysis of Gene Expression Data with Small Samples
Takashi Kawamura, Hiro Takahashi, Hiroyuki Honda

Prediction of Glycan Structures from Gene Expression Data Based on Improved Scoring Scheme
Akitsugu Suga, Yoshihiro Yamanishi, Kosuke Hashimoto, Minoru Kanehisa

Integrative Estimation of Gene Regulatory Network by Means of AdaBoost
Shinya Nabatame, Hitoshi Iba

Analysis and Discrimination of Ligand Binding Membrane Proteins Using a Simple Statistical Approach
M.Xavier Suresh, M.Michael Gromiha, Makiko Suwa

Prediction of Protein Subcellular Localization Using an Artificial Neural Network
Anton Kratz, Rintaro Saito, Arun Krishnan, Masaru Tomita

A Statistical Framework for Genome Wide Discovery of Biomarker Splice Variations with GeneChip Human Exon 1.0 ST Arrays
Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano

A Calibration Technique for Single-Dimensional Distribution of Local GC Content
Tomoyuki Fujimoto, Tadao Sugiura, Takeshi Nagaya, Tetsuo Sato, Kotaro Minato

Nonmetric Distances for Barcode of Life
Hisamitsu Akiba, Y-h. Taguchi

modEst: A GMOD-Based Framework for Integrating Partial Polyploid Transcripts into Closely-Related Genomes
Aaron Chuah, Richard Bartfai, Laszlo Orban, Alan Christoffels

In Silico Functional Profiling of Small Molecules for Assessing their Physiological Effects.
Tomohiro Sato, Yo Matsuo, Shigeyuki Yokoyama

Probabilistic Ranking for Analyzing Transcriptional Response Variations of Metabolic Gene Paths
Ichigaku Takigawa, Hiroshi Mamitsuka

Interpreting Patterns of Gene Expression with spherical Self-Organizing Maps (sSOM): Application to Search for Cell Surface Markers
Tuoya, Yuh Sugii, Tadahiro Nagaoka, Takayuki Fukuda, Hiroko Tada, Hidenori Yamada, Yasaburo Matsuura, Heizo Tokutaka, Masaharu Seno

Gene Subset Selection for Kernel-Based Classifiers
Satoshi Niijima, Satoru Kuhara

Improvement of a Gene Network Discovery Method via Frequent Subtree Mining
Alexandre Termier, Yoshinori Tamada, Kazuyuki Numata, Seiya Imoto, Takashi Washio, Tomoyuki Higuchi

A Graph Mining Approach to Gene Network Motif Extraction
Kazuyuki Numata, Alexandre Termier, Ryo Yoshida, Seiya Imoto, Yoshinori Tamada, Tomoyuki Higuchi, Satoru Miyano

Considering False Negatives in Mixture Oncogenetic Trees Model for Chromosomal Alteration Data
Kosei Yamamoto, Shigeyuki Oba, Shin Ishii

A Novel Clustering Method for Analysis of Biological Networks Using Maximal Components of Graphs
Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi

Extending Multivariate Bernoulli and Multinomial Models for Clustering MEDLINE Records
Shanfeng Zhu, Ichigaku Takigawa, Shuqin Zhang, Hiroshi Mamitsuka

A Recommendation System of PubMed Articles Based on Content-Based Filtering
Takashi Yoneya, Hiroshi Mamitsuka

Automated Genome Annotation and Analysis of Eukaryotes
Igor Grigoriev, Andrea Aerts, Alan Kuo, Robert Otillar, Asaf Salamov, Astrid Terry, Kemin Zhou, Kelly Felkins, Jinal Jhavery, Wayne Huang, Lukasz Szajkowski, Gregory Werner

A Resolution of the Problem of Multiple Inheritance in Gene Ontology
Takako Takai-Igarashi, Hiroshi Tanaka

A Gene Annotation Tool Based on Sequence Similarity and Biomedical Text
Daisuke Yamaguchi, Asako Koike, Yasunori Yamamoto, Toshihisa Takagi

Classification of Figures in Biomedical Literature toward a Figure Finding System
Natsu Ishii, Asako Koike, Yasunori Yamamoto, Toshihisa Takagi

A Biomedical Text Mining System from PubMed Abstracts and Patents
Jaesoo Lim, Hyunchul Jang, Joon-Ho Lim, Soo-Jun Park

Ontology-Based Representation for Cell Systems Markup Language
Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano

A New Grid Layout Algorithm with Swap Operation that Extends the Search Space while Keeping the Time Complexity
Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano

A Visualization Method for Detecting Pathway Alteration among Subtypes of Lung Carcinoma
Makoto Kano, Shumpei Ishikawa, Michitaka Hirose, Hiroyuki Aburatani

eXpanda: An Integrated Platform for Network Analysis and Visualization
Yoshiteru Negishi, Hiroyuki Nakamura, Nozomu Yachie, Rintaro Saito, Masaru Tomita

Pathway Mapping Web-Service Based on KEGG and SVG
Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita

Visualization of Metabolic Networks as Networks of Atoms by Pajek: An Application of Connectivity Matrix Method
Jun Ohta

A Hub-Seeded Multilevel Algorithm for Fast Layout of Protein-Protein Interaction Networks
SunLee Bang, JaeHun Choi, JongMin Park, SooJun Park

Analyzing and Visualizing Complex Metabolite Profiles with MathDAMP
Richard Baran, Hayataro Kochi, Natsumi Saito, Makoto Suematsu, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita

Correlation Analysis of Sequence and Activity Based on Translation Signal Database, TRSIG
Takahiro Ishimoto, Alex V. Kochetov, Akinori Sarai

New Features of MutationView : A Module to Search for Disease-Causing Genes from Protein Functional Domain
Masafumi Ohtsubo, Takashi Kawamura, Susumu Mitsuyama, Nobuyoshi Shimizu, Shinsei Minoshima

Construction of Biomolecular Network in Structurome and Analysis of Cooperativity
Mitsunobu Sekitou, Akinori Sarai

INOH Pathway Data Ontologies
Noriko Sakai, Satoko Yamamoto, Hiromi Nakamura, Yukiko Nakanishi, Toshihisa Takagi, KenIchiro Fukuda

Application of AI-Based Database Methods in Purification of Traditional Chinese Pharmacy Recipes
Yini Cui

Restauro-G: A Rapid Genome Re-Annotation System
Satoshi Tamaki, Kazuharu Arakawa, Nobuaki Kono, Masaru Tomita

A Web-Based Resource for Glycome Informatics
Kiyoko F. Aoki-Kinoshita, Masao Ichikawa, Shuichi Ikeda, Kouichi Yamada, Takako Yamaguchi

Gclust Server: Phylogenetic Profiling with Pre-Defined Organism Sets
Naoki Sato

TACT: Transcriptome Auto-Annotation Conducting Tool of H-InvDB
Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino, Takeshi Itoh, Takashi Gojobori, Tadashi Imanishi