Software Demonstration AbstractsMass Spectral Database for Metabolome Analysis CADLIVE: Integration for Large-Scale Network Data RIKEN Natural Products Depository (RIKEN NPDepo) PreSPI: Prediction System for Protein Interaction Construction of Candida Albicans Protein Network from Yeast Protein Interactions in System Biology ExPlain: Causal Analysis of Gene Expression Data from Promoter Models to Signaling Pathways Cell Illustrator3.0: A Platform for Biopathway Modeling and Simulation Ajax for Networks and Ontologies Poster AbstractsSerial Regulation on Cell Cycle System in S.cerevisiae Efficient Inferring Method for Extracting Reliable Interactions from Time Series of Gene Expression Profile Emerging Needs for Restructuring Biomedical Knowledge and Education System Relation between Cell Division and Gene Expression by Using Single Cell Tracking System Identification of Apoptosis-Induced Gene Networks from Time Course Expression Profiles with Replicated Measurements p53 Pathways to Simulate the p53 Transcriptional Activity An S-System Application for Mammalian Circadian Clock System Noise-Induced Robust Synchronization in a Multicellular System Mathematical Modeling of G1/S Phase in the Cell Cycle with Involving the p53/Mdm2 Network Sensitivity Analysis for the E.coli Nitrogen Assimilation System Analysis for the Conflict between G2/M Phase Arrest in the Cell Cycle and Apoptosis Induction Spatio-Temporal Dynamics of Molecules on the Cell Surface Studied by Particle Simulation Consistency of the Transition Theory in Computer Simulation of a Genetic Toggle Switch Regulation of Metabolic Networks By Small Molecule Metabolites The Finitely Numerable Effect in the Coupled Molecular Motor Model A Steady-State Approximation-Based Solver for Stiff Biochemical Models Genomic Data Assimilation for a Hybrid Functional Petri Net Model of Circadian Rhythm with Time Course Gene Expression Data Cell Fate Simulation of ASE Cell in eCaenorhabditis elegans Using Hybrid Functional Petri Net with Extension A Cluster Identification Method without Using a Threshold of Correlation Coefficient in Hierarchical Cluster Analysis Cluster Analysis of Transcription Factor Binding Sites in the Promoter Regions of Cardiac Genes in Failing Hearts Module Discovery in Gene Expression Data Using Closed Itemset Mining Algorithm A Gene Clustering Method Using Gene Expression Data and Gene Networks Applying Gaussian Distribution-Dependent Criteria to Decision Trees for High-Dimensional Microarray Data Computational Analysis of Global Expression Profiles in Mouse Natural Antisense Transcripts Quantitative Control of Early Transcription by ERK and Akt Signal Transduction Prediction of Ligand- and ErbB Receptor-Specific Transcription Factors from Time-Course Gene Expression Data of Cancer Cells Modeling of Extracellular Matrix Degradation Processes in Cancer Metastasis Using Covariance Structure Analysis Gene Expression Profiling of Hepatocellular Carcinoma Using Independent Component Analysis ROKU: An Improved Method for the Detection of Tissue-Specific Expression Patterns Identification of Tissue Specific Transcription Factors Using Microarray Gene Expression Data Profiling Prostate Cancer Signatures by Statistical Analysis of mRNA Isoform Expression A Comparative Study of Exploratory Analysis versus Statistical Analysis for Oligo-DNA Microarrays Genome-Wide Detection of Human Copy Number Variations Using High-Density DNA Oligonucleotide Arrays Experimental Design for Time-Series Microarray Analysis New Gene Filtering Method Using S2N' Based on the Concept of PART Filtering Method Gene Alignment for Cell Division Cycle Microarray Experiments without Sinusoidal Fittings Power Spectra of Bird-Influenza A Virus (BIV) H5N1 ssRNA Base Sequences : Possibility of Cooperative Genes or Interferences Gene Finding for Microbial Metagenomics Conservation of Regulation Systems in Firmicutes Comprehensive Detection of Terminal Oligo-Pyrimidine (TOP)Genes in the Human Genome Autoimmune Diseases and Evolutionary Trace of the T-Cell Epitopes Analysis of Tissue Specific Expression Patterns of Isozymes A Web Application for Identification of Glycosaminoglycan (GAG) Binding Motifs in Plasmodium Falciparum Analysis of the Sub-Telomeric Region of the Malaria Parasite P. Falciparum Using aCGH Data Proteins with Charge Periodicity of 28 Residues in Amino Acid Sequences from Total Genomes Characteristic Distribution of GC Contents for Proteins with Charge Periodicity of 28 Residues Analysis and Estimation for the Substituted Sequences of DNA Sequences for Saccharomyces Cerevisiae with a Kind of Marcov Model Stochastic Local Genome Alignment and Comprehensive Search for Conserved Gene Clusters Computational Analysis of Human mRNAs Regulated by GRSF-1, a Positive Regulator of Influenza Virus Significant Deviation in the Configuration of Tandem Repeats in Prokaryotic Genomes RNA Base Pairing Probability Alignment by Genetic Algorithm Detailed Analysis of Reentrant Loops and Neighboring Sites in Alpha-Helical Transmembrane Proteins Distribution of Relative Mutation Frequency MotifCombinator: A Web Tool to Search for Combinations of Cis-Regulatory Motifs Frame-Cluster Mapping: Genomewide Analysis for Detection of Localized Signal Regions Analysis of Aspergillus oryzae tRNA Genes Using Multivariate Analysis Analysis of Amino Acid Sequence by Self Organization Maps Prediction of Transcription Factor Binding Sites in Saccharomyces cerevisiae Structural Breakpoint Prediction and its Application Based on Dimers in Amino Acid Sequence Ab-initio Identification of Promoter Elements in Antimicrobial Peptide-Coding Genes Structural Analysis on Functional Epitope A GP Based Algorithm for HP-Model Problem Combining Molecular Dynamics Simulation with a Graph Theoretical Approach to Study Protein Complex Flexibility Inferring Domain Combination Pattern and its Biological Meaning via Association Rules A Novel Method to Determine the Assembling Space between Two Protein Subunits Biomolecular Computations toward Enzyme-Catalyzed Transformations of Non-Natural Organic Compounds: Ab initio Fragment Molecular Orbital Calculations Can Brownian Dynamics be a Useful Tool for Structure-Based Drug Design? A Benchmark Study of the “Soft Docking” Module of MIAX,Using a Set of Unbound Proteins Supervised Consensus Scoring Methods for Structure-Based Drug Design Scoring Analysis of DNA Binding Sites of DNA Binding Proteins Classification of Protein-DNA Complexes Based on Structural Descriptiors Comparative Analysis of Amino Acid Residues and Structures between RNase HII and Argonaute Proteins from Pyrococcus furiosus Murlet: A Practical Multiple Alignment Tool for Structural RNA Sequences fRNAdb: A Platform for Mining/Annotating Functional RNA Candidates from Non-Coding RNA Sequences RNAmine: Frequent Stem Pattern Miner from RNAs An Evolving Zipper Automaton for RNA Secondary Structure Prediction: Improvement by Sequence Homology Inclusion Comprehensive Analysis of miRNA Effect to the Transcripts Multiple Alignment of RNAs by Maximizing the Sum of the Matching Probability of Stem Fragments Phylogenetic Analysis of Essential Genes by Using ORI-GENE Evidence for ‘Introns-Late’ from Intron Phase Distribution Algebraic Evolution of the Genetic Code Distance Structure of Homologous Gene Cluster in Cyanobacteria Tracing Back Xenobiotic Responsive and NR Mediated Pathways/Networks Analyses of the Nutrient Dependency of Parasites to Hosts Using KEGG Database Identification of Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture Comprehensive Analysis of Domain Architectures of Transmembrane Proteins Gene Expression Profile Analysis for Circadian Promoter Activities of Cyanobacterial Bioluminescent Reporter Strains Using Non-Metric Multidimensional Scaling Comparative Sequence Analysis between Human and Mouse: Promoter Conservation and Protein Conservation Whole-Genome Functional Linkage Network Construction in the Domain Level by Probabilistic Model Systematic Analysis of Functional SNP with Type 2 Diabetes Mellitus (T2DM) in the Korean Population Analysis of Disease-Associated Mutations and SNP in Relationship with Protein Structure Adaptive Threshold for Detecting Significant Fold Changes in Microarray Data Precise Correlation between MLV Integration Sites and Transcription Start Sites in the Human Genome Hierarchical Bayes Approach to Array CGH Data Normalization Development of a Platform for Functional Genomics under the Generation Challenge Programme (GCP) Annotating Genes with Labelled and Unlabelled Data Developing SVM Classifier for GPI-(Like)-Anchored Proteins Prediction Enrichment of Protein Utilization in Protein-Protein Interaction Prediction by Adjusting e-value of InterProScan and Using Gene Ontology An Approach to Identify Unknown Gene Function through Higher Order Correlations for Gene Clusters Proposal of Graphic Assessment Method of Attribute Significance for Comprehensive Combination Analysis Predicting Types of Protein-Protein Interactions Using Various Multiple-Instance Learning Algorithms Relationship between Data Size and Accuracy of Prediction of Protein-Protein Interactions by Co-Evolutionary Information Prediction Accuracy Evaluation of Domain and Domain Combination Based Prediction Methods for Protein-Protein Interaction Protein Feature Prediction Using Chi-Square in PPI Networks Predicting Ligand Binding Sites of Uncharacterized Protein Explore MicroRNA Precursors through a High-Throughput Computational Prediction Comparison of the Prediction Abilities of FBA, MOMA and ROOM for a pykF Mutant of E. coli DNA Repair Recognition via Support Vector Machines Discrimination of β-Barrel Membrane Proteins Using Machine Learning Techniques Prediction of Protein-Protein Interaction Sites with Two-Stage Support Vector Machine Prediction of Mucin-Type O-Glycosylation by Layered Neural Networks and Support Vector Machines Computational Prediction of Drosophila MicroRNA Targets and Analysis of their Negative Feedback Control Detection of Transcription Units Based on Integration of Non-Targeted Analyses Prediction of Glycosphingolipid Chemical Structure from MALDI-TOF MS Data An Expectation-Maximization Algorithm for Reconstructing Heterogeneous Gene-Content Evolution From Function Prediction to Pathway Prediction: A New Pipeline Based on KAAS and GENIES Proposal of PART (Projective Adaptive Resonance Theory) for Analysis of Gene Expression Data with Small Samples Prediction of Glycan Structures from Gene Expression Data Based on Improved Scoring Scheme Integrative Estimation of Gene Regulatory Network by Means of AdaBoost Analysis and Discrimination of Ligand Binding Membrane Proteins Using a Simple Statistical Approach Prediction of Protein Subcellular Localization Using an Artificial Neural Network A Statistical Framework for Genome Wide Discovery of Biomarker Splice Variations with GeneChip Human Exon 1.0 ST Arrays A Calibration Technique for Single-Dimensional Distribution of Local GC Content Nonmetric Distances for Barcode of Life modEst: A GMOD-Based Framework for Integrating Partial Polyploid Transcripts into Closely-Related Genomes In Silico Functional Profiling of Small Molecules for Assessing their Physiological Effects Probabilistic Ranking for Analyzing Transcriptional Response Variations of Metabolic Gene Paths Interpreting Patterns of Gene Expression with spherical Self-Organizing Maps (sSOM): Application to Search for Cell Surface Markers Gene Subset Selection for Kernel-Based Classifiers Improvement of a Gene Network Discovery Method via Frequent Subtree Mining A Graph Mining Approach to Gene Network Motif Extraction Considering False Negatives in Mixture Oncogenetic Trees Model for Chromosomal Alteration Data A Novel Clustering Method for Analysis of Biological Networks Using Maximal Components of Graphs Extending Multivariate Bernoulli and Multinomial Models for Clustering MEDLINE Records A Recommendation System of PubMed Articles Based on Content-Based Filtering Automated Genome Annotation and Analysis of Eukaryotes A Resolution of the Problem of Multiple Inheritance in Gene Ontology A Gene Annotation Tool Based on Sequence Similarity and Biomedical Text Classification of Figures in Biomedical Literature toward a Figure Finding System A Biomedical Text Mining System from PubMed Abstracts and Patents Ontology-Based Representation for Cell Systems Markup Language A New Grid Layout Algorithm with Swap Operation that Extends the Search Space while Keeping the Time Complexity A Visualization Method for Detecting Pathway Alteration among Subtypes of Lung Carcinoma eXpanda: An Integrated Platform for Network Analysis and Visualization Pathway Mapping Web-Service Based on KEGG and SVG Visualization of Metabolic Networks as Networks of Atoms by Pajek: An Application of Connectivity Matrix Method A Hub-Seeded Multilevel Algorithm for Fast Layout of Protein-Protein Interaction Networks Analyzing and Visualizing Complex Metabolite Profiles with MathDAMP Correlation Analysis of Sequence and Activity Based on Translation Signal Database, TRSIG New Features of MutationView : A Module to Search for Disease-Causing Genes from Protein Functional Domain Construction of Biomolecular Network in Structurome and Analysis of Cooperativity INOH Pathway Data Ontologies Application of AI-Based Database Methods in Purification of Traditional Chinese Pharmacy Recipes Restauro-G: A Rapid Genome Re-Annotation System A Web-Based Resource for Glycome Informatics Gclust Server: Phylogenetic Profiling with Pre-Defined Organism Sets TACT: Transcriptome Auto-Annotation Conducting Tool of H-InvDB  |
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- Genome Informatics vol.19 (2007)
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