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Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models

Background To facilitate new drug development, physiologically-based pharmacokinetic (PBPK) modeling methods receive growing attention as a tool to fully understand and predict complex pharmacokinetic phenomena. As the number of parameters to reproduce physiological functions tend to be large in PBPK models, efficient parameter estimation methods are essential. We have successfully ...

Molecular Robotics: A New Paradigm for Artifacts

of IEEE, ISNSCE, RSJ, SICE, JSME, Katachi no Kagakukai and JACG. Akihiko Konagaya: He is a Professor in the Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology

Trends in life science grid: from computing grid to knowledge grid

Background Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity of a single institution. Results This survey reviews the latest grid technologies from the viewpoints of computing grid, data grid and knowledge grid. Computing grid ...

Selecting effective siRNA sequences by using radial basis function network and decision tree learning

Shigeru Takasaki 0 Yoshihiro Kawamura 0 Akihiko Konagaya 0 0 Address: RIKEN Genomic Sciences Center (GSC) , Suehiro-cho 1-7-22-E216, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 , Japan Background

KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data

Summary: KnowledgeEditor is a graphical workbench for biological experts to model biomolecular network graphs. The modeled network data are represented by SRML, and can be published via the internet with the help of plug-in module ‘GSCope’. KnowledgeEditor helps us to model and analyze biological pathways based on microarray data. It is possible to analyze the drawn networks by ...

Particle simulation approach for subcellular dynamics and interactions of biological molecules

Background Spatio-temporal dynamics within cells can now be visualized at appropriate resolution, due to the advances in molecular imaging technologies. Even single-particle tracking (SPT) and single fluorophore video imaging (SFVI) are now being applied to observation of molecular-level dynamics. However, little is known concerning how molecular-level dynamics affect properties at ...

Coincidence between Transcriptome Analyses on Different Microarray Platforms Using a Parametric Framework

A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Microarrays are widely employed to acquire transcriptome information, and several platforms of chips are currently in use. However, discrepancies among studies are frequently reported, particularly among ...

Efficient filtering methods for clustering cDNAs with spliced sequence alignment

Motivation: Clustering sequences of a full-length cDNA library into alternative splice form candidates is a very important problem. Results: We developed a new efficient algorithm to cluster sequences of a full-length cDNA library into alternative splice form candidates. Current clustering algorithms for cDNAs tend to produce too many clusters containing incorrect splice form ...

Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation

when he studied in TITECH. Akihiko Konagaya conceived of the study, partcipated in its design and coordination, and helped to draft the manuscript. Additional material Additional file 1 owl file for

GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs

Summary: A graphical tool to visualize highly complicated biomolecular network graphs is described. It helps us to understand the graphs from macroscopic and microscopic viewpoints by incorporating continuous transition from global to clipped hyperbolic projection. GSCope also helps us to find a molecule in the graphs by offering several searching functions. It is useful to publish ...

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks

Motivation: Most ordinary traits are well described by multiple measurable parameters. Thus, in the course of elucidating the genes responsible for a given trait, it is necessary to conduct and integrate the genetic mapping of each parameter. However, the integration of multiple mapping results from different publications is prevented by the fact that they are conventionally ...

OBIYagns: a grid-based biochemical simulator with a parameter estimator

Summary: OBIYagns (yet another gene network simulator) is a biochemical system simulator that comprises a multiple-user Web-based graphical interface, an ordinary differential equation solver and a parameter estimators distributed over an open bioinformatics grid (OBIGrid). This grid-based biochemical simulation system can achieve high performance and provide a secure simulation ...

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences

We mapped RIKEN Arabidopsis full-length (RAFL) cDNAs to the Arabidopsis thaliana genome to search for alternative splicing events. We used 278 734 full-length and 3′/5′ terminal reads of the sequences of 220 214 RAFL cDNA clones for the analysis. Eighty-nine percent of the cDNA sequences could be mapped to the genome and were clustered in 17 130 transcription units (TUs). ...

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm

Motivation: To resolve the high-dimensionality of the genetic network inference problem in the S-system model, a problem decomposition strategy has been proposed. While this strategy certainly shows promise, it cannot provide a model readily applicable to the computational simulation of the genetic network when the given time-series data contain measurement noise. This is a ...

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome

The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, ...

Integrative Genome-Wide Expression Analysis Bears Evidence of Estrogen Receptor-Independent Transcription in Heregulin-Stimulated MCF-7 Cells

Heregulin ß-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive ...

FREP: a database of functional repeats in mouse cDNAs

Takeshi Nagashima Hideo Matsuda Diego G. Silva Nikolai Petrovsky RIKEN GER Group GSL Members Akihiko Konagaya Christian Scho nbach The FREP database (http://facts.gsc.riken.go.jp/ FREP/) contains 31