Akihiko Konagaya

According to our database1, Akihiko Konagaya authored at least 83 papers between 1984 and 2017.

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Bibliography

2017
Parallel Interaction Detection Algorithms for a Particle-based Live Controlled Real-time Microtubule Gliding Simulation System Accelerated by GPGPU.
New Generation Comput., 2017

Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model.
BMC Systems Biology, 2017

2015
Molecular Robotics and Controlling.
New Generation Comput., 2015

Automatic Recognition of DNA Pliers in Atomic Force Microscopy Images.
New Generation Comput., 2015

Improvements to the cluster Newton method for underdetermined inverse problems.
J. Computational Applied Mathematics, 2015

2014
Cluster Newton Method for Sampling Multiple Solutions of Underdetermined Inverse Problems: Application to a Parameter Identification Problem in Pharmacokinetics.
SIAM J. Scientific Computing, 2014

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.
J. Bioinformatics and Computational Biology, 2014

Tracking single microtubules by using B-spline curves and Hausdorff distance.
Proceedings of the 4th International Conference on Image Processing Theory, 2014

2013
Molecular Robotics: A New Paradigm for Artifacts.
New Generation Comput., 2013

Turing Test Considered Mostly Harmless.
New Generation Comput., 2013

Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models.
BMC Systems Biology, 2013

2008
Guest Editorial Introduction to the Special Section on BioGrid: Biomedical Computations on the Grid.
IEEE Trans. Information Technology in Biomedicine, 2008

Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation.
BMC Bioinformatics, 2008

2007
Mesoscopic-level Simulation of Dynamics and Interactions of Biological Molecules Using Monte Carlo Simulation.
VLSI Signal Processing, 2007

Life Science Grid.
New Generation Comput., 2007

Discovering Dynamic Characteristics of Biochemical Pathways using Geometric Patterns among Parameter-Parameter Dependencies in Differential Equations.
New Generation Comput., 2007

Multiple Sequence Alignment Based on Dynamic Programming Using FPGA.
IEICE Transactions, 2007

Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction.
Proceedings of the Proceeding of the Second International Multi-Symposium of Computer and Computational Sciences (IMSCCS 2007), 2007

High speed tablation system using an FPGA designed for distribution tables of frequent DNA subsequences.
Proceedings of the FPL 2007, 2007

An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method.
Proceedings of the FPL 2007, 2007

RABC: A Conceptual Design of Pervasive Infrastructure for Browser Computing based on Ajax technologies.
Proceedings of the Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2007), 2007

Kinetic Analysis of Ligand-Receptor Complex Formation with the Aid of Computer Simulation.
Proceedings of the 21st International Conference on Advanced Information Networking and Applications (AINA 2007), 2007

2006
Selecting effective siRNA sequences based on the self-organizing map and statistical techniques.
Computational Biology and Chemistry, 2006

Selecting effective siRNA sequences by using radial basis function network and decision tree learning.
BMC Bioinformatics, 2006

Trends in life science grid: from computing grid to knowledge grid.
BMC Bioinformatics, 2006

Particle simulation approach for subcellular dynamics and interactions of biological molecules.
BMC Bioinformatics, 2006

Particle Simulation Approach for Sub-cellular Dynamics and Interactions of Biological Molecules.
Proceedings of the Interdisciplinary and Multidisciplinary Research in Computer Science, 2006

Topic 17: High-Performance Bioinformatics.
Proceedings of the Euro-Par 2006, Parallel Processing, 12th International Euro-Par Conference, Dresden, Germany, August 28, 2006

Multidimensional Dynamic Programming for Homology Search on Distributed Systems.
Proceedings of the Euro-Par 2006, Parallel Processing, 12th International Euro-Par Conference, Dresden, Germany, August 28, 2006

Improving the Research Environment of High Performance Computing for Non-cluster Experts Based on Knoppix Instant Computing Technology.
Proceedings of the Euro-Par 2006, Parallel Processing, 12th International Euro-Par Conference, Dresden, Germany, August 28, 2006

OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics.
Proceedings of the Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006), 2006

Drug Interaction Ontology (DIO) and the Resource-Sensitive Logical Inferences.
Proceedings of the Algebra, Meaning, and Computation, 2006

2005
RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.
Nucleic Acids Research, 2005

Three-dimensional Definition of Leaf Morphological Traits of arabidopsis in Silico Phenotypic Analysis.
J. Bioinformatics and Computational Biology, 2005

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.
Bioinformatics, 2005

Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways.
Proceedings of the 21st International Conference on Data Engineering Workshops, 2005

Spatiotemporal Simulation of a Single Living Cell.
Proceedings of the 2005 IEEE International Conference on Field-Programmable Technology, 2005

Multidimensional Dynamic Programming for Homology Search.
Proceedings of the 2005 International Conference on Field Programmable Logic and Applications (FPL), 2005

2004
The Superstructure toward Open Bioinformatics Grid.
New Generation Comput., 2004

Life Sciences and Cyberinfrastructure: Dual and Interacting Revolutions that will Drive Future Science.
New Generation Comput., 2004

FREP: a database of functional repeats in mouse cDNAs.
Nucleic Acids Research, 2004

Use of morphological analysis in protein name recognition.
Journal of Biomedical Informatics, 2004

Efficient filtering methods for clustering cDNAs with spliced sequence alignment.
Bioinformatics, 2004

OBIYagns: a grid-based biochemical simulator with a parameter estimator.
Bioinformatics, 2004

Prediction of Protein Secondary Structure from PDB Structure Information Based on Sequence Segments Homology Searching.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2004

Drug Interaction Ontology (DIO) for Inferences of Possible Drug-drug Interactions.
Proceedings of the MEDINFO 2004, 2004

An Integrated System for Distributed Bioinformatics Environment on Grids.
Proceedings of the Grid Computing in Life Science, 2004

The Architectural Design of High-Throughput BLAST Services on OBIGrid.
Proceedings of the Grid Computing in Life Science, 2004

Genome-Wide Functional Annotation Environment forin OBIGrid.
Proceedings of the Grid Computing in Life Science, 2004

PBIE: A Data Preparation Toolkit Toward Developing a Parsing-Based Information Extraction System.
Proceedings of the Fourth International Conference on Language Resources and Evaluation, 2004

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Three-Dimensional Dynamic Programming for Homology Search.
Proceedings of the Field Programmable Logic and Application, 2004

2003
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs.
Bioinformatics, 2003

KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data.
Bioinformatics, 2003

High dimensional function optimization using a new genetic local search suitable for parallel computers.
Proceedings of the IEEE International Conference on Systems, 2003

Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations.
Proceedings of the ACM/IEEE SC2003 Conference on High Performance Networking and Computing, 2003

MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations.
Proceedings of the Parallel Computing: Software Technology, 2003

DIO: Drug Interaction Ontology - Application to Inferences in Possible Drug-Drug Interactions.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2003

Development of Support Tool for NMR Spectrum Analysis.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2003

Prediction of Protein-Protein Interaction Sites Using Support Vector Machines.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2003

Effect of utilizing terminology on extraction of protein-protein interaction information from biomedical literature.
Proceedings of the EACL 2003, 2003

Inference of S-system models of genetic networks using a genetic local search.
Proceedings of the IEEE Congress on Evolutionary Computation, CEC 2003, 8, 2003

Protein Name Tagging for Biomedical Annotation in Text.
Proceedings of the Workshop on Natural Language Processing in Biomedicine, 2003

2002
OBIGrid: Towards a New Distributed Platform for Bioinformatics.
Proceedings of the 21st Symposium on Reliable Distributed Systems (SRDS 2002), 2002

High Speed Homology Search with FPGAs.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Circle formation for oblivious anonymous mobile robots with no common sense of orientation.
Proceedings of the 2002 Workshop on Principles of Mobile Computing, 2002

High Speed Homology Search Using Run-Time Reconfiguration.
Proceedings of the Field-Programmable Logic and Applications, 2002

1995
A combination of a functional motif model and a structural motif model for a database validation.
Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS-28), 1995

Ordered multithreading: a novel technique for exploiting thread-level parallelism.
Proceedings of the IFIP WG10.3 working conference on Parallel architectures and compilation techniques, 1995

1994
Stochastic Motif Extraction Using Hidden Markov Model.
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994

1993
Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993

A Fine-Grained Parallel Genetic Algorithm for Distributed Parallel Systems.
Proceedings of the 5th International Conference on Genetic Algorithms, 1993

1992
An Asynchronous Fine-Grained Parallel Genetic Algorithm.
Proceedings of the Parallel Problem Solving from Nature 2, 1992

Implementing Streams on Parallel Machines with Distributed Memory.
FGCS, 1992

A Stochastic Approach to Genetic Information Processing.
Proceedings of the Algorithmic Learning Theory, Third Workshop, 1992

1991
Learning Stochastic Motifs from Genetic Sequences.
Proceedings of the Eighth International Workshop (ML91), 1991

1990
Implementation and Evaluation of Dynamic Predicates on the Sequential Inference Machine CHI.
Proceedings of the 1990 Internation Conference on Computer Languages, 1990

1989
Performance Evaluation of a Sequential Inference Machine CHI.
Proceedings of the Logic Programming, 1989

1988
Knowledge Base System in Logic Programming Paradigm.
FGCS, 1988

1987
A Co-Operative Programming Environment for a Back-End Type Sequential Inference Machine CHI.
Proceedings of the Parallel Algorithms and Architectures, 1987

1985
Design of a High-speed Prolog Machine (HPM).
Proceedings of the 12th Annual Symposium on Computer Architecture, 1985

1984
Knowledge Information Processing Language: ShapeUp.
New Generation Comput., 1984

Comparison of Closure Reduction and Combinatory Reduction Schemes.
Proceedings of the RIMS Symposia on Software Science and Engineering II, 1984


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