Masao Nagasaki

According to our database1, Masao Nagasaki authored at least 61 papers between 2003 and 2021.

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Bibliography

2021
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net.
Biosyst., 2021

2018
Time-Series Filtering for Replicated Observations via a Kernel Approximate Bayesian Computation.
IEEE Trans. Signal Process., 2018

2017
Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design.
BMC Medical Informatics Decis. Mak., 2017

2016
Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling.
Proceedings of the Modeling in Systems Biology, The Petri Net Approach, 2016

A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes.
BMC Genom., 2016

2015
HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data.
BMC Genom., 2015

Estimating copy numbers of alleles from population-scale high-throughput sequencing data.
BMC Bioinform., 2015

2014
An efficient method of exploring simulation models by assimilating literature and biological observational data.
Biosyst., 2014

CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML.
Biosyst., 2014

SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints.
Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads.
Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

2013
iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data.
BMC Syst. Biol., 2013

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.
Bioinform., 2013

XiP: a computational environment to create, extend and share workflows.
Bioinform., 2013

A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads.
Bioinform., 2013

2012
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.
BMC Bioinform., 2012

IRView: a database and viewer for protein interacting regions.
Bioinform., 2012

2011
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011

High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Hybrid Petri net based modeling for biological pathway simulation.
Nat. Comput., 2011

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.
BMC Bioinform., 2011

Ontology-based instance data validation for high-quality curated biological pathways.
BMC Bioinform., 2011

SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinform., 2011

Systems biology model repository for macrophage pathway simulation.
Bioinform., 2011

MIRACH: efficient model checker for quantitative biological pathway models.
Bioinform., 2011

CSO validator: improving manual curation workflow for biological pathways.
Bioinform., 2011

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation.
Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

Poster: Comprehensive pharmacogenomic pathway screening by data assimilation.
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2010
Identification of Granger Causality between Gene Sets.
J. Bioinform. Comput. Biol., 2010

Cell Illustrator 4.0: A Computational Platform for Systems Biology.
Silico Biol., 2010

Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana.
Silico Biol., 2010

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram.
BMC Syst. Biol., 2010

An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.
BMC Bioinform., 2010

The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis.
Biosyst., 2010

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
Bioinform., 2010

Model-free unsupervised gene set screening based on information enrichment in expression profiles.
Bioinform., 2010

DA 1.0: parameter estimation of biological pathways using data assimilation approach.
Bioinform., 2010

Network profiling analysis for generating modulator-dependent gene networks.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009
Recursive regularization for inferring gene networks from time-course gene expression profiles.
BMC Syst. Biol., 2009

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.
BMC Syst. Biol., 2009

BFL: a node and edge betweenness based fast layout algorithm for large scale networks.
BMC Bioinform., 2009

Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality.
Proceedings of the Discovery Science, 12th International Conference, 2009

Gene Networks Viewed through Two Models.
Proceedings of the Bioinformatics and Computational Biology, 2009

Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases.
Computational Biology 13, Springer, ISBN: 978-1-84882-022-7, 2009

2008
Systematic reconstruction of TRANSPATH data into Cell System Markup Language.
BMC Syst. Biol., 2008

ExonMiner: Web service for analysis of GeneChip Exon array data.
BMC Bioinform., 2008

Bayesian learning of biological pathways on genomic data assimilation.
Bioinform., 2008

Fast grid layout algorithm for biological networks with sweep calculation.
Bioinform., 2008

2007
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways.
Silico Biol., 2007

AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction.
BMC Bioinform., 2007

An efficient grid layout algorithm for biological networks utilizing various biological attributes.
BMC Bioinform., 2007

Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.
Silico Biol., 2006

2004
Constructing biological pathway models with hybrid functional Petri net.
Silico Biol., 2004

Integrating Biopathway Databases for Large-scale Modeling and Simulation.
Proceedings of the Second Asia-Pacific Bioinformatics Conference (APBC 2004), 2004

2003
Recreating Biopathway Databases towards Simulation.
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003

Towards Biopathway Modeling and Simulation.
Proceedings of the Applications and Theory of Petri Nets 2003, 2003


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