Masao Nagasaki
Orcid: 0000-0002-4292-8785
According to our database1,
Masao Nagasaki
authored at least 61 papers
between 2003 and 2021.
Collaborative distances:
Collaborative distances:
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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
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
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
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
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
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
Bioinform., 2011
Bioinform., 2011
Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011
2010
J. Bioinform. Comput. Biol., 2010
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
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
Proceedings of the Bioinformatics and Computational Biology, 2009
Computational Biology 13, Springer, ISBN: 978-1-84882-022-7, 2009
2008
BMC Syst. Biol., 2008
BMC Bioinform., 2008
Bioinform., 2008
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
Silico Biol., 2004
Proceedings of the Second Asia-Pacific Bioinformatics Conference (APBC 2004), 2004
2003
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003
Proceedings of the Applications and Theory of Petri Nets 2003, 2003