Masao Nagasaki

62 papers B 2C 1Misc 2Journal 46Unranked 9
YearRankTypeTitle / Venue / Authors
2025 J jnl
QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution.
Briefings Bioinform.
Taichi Matsubara, Shuto Machida, Samuel Papa Kwesi Owusu, Akihiro Asakura, Hiroki Hashimoto, Masanori Matsuoka, Masao Nagasaki
2021 J jnl
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net.
Biosyst.
Chen Li, Jiale Qin, Keisuke Kuroyanagi, Lu Lu, Masao Nagasaki, Satoru Miyano
2018 J jnl
Time-Series Filtering for Replicated Observations via a Kernel Approximate Bayesian Computation.
IEEE Trans. Signal Process.
Takanori Hasegawa, Kaname Kojima, Yosuke Kawai, Masao Nagasaki
2017 J jnl
Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design.
BMC Medical Informatics Decis. Mak.
Takako Takai-Igarashi, Kengo Kinoshita, Masao Nagasaki, Soichi Ogishima, Naoki Nakamura, Sachiko Nagase, Satoshi Nagaie, Tomo Saito, Fuji Nagami, Naoko Minegishi, Yoichi Suzuki, Kichiya Suzuki, Hiroaki Hashizume, Shinichi Kuriyama, Atsushi Hozawa, Nobuo Yaegashi, Shigeo Kure, Gen Tamiya, Yoshio Kawaguchi, Hiroshi Tanaka, Masayuki Yamamoto
2016 J jnl
A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes.
BMC Genom.
Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yosuke Kawai, Masao Nagasaki
2016 — ch.
Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling.
Modeling in Systems Biology, The Petri Net Approach
Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano
2015 J jnl
Estimating copy numbers of alleles from population-scale high-throughput sequencing data.
BMC Bioinform.
Takahiro Mimori, Naoki Nariai, Kaname Kojima, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki
2015 J jnl
HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data.
BMC Genom.
Naoki Nariai, Kaname Kojima, Sakae Saito, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Jun Yasuda, Masao Nagasaki
2014 J jnl
An efficient method of exploring simulation models by assimilating literature and biological observational data.
Biosyst.
Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2014 J jnl
CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML.
Biosyst.
Chen Li, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Satoru Miyano
2014 — conf
HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads.
AlCoB
Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai, Masao Nagasaki
2014 — conf
SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints.
AlCoB
Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Tetsuo Shibuya, Masao Nagasaki
2013 J jnl
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads.
Bioinform.
Kaname Kojima, Naoki Nariai, Takahiro Mimori, Mamoru Takahashi, Yumi Yamaguchi-Kabata, Yukuto Sato, Masao Nagasaki
2013 J jnl
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.
Bioinform.
Naoki Nariai, Osamu Hirose, Kaname Kojima, Masao Nagasaki
2013 J jnl
XiP: a computational environment to create, extend and share workflows.
Bioinform.
Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li, Satoru Miyano
2013 J jnl
iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data.
BMC Syst. Biol.
Takahiro Mimori, Naoki Nariai, Kaname Kojima, Mamoru Takahashi, Akira Ono, Yukuto Sato, Yumi Yamaguchi-Kabata, Masao Nagasaki
2012 J jnl
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.
BMC Bioinform.
Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki, Satoru Miyano
2012 J jnl
IRView: a database and viewer for protein interacting regions.
Bioinform.
Shigeo Fujimori, Naoya Hirai, Kazuyo Masuoka, Tomohiro Oshikubo, Tatsuhiro Yamashita, Takanori Washio, Ayumu Saito, Masao Nagasaki, Satoru Miyano, Etsuko Miyamoto-Sato
2012 J jnl
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
2011 J jnl
CSO validator: improving manual curation workflow for biological pathways.
Bioinform.
Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano
2011 J jnl
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.
BMC Bioinform.
Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki
2011 — conf
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation.
ISBRA
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
2011 J jnl
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin G. Print, Stephen D. Charnock-Jones, Satoru Miyano
2011 J jnl
High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA.
IEEE ACM Trans. Comput. Biol. Bioinform.
Georgios Chalkidis, Masao Nagasaki, Satoru Miyano
2011 J jnl
Hybrid Petri net based modeling for biological pathway simulation.
Nat. Comput.
Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano
2011 J jnl
MIRACH: efficient model checker for quantitative biological pathway models.
Bioinform.
Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano
2011 J jnl
Ontology-based instance data validation for high-quality curated biological pathways.
BMC Bioinform.
Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano
2011 — conf
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation.
ICCABS
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
2011 J jnl
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinform.
Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano
2011 J jnl
Systems biology model repository for macrophage pathway simulation.
Bioinform.
Masao Nagasaki, Ayumu Saito, André Fujita, Georg Tremmel, Kazuko Ueno, Emi Ikeda, Euna Jeong, Satoru Miyano
2010 J jnl
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.
BMC Bioinform.
Kaname Kojima, Masao Nagasaki, Satoru Miyano
2010 J jnl
Cell Illustrator 4.0: A Computational Platform for Systems Biology.
Silico Biol.
Masao Nagasaki, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda, Satoru Miyano
2010 J jnl
DA 1.0: parameter estimation of biological pathways using data assimilation approach.
Bioinform.
Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Limsoon Wong, Satoru Miyano
2010 — conf
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning.
BIBM
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
2010 J jnl
Identification of Granger Causality between Gene Sets.
J. Bioinform. Comput. Biol.
André Fujita, João Ricardo Sato, Kaname Kojima, Luciana Rodrigues Gomes, Masao Nagasaki, Mari Cleide Sogayar, Satoru Miyano
2010 J jnl
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
Bioinform.
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
2010 J jnl
Model-free unsupervised gene set screening based on information enrichment in expression profiles.
Bioinform.
Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano
2010 J jnl
Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana.
Silico Biol.
Kerstin Kaufmann, Masao Nagasaki, Ruy Jáuregui
2010 — conf
Network profiling analysis for generating modulator-dependent gene networks.
BIBM Workshops
Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano
2010 J jnl
The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis.
Biosyst.
Jin Hwan Do, Masao Nagasaki, Satoru Miyano
2010 J jnl
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram.
BMC Syst. Biol.
Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano
2009 J jnl
BFL: a node and edge betweenness based fast layout algorithm for large scale networks.
BMC Bioinform.
Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano
2009 B conf
Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality.
Discovery Science
Takanori Yamamoto, Hideo Bannai, Masao Nagasaki, Satoru Miyano
2009 — book
Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases.
Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
2009 — conf
Gene Networks Viewed through Two Models.
BICoB
Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto
2009 Misc conf
Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing.
Pacific Symposium on Biocomputing
Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi
2009 J jnl
Recursive regularization for inferring gene networks from time-course gene expression profiles.
BMC Syst. Biol.
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano
2009 J jnl
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.
BMC Syst. Biol.
Chen Li, Masao Nagasaki, Kazuko Ueno, Satoru Miyano
2009 Misc conf
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks.
Pacific Symposium on Biocomputing
Yoshinori Tamada, Hiromitsu Araki, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Yukiko Nakanishi, Yuki Tomiyasu, Kaori Yasuda, Ben Dunmore, Deborah Sanders, Sally Humphreys, Cristin G. Print, Stephen D. Charnock-Jones, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2008 J jnl
Bayesian learning of biological pathways on genomic data assimilation.
Bioinform.
Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi
2008 J jnl
ExonMiner: Web service for analysis of GeneChip Exon array data.
BMC Bioinform.
Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano
2008 J jnl
Fast grid layout algorithm for biological networks with sweep calculation.
Bioinform.
Kaname Kojima, Masao Nagasaki, Satoru Miyano
2008 J jnl
Systematic reconstruction of TRANSPATH data into Cell System Markup Language.
BMC Syst. Biol.
Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano
2007 J jnl
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.
Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto, Satoru Miyano
2007 J jnl
An efficient grid layout algorithm for biological networks utilizing various biological attributes.
BMC Bioinform.
Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano
2007 J jnl
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways.
Silico Biol.
Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano
2007 C conf
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles.
BIBE
Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano
2006 J jnl
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.
Silico Biol.
Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano
2004 J jnl
Constructing biological pathway models with hybrid functional Petri net.
Silico Biol.
Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano
2004 B conf
Integrating Biopathway Databases for Large-scale Modeling and Simulation.
APBC
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
2003 — conf
Recreating Biopathway Databases towards Simulation.
CMSB
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
2003 — conf
Towards Biopathway Modeling and Simulation.
ICATPN
Hiroshi Matsuno, Sachie Fujita, Atsushi Doi, Masao Nagasaki, Satoru Miyano