Masao Nagasaki

Publication Activity (10 Years)

Years Active: 2003-2021
Publications (10 Years): 6

Top Topics

Biological Pathways

Differential Expression

Top Venues

Publications

Chen Li, Jiale Qin, Keisuke Kuroyanagi, Lu Lu, Masao Nagasaki, Satoru Miyano
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net. Biosyst. 201 (2021)
Takanori Hasegawa, Kaname Kojima, Yosuke Kawai, Masao Nagasaki
Time-Series Filtering for Replicated Observations via a Kernel Approximate Bayesian Computation. IEEE Trans. Signal Process. 66 (23) (2018)
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
Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design. BMC Medical Informatics Decis. Mak. 17 (1) (2017)
Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yosuke Kawai, Masao Nagasaki
A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. BMC Genom. 17 (S-1) (2016)
Takahiro Mimori, Naoki Nariai, Kaname Kojima, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki
Estimating copy numbers of alleles from population-scale high-throughput sequencing data. BMC Bioinform. 16 (S-1) (2015)
Naoki Nariai, Kaname Kojima, Sakae Saito, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Jun Yasuda, Masao Nagasaki
HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. BMC Genom. 16 (S-2) (2015)
Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
An efficient method of exploring simulation models by assimilating literature and biological observational data. Biosyst. 121 (2014)
Chen Li, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Satoru Miyano
CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML. Biosyst. 121 (2014)
Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai, Masao Nagasaki
HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads. AlCoB (2014)
Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Tetsuo Shibuya, Masao Nagasaki
SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints. AlCoB (2014)
Takahiro Mimori, Naoki Nariai, Kaname Kojima, Mamoru Takahashi, Akira Ono, Yukuto Sato, Yumi Yamaguchi-Kabata, Masao Nagasaki
iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Syst. Biol. 7 (S-6) (2013)
Kaname Kojima, Naoki Nariai, Takahiro Mimori, Mamoru Takahashi, Yumi Yamaguchi-Kabata, Yukuto Sato, Masao Nagasaki
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. Bioinform. 29 (22) (2013)
Naoki Nariai, Osamu Hirose, Kaname Kojima, Masao Nagasaki
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. Bioinform. 29 (18) (2013)
Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li, Satoru Miyano
XiP: a computational environment to create, extend and share workflows. Bioinform. 29 (1) (2013)
Shigeo Fujimori, Naoya Hirai, Kazuyo Masuoka, Tomohiro Oshikubo, Tatsuhiro Yamashita, Takanori Washio, Ayumu Saito, Masao Nagasaki, Satoru Miyano, Etsuko Miyamoto-Sato
IRView: a database and viewer for protein interacting regions. Bioinform. 28 (14) (2012)
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki, Satoru Miyano
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinform. 13 (2012)
Georgios Chalkidis, Masao Nagasaki, Satoru Miyano
High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (6) (2011)
Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano
CSO validator: improving manual curation workflow for biological pathways. Bioinform. 27 (17) (2011)
Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin G. Print, Stephen D. Charnock-Jones, Satoru Miyano
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano
Hybrid Petri net based modeling for biological pathway simulation. Nat. Comput. 10 (3) (2011)
Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano
Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinform. 12 (S-1) (2011)
Masao Nagasaki, Ayumu Saito, André Fujita, Georg Tremmel, Kazuko Ueno, Emi Ikeda, Euna Jeong, Satoru Miyano
Systems biology model repository for macrophage pathway simulation. Bioinform. 27 (11) (2011)
Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinform. 12 (S-14) (2011)
Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano
MIRACH: efficient model checker for quantitative biological pathway models. Bioinform. 27 (5) (2011)
Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano
SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinform. 27 (8) (2011)
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. ISBRA (2011)
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. ICCABS (2011)
Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Limsoon Wong, Satoru Miyano
DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinform. 26 (14) (2010)
Jin Hwan Do, Masao Nagasaki, Satoru Miyano
The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosyst. 100 (3) (2010)
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinform. 26 (8) (2010)
Kerstin Kaufmann, Masao Nagasaki, Ruy Jáuregui
Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana. Silico Biol. 10 (1-2) (2010)
Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Syst. Biol. 4 (2010)
Kaname Kojima, Masao Nagasaki, Satoru Miyano
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinform. 11 (2010)
Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano
Network profiling analysis for generating modulator-dependent gene networks. BIBM Workshops (2010)
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. BIBM (2010)
Masao Nagasaki, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda, Satoru Miyano
Cell Illustrator 4.0: A Computational Platform for Systems Biology. Silico Biol. 10 (1-2) (2010)
André Fujita, João Ricardo Sato, Kaname Kojima, Luciana Rodrigues Gomes, Masao Nagasaki, Mari Cleide Sogayar, Satoru Miyano
Identification of Granger Causality between Gene Sets. J. Bioinform. Comput. Biol. 8 (4) (2010)
Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano
Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinform. 26 (24) (2010)
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
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks. Pacific Symposium on Biocomputing (2009)
Chen Li, Masao Nagasaki, Kazuko Ueno, Satoru Miyano
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst. Biol. 3 (2009)
Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi
Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing. Pacific Symposium on Biocomputing (2009)
Takanori Yamamoto, Hideo Bannai, Masao Nagasaki, Satoru Miyano
Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality. Discovery Science (2009)
Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto
Gene Networks Viewed through Two Models. BICoB (2009)
Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano
BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinform. 10 (2009)
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst. Biol. 3 (2009)
Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi
Bayesian learning of biological pathways on genomic data assimilation. Bioinform. 24 (22) (2008)
Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano
Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Syst. Biol. 2 (2008)
Kaname Kojima, Masao Nagasaki, Satoru Miyano
Fast grid layout algorithm for biological networks with sweep calculation. Bioinform. 24 (12) (2008)
Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano
ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinform. 9 (2008)
Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto, Satoru Miyano
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. 8 (2007)
Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles. BIBE (2007)
Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways. Silico Biol. 7 (6) (2007)
Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano
An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinform. 8 (2007)
Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net. Silico Biol. 6 (1-2) (2006)
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
Integrating Biopathway Databases for Large-scale Modeling and Simulation. APBC (2004)
Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano
Constructing biological pathway models with hybrid functional Petri net. Silico Biol. 4 (3) (2004)
Hiroshi Matsuno, Sachie Fujita, Atsushi Doi, Masao Nagasaki, Satoru Miyano
Towards Biopathway Modeling and Simulation. ICATPN (2003)
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
Recreating Biopathway Databases towards Simulation. CMSB (2003)