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ORCIDMasao Nagasaki
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2020 – today
- 2021
[j45]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: 104332 (2021)
2010 – 2019
- 2018
- [j44]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): 6148-6161 (2018) - 2017
- [j43]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): 100:1-100:12 (2017) - 2016
- [j42]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): 2 (2016) - [p1]Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano:
Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. Modeling in Systems Biology, The Petri Net Approach 2016: 101-120 - 2015
- [j41]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): S4 (2015) - [j40]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): S7 (2015) - 2014
- [j39]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: 22-28 (2014) - [j38]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: 54-66 (2014) - [c14]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: 107-118 - [c13]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: 208-219 - 2013
- [j37]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): 137-139 (2013) - [j36]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): 2292-2299 (2013) - [j35]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): 2835-2843 (2013) - [j34]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): S8 (2013) - 2012
- [j33]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): 1949-1950 (2012) - [j32]Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki, Satoru Miyano:
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinform. 13: 279 (2012) - [j31]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): 966-972 (2012) - 2011
- [j30]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): 734-735 (2011) - [j29]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): 1172-1173 (2011) - [j28]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): 1591-1593 (2011) - [j27]Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano:
CSO validator: improving manual curation workflow for biological pathways. Bioinform. 27(17): 2471-2472 (2011) - [j26]Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano:
Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinform. 12(S-1): S8 (2011) - [j25]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): S7 (2011) - [j24]Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano:
Hybrid Petri net based modeling for biological pathway simulation. Nat. Comput. 10(3): 1099-1120 (2011) - [j23]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): 683-697 (2011) - [j22]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): 1545-1556 (2011) - [c12]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. ICCABS 2011: 246 - [c11]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. ISBRA 2011: 160-171 - 2010
- [j21]Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano:
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinform. 26(8): 1064-1072 (2010) - [j20]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): 1794-1796 (2010) - [j19]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): 3090-3097 (2010) - [j18]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): 178-184 (2010) - [j17]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: 335 (2010) - [j16]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: 39 (2010) - [j15]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): 5-26 (2010) - [j14]Kerstin Kaufmann, Masao Nagasaki, Ruy Jáuregui:
Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana. Silico Biol. 10(1-2): 125-143 (2010) - [j13]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): 679-701 (2010) - [c10]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: 253-258 - [c9]Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano:
Network profiling analysis for generating modulator-dependent gene networks. BIBM Workshops 2010: 836
2000 – 2009
- 2009
- [b1]Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano:
Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases. Computational Biology 13, Springer 2009, ISBN 978-1-84882-022-7, pp. I-XII, 1-155 - [j12]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) - [j11]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: 41 (2009) - [j10]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: 42 (2009) - [c8]Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto:
Gene Networks Viewed through Two Models. BICoB 2009: 54-66 - [c7]Takanori Yamamoto, Hideo Bannai, Masao Nagasaki, Satoru Miyano:
Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality. Discovery Science 2009: 465-472 - [c6]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: 227-238 - [c5]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: 251-263 - 2008
- [j9]Kaname Kojima, Masao Nagasaki, Satoru Miyano:
Fast grid layout algorithm for biological networks with sweep calculation. Bioinform. 24(12): 1433-1441 (2008) - [j8]Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi:
Bayesian learning of biological pathways on genomic data assimilation. Bioinform. 24(22): 2592-2601 (2008) - [j7]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) - [j6]Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano:
Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Syst. Biol. 2: 53 (2008) - 2007
- [j5]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) - [j4]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) - [j3]Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano:
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways. Silico Biol. 7(6): 623-638 (2007) - [c4]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: 715-722 - 2006
- [j2]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): 1-13 (2006) - 2004
- [j1]Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano:
Constructing biological pathway models with hybrid functional Petri net. Silico Biol. 4(3): 271-291 (2004) - [c3]Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano:
Integrating Biopathway Databases for Large-scale Modeling and Simulation. APBC 2004: 43-52 - 2003
- [c2]Hiroshi Matsuno, Sachie Fujita, Atsushi Doi, Masao Nagasaki, Satoru Miyano:
Towards Biopathway Modeling and Simulation. ICATPN 2003: 3-22 - [c1]Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano:
Recreating Biopathway Databases towards Simulation. CMSB 2003: 168-169
Coauthor Index
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