Towards Biopathway Modeling and Simulation. - Hiroshi Matsuno; Sachie Fujita; Atsushi Doi; Masao Nagasaki; Satoru Miyano (ICATPN, 2003)

Recreating Biopathway Databases towards Simulation. - Masao Nagasaki; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano (CMSB, 2003)

Integrating Biopathway Databases for Large-scale Modeling and Simulation. - Masao Nagasaki; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano (APBC, 2004)

Constructing biological pathway models with hybrid functional Petri net. - Atsushi Doi; Sachie Fujita; Hiroshi Matsuno; Masao Nagasaki; Satoru Miyano (Silico Biol., 2004)

Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net. - Atsushi Doi; Masao Nagasaki; Hiroshi Matsuno; Satoru Miyano (Silico Biol., 2006)

Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles. - Ryo Yoshida; Kazuyuki Numata; Seiya Imoto; Masao Nagasaki; Atsushi Doi; Kazuko Ueno; Satoru Miyano (BIBE, 2007)

An efficient grid layout algorithm for biological networks utilizing various biological attributes. - Kaname Kojima; Masao Nagasaki; Euna Jeong; Mitsuru Kato; Satoru Miyano (BMC Bioinform., 2007)

AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. - Ayumu Saito; Masao Nagasaki; Masaaki Oyama; Hiroko Kozuka-Hata; Kentaro Semba; Sumio Sugano; Tadashi Yamamoto; Satoru Miyano (BMC Bioinform., 2007)

Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways. - Euna Jeong; Masao Nagasaki; Ayumu Saito; Satoru Miyano (Silico Biol., 2007)

Fast grid layout algorithm for biological networks with sweep calculation. - Kaname Kojima; Masao Nagasaki; Satoru Miyano (Bioinform., 2008)

Bayesian learning of biological pathways on genomic data assimilation. - Ryo Yoshida; Masao Nagasaki; Rui Yamaguchi; Seiya Imoto; Satoru Miyano; Tomoyuki Higuchi (Bioinform., 2008)

ExonMiner: Web service for analysis of GeneChip Exon array data. - Kazuyuki Numata; Ryo Yoshida; Masao Nagasaki; Ayumu Saito; Seiya Imoto; Satoru Miyano (BMC Bioinform., 2008)

Systematic reconstruction of TRANSPATH data into Cell System Markup Language. - Masao Nagasaki; Ayumu Saito; Chen Li 007; Euna Jeong; Satoru Miyano (BMC Syst. Biol., 2008)

Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases. - Masao Nagasaki; Ayumu Saito; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano (Springer, 2009)

Gene Networks Viewed through Two Models. - Satoru Miyano; Rui Yamaguchi; Yoshinori Tamada; Masao Nagasaki; Seiya Imoto (BICoB, 2009)

Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality. - Takanori Yamamoto; Hideo Bannai; Masao Nagasaki; Satoru Miyano (Discovery Science, 2009)

Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing. - Kazuyuki Nakamura; Ryo Yoshida; Masao Nagasaki; Satoru Miyano; Tomoyuki Higuchi (Pacific Symposium on Biocomputing, 2009)

Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks. - 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; et al. (Pacific Symposium on Biocomputing, 2009)

BFL: a node and edge betweenness based fast layout algorithm for large scale networks. - Tatsunori B. Hashimoto; Masao Nagasaki; Kaname Kojima; Satoru Miyano (BMC Bioinform., 2009)

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. - Chen Li 007; Masao Nagasaki; Kazuko Ueno; Satoru Miyano (BMC Syst. Biol., 2009)

Recursive regularization for inferring gene networks from time-course gene expression profiles. - Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; André Fujita; Masao Nagasaki; Satoru Miyano (BMC Syst. Biol., 2009)

Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. - Shuichi Kawano; Teppei Shimamura; Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Ryo Yoshida; Cristin G. Print; Satoru Miyano (BIBM, 2010)

Network profiling analysis for generating modulator-dependent gene networks. - Teppei Shimamura; Seiya Imoto; Atsushi Niida; Masao Nagasaki; Rui Yamaguchi; Satoru Miyano (BIBM Workshops, 2010)

DA 1.0: parameter estimation of biological pathways using data assimilation approach. - Chuan Hock Koh; Masao Nagasaki; Ayumu Saito; Limsoon Wong; Satoru Miyano (Bioinform., 2010)

Model-free unsupervised gene set screening based on information enrichment in expression profiles. - Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; André Fujita; Teppei Shimamura; Satoru Miyano (Bioinform., 2010)

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. - Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Satoru Miyano (Bioinform., 2010)

The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. - Jin Hwan Do; Masao Nagasaki; Satoru Miyano (Biosyst., 2010)

An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. - Kaname Kojima; Masao Nagasaki; Satoru Miyano (BMC Bioinform., 2010)

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. - Chen Li 007; Masao Nagasaki; Ayumu Saito; Satoru Miyano (BMC Syst. Biol., 2010)

Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana. - Kerstin Kaufmann; Masao Nagasaki; Ruy Jáuregui (Silico Biol., 2010)

Cell Illustrator 4.0: A Computational Platform for Systems Biology. - Masao Nagasaki; Ayumu Saito; Euna Jeong; Chen Li 007; Kaname Kojima; Emi Ikeda; Satoru Miyano (Silico Biol., 2010)

Identification of Granger Causality between Gene Sets. - André Fujita; João Ricardo Sato; Kaname Kojima; Luciana Rodrigues Gomes; Masao Nagasaki; Mari Cleide Sogayar; Satoru Miyano (J. Bioinform. Comput. Biol., 2010)

Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. - Takanori Hasegawa; Rui Yamaguchi; Masao Nagasaki; Seiya Imoto; Satoru Miyano (ICCABS, 2011)

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. - Takanori Hasegawa; Rui Yamaguchi; Masao Nagasaki; Seiya Imoto; Satoru Miyano (ISBRA, 2011)

CSO validator: improving manual curation workflow for biological pathways. - Euna Jeong; Masao Nagasaki; Emi Ikeda; Yayoi Sekiya; Ayumu Saito; Satoru Miyano (Bioinform., 2011)

MIRACH: efficient model checker for quantitative biological pathway models. - Chuan Hock Koh; Masao Nagasaki; Ayumu Saito; Chen Li 007; Limsoon Wong; Satoru Miyano (Bioinform., 2011)

Systems biology model repository for macrophage pathway simulation. - Masao Nagasaki; Ayumu Saito; André Fujita; Georg Tremmel; Kazuko Ueno; Emi Ikeda; Euna Jeong; Satoru Miyano (Bioinform., 2011)

SiGN-SSM: open source parallel software for estimating gene networks with state space models. - Yoshinori Tamada; Rui Yamaguchi; Seiya Imoto; Osamu Hirose; Ryo Yoshida; Masao Nagasaki; Satoru Miyano (Bioinform., 2011)

Ontology-based instance data validation for high-quality curated biological pathways. - Euna Jeong; Masao Nagasaki; Kazuko Ueno; Satoru Miyano (BMC Bioinform., 2011)

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. - Shin Suzuki; Tomohiro Yasuda; Yuichi Shiraishi; Satoru Miyano; Masao Nagasaki (BMC Bioinform., 2011)

Hybrid Petri net based modeling for biological pathway simulation. - Hiroshi Matsuno; Masao Nagasaki; Satoru Miyano (Nat. Comput., 2011)

High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA. - Georgios Chalkidis; Masao Nagasaki; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. - Yoshinori Tamada; Seiya Imoto; Hiromitsu Araki; Masao Nagasaki; Cristin G. Print; Stephen D. Charnock-Jones; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

IRView: a database and viewer for protein interacting regions. - Shigeo Fujimori; Naoya Hirai; Kazuyo Masuoka; Tomohiro Oshikubo; Tatsuhiro Yamashita; Takanori Washio; Ayumu Saito; Masao Nagasaki; Satoru Miyano; Etsuko Miyamoto-Sato (Bioinform., 2012)

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. - Tomohiro Yasuda; Shin Suzuki; Masao Nagasaki; Satoru Miyano (BMC Bioinform., 2012)

Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. - Shuichi Kawano; Teppei Shimamura; Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Ryo Yoshida; Cristin G. Print; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. - Kaname Kojima; Naoki Nariai; Takahiro Mimori; Mamoru Takahashi; Yumi Yamaguchi-Kabata; Yukuto Sato; Masao Nagasaki (Bioinform., 2013)

XiP: a computational environment to create, extend and share workflows. - Masao Nagasaki; André Fujita; Yayoi Sekiya; Ayumu Saito; Emi Ikeda; Chen Li 007; Satoru Miyano (Bioinform., 2013)

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. - Naoki Nariai; Osamu Hirose; Kaname Kojima; Masao Nagasaki (Bioinform., 2013)

iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. - Takahiro Mimori; Naoki Nariai; Kaname Kojima; Mamoru Takahashi; Akira Ono; Yukuto Sato; Yumi Yamaguchi-Kabata; Masao Nagasaki (BMC Syst. Biol., 2013)

HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads. - Kaname Kojima; Naoki Nariai; Takahiro Mimori; Yumi Yamaguchi-Kabata; Yukuto Sato; Yosuke Kawai; Masao Nagasaki (AlCoB, 2014)

SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints. - Tomohiko Ohtsuki; Naoki Nariai; Kaname Kojima; Takahiro Mimori; Yukuto Sato; Yosuke Kawai; Yumi Yamaguchi-Kabata; Tetsuo Shibuya; Masao Nagasaki (AlCoB, 2014)

CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML. - Chen Li 007; Masao Nagasaki; Emi Ikeda; Yayoi Sekiya; Satoru Miyano (Biosyst., 2014)

An efficient method of exploring simulation models by assimilating literature and biological observational data. - Takanori Hasegawa; Masao Nagasaki; Rui Yamaguchi; Seiya Imoto; Satoru Miyano (Biosyst., 2014)

Estimating copy numbers of alleles from population-scale high-throughput sequencing data. - Takahiro Mimori; Naoki Nariai; Kaname Kojima; Yukuto Sato; Yosuke Kawai; Yumi Yamaguchi-Kabata; Masao Nagasaki (BMC Bioinform., 2015)

HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. - Naoki Nariai; Kaname Kojima; Sakae Saito; Takahiro Mimori; Yukuto Sato; Yosuke Kawai; Yumi Yamaguchi-Kabata; Jun Yasuda; Masao Nagasaki (BMC Genom., 2015)

A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. - Naoki Nariai; Kaname Kojima; Takahiro Mimori; Yosuke Kawai; Masao Nagasaki (BMC Genom., 2016)

Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. - Ayumu Saito; Masao Nagasaki; Hiroshi Matsuno; Satoru Miyano (Modeling in Systems Biology, The Petri Net Approach, 2016)

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

Time-Series Filtering for Replicated Observations via a Kernel Approximate Bayesian Computation. - Takanori Hasegawa; Kaname Kojima; Yosuke Kawai; Masao Nagasaki (IEEE Trans. Signal Process., 2018)

High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net. - Chen Li 007; Jiale Qin; Keisuke Kuroyanagi; Lu Lu; Masao Nagasaki; Satoru Miyano (Biosyst., 2021)