Masao Nagasaki

Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li, Satoru Miyano: XiP: a computational environment to create, extend and share workflows. Bioinformatics 29(1): 137-139 (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. Bioinformatics 28(14): 1949-1950 (2012)

Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki, Satoru Miyano: ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinformatics 13: 279 (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. Biology Bioinform. 9(4): 966-972 (2012)

Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano: MIRACH: efficient model checker for quantitative biological pathway models. Bioinformatics 27(5): 734-735 (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. Bioinformatics 27(8): 1172-1173 (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. Bioinformatics 27(11): 1591-1593 (2011)

Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano: CSO validator: improving manual curation workflow for biological pathways. Bioinformatics 27(17): 2471-2472 (2011)

Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano: Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics 12(S-1): S8 (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 Bioinformatics 12(S-14): S7 (2011)

Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano: Hybrid Petri net based modeling for biological pathway simulation. Natural Computing 10(3): 1099-1120 (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. Biology Bioinform. 8(3): 683-697 (2011)

Georgios Chalkidis, Masao Nagasaki, Satoru Miyano: High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA. IEEE/ACM Trans. Comput. Biology Bioinform. 8(6): 1545-1556 (2011)

Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano: Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. ICCABS 2011: 246

Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano: Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. ISBRA 2011: 160-171

Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano: Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics 26(8): 1064-1072 (2010)

Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Limsoon Wong, Satoru Miyano: DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics 26(14): 1794-1796 (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. Bioinformatics 26(24): 3090-3097 (2010)

Jin Hwan Do, Masao Nagasaki, Satoru Miyano: The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosystems 100(3): 178-184 (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 Bioinformatics 11: 335 (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. Bioinformatics and Computational Biology 8(4): 679-701 (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: 253-258

Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano: BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinformatics 10 (2009)

Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto: Gene Networks Viewed through Two Models. BICoB 2009: 54-66

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

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

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

Kaname Kojima, Masao Nagasaki, Satoru Miyano: Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics 24(12): 1433-1441 (2008)

Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi: Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics 24(22): 2592-2601 (2008)

Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano: ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinformatics 9 (2008)

Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano: An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics 8 (2007)

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 Bioinformatics 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: 715-722

Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano: Constructing biological pathway models with hybrid functional Petri net. In Silico Biology 4 (2004)

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano: Integrating Biopathway Databases for Large-scale Modeling and Simulation. APBC 2004: 43-52

Hiroshi Matsuno, Sachie Fujita, Atsushi Doi, Masao Nagasaki, Satoru Miyano: Towards Biopathway Modeling and Simulation. ICATPN 2003: 3-22

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano: Recreating Biopathway Databases towards Simulation. CMSB 2003: 168-169