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Satoru Miyano

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Oligonucleotide Array Sequence Analysis

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Saccharomyces cerevisiae

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Rui Yamaguchi; Seiya Imoto; Masahiro Kami; Satoru Miyano; Kenji Watanabe; Koichiro Yuji
Does Twitter trigger bursts in signature collections?
Muna Affara; Hiromitsu Araki; Benjamin J Dunmore; Sally Humphreys; Seiya Imoto; David Jeffries; Satoru Kuhara; Satoru Miyano; Cristin G Print; Debbie Sanders; Christopher Savoie; Yoshinori Tamada; D Stephen Charnock-Jones
Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis.
Masao Nagasaki; Ayumu Saito; Yayoi Sekiya; André Fujita; Emi Ikeda; Chen Li; Satoru Miyano
XiP: a computational environment to create, extend and share workflows.

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All Publications

2013: Rui Yamaguchi; Seiya Imoto; Masahiro Kami; Satoru Miyano; Kenji Watanabe; Koichiro Yuji
Does Twitter trigger bursts in signature collections?
PloS one 2013;8(3):e58252.
2013: Muna Affara; Hiromitsu Araki; Benjamin J Dunmore; Sally Humphreys; Seiya Imoto; David Jeffries; Satoru Kuhara; Satoru Miyano; Cristin G Print; Debbie Sanders; Christopher Savoie; Yoshinori Tamada; D Stephen Charnock-Jones
Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis.
BMC genomics 2013;14():23.
2013: Masao Nagasaki; Ayumu Saito; Yayoi Sekiya; André Fujita; Emi Ikeda; Chen Li; Satoru Miyano
XiP: a computational environment to create, extend and share workflows.
Bioinformatics (Oxford, England) 2013;29(1):137-9.
2012: Alok Sharma; Seiya Imoto; Satoru Miyano
A between-class overlapping filter-based method for transcriptome data analysis.
Journal of bioinformatics and computational biology 2012;10(5):1250010.
2012: Shigeo Fujimori; Naoya Hirai; Kazuyo Masuoka; Satoru Miyano; Masao Nagasaki; Tomohiro Oshikubo; Ayumu Saito; Takanori Washio; Tatsuhiro Yamashita; Etsuko Miyamoto-Sato
IRView: a database and viewer for protein interacting regions.
Bioinformatics (Oxford, England) 2012;28(14):1949-50.
2012: Atushi Niida; Teppei Shimamura; Seiya Imoto; Satoru Miyano
Statistical model-based testing to evaluate the recurrence of genomic aberrations.
Bioinformatics (Oxford, England) 2012;28(12):i115-20.
2012: Alok Sharma; Seiya Imoto; Satoru Miyano
A top-r feature selection algorithm for microarray gene expression data.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2012;9(3):754-64.
2012: Kentaro Ogami; Cristin Print; Yoshinori Tamada; Rui Yamaguchi; Hiromitsu Araki; Seiya Imoto; Satoru Miyano
Computational gene network analysis reveals TNF-induced angiogenesis.
BMC systems biology 2012;6 Suppl 2():S12.
2012: Tomohiro Yasuda; Masao Nagasaki; Shin Suzuki; Satoru Miyano
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.
BMC bioinformatics 2012;13():279.
2012: Shigeo Fujimori; Katsuya Hino; Satoru Miyano; Ayumu Saito; Etsuko Miyamoto-Sato
PRD: A protein-RNA interaction database.
Bioinformation 2012;8(15):729-30.
2012: Mai Yamauchi; Jun Yokota; Ryo Yoshida; David G Beer; Yousuke Hatanaka; Tomoyuki Higuchi; Seiya Imoto; Takashi Kohno; Satoru Miyano; Masao Nagasaki; Asuka Nakata; Masaharu Nomura; Ayumu Saito; Teppei Shimamura; Kazuko Ueno; Rui Yamaguchi; Noriko Gotoh
Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma.
PloS one 2012;7(9):e43923.
2012: Kaname Kojima; André Fujita; Noriko Gotoh; Seiya Imoto; Rui Yamaguchi; Mai Yamauchi; Satoru Miyano
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing.
BMC genomics 2012;13 Suppl 1():S6.
2011: Georgios Chalkidis; Masao Nagasaki; Satoru Miyano
High performance hybrid functional Petri net simulations of biological pathway models on CUDA.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2011;8(6):1545-56.
2011: Euna Jeong; Masao Nagasaki; Ayumu Saito; Yayoi Sekiya; Emi Ikeda; Satoru Miyano
CSO validator: improving manual curation workflow for biological pathways.
Bioinformatics (Oxford, England) 2011;27(17):2471-2.
2011: Yuichi Shiraishi; Mariko Okada-Hatakeyama; Satoru Miyano
A rank-based statistical test for measuring synergistic effects between two gene sets.
Bioinformatics (Oxford, England) 2011;27(17):2399-405.
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 (Oxford, England) 2011;27(11):1591-3.
2011: Chen Li; Masao Nagasaki; Chuan Hock Koh; Satoru Miyano
Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.
Molecular bioSystems 2011;7(5):1576-92.
2011: Yoshinori Tamada; Seiya Imoto; Hiromitsu Araki; Masao Nagasaki; Cristin G Print; D Stephen Charnock-Jones; Satoru Miyano
Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2011;8(3):683-97.
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 (Oxford, England) 2011;27(8):1172-3.
2011: Chuan Hock Koh; Masao Nagasaki; Ayumu Saito; Chen Li; Limsoon Wong; Satoru Miyano
MIRACH: efficient model checker for quantitative biological pathway models.
Bioinformatics (Oxford, England) 2011;27(5):734-5.
2011: Shin Suzuki; Tomohiro Yasuda; Satoru Miyano; Yuichi Shiraishi; Masao Nagasaki
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.
BMC bioinformatics 2011;12 Suppl 14():S7.
2011: Tsutomu Osoda; Satoru Miyano
2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope.
Journal of cheminformatics 2011;3(1):50.
2011: Teppei Shimamura; Takashi Takahashi; Rui Yamaguchi; Yasuyuki Hosono; Seiya Imoto; Masao Nagasaki; Atsushi Niida; Yukako Shimada; Satoru Miyano
A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition.
PloS one 2011;6(6):e20804.
2011: Masao Nagasaki; Ayumu Saito; Emi Ikeda; Euna Jeong; Kaname Kojima; Chen Li; Satoru Miyano
Cell illustrator 4.0: a computational platform for systems biology.
Studies in health technology and informatics 2011;162():160-81.
2011: Atsushi Doi; Hiroshi Matsuno; Masao Nagasaki; Satoru Miyano
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.
Studies in health technology and informatics 2011;162():130-42.
2011: Euna Jeong; Masao Nagasaki; Kazuko Ueno; Satoru Miyano
Ontology-based instance data validation for high-quality curated biological pathways.
BMC bioinformatics 2011;12 Suppl 1():S8.
2010: Atushi 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 (Oxford, England) 2010;26(24):3090-7.
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 (Oxford, England) 2010;26(14):1794-6.
2010: Teppei Shimamura; Yoshinori Tamada; Rui Yamaguchi; Mai Yamauchi; André Fujita; Noriko Gotoh; Seiya Imoto; Masao Nagasaki; Satoru Miyano
Collocation-based sparse estimation for constructing dynamic gene networks.
Genome informatics. International Conference on Genome Informatics 2010;24(1):164-78.
2010: Kaname Kojima; Seiya Imoto; Masao Nagasaki; Satoru Miyano
Gene regulatory network clustering for graph layout based on microarray gene expression data.
Genome informatics. International Conference on Genome Informatics 2010;24(1):84-95.
2010: Jin Hwan Do; Masao Nagasaki; Satoru Miyano
The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis.
Bio Systems 2010;100(3):178-84.
2010: Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Satoru Miyano
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
Bioinformatics (Oxford, England) 2010;26(8):1064-72.
2010: Masao Nagasaki; Ayumu Saito; Emi Ikeda; Euna Jeong; Kaname Kojima; Chen Li; Satoru Miyano
Cell Illustrator 4.0: a computational platform for systems biology.
In silico biology 2010;10(1):5-26.
2010: Shinya Tasaki; Masao Nagasaki; Hiroko Kozuka-Hata; Kentaro Semba; Noriko Gotoh; Seisuke Hattori; Jun-Ichiro Inoue; Tadashi Yamamoto; Satoru Miyano; Sumio Sugano; Masaaki Oyama
Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling.
PloS one 2010;5(11):e13926.
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 2010;11():335.
2010: Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Satoru Miyano
Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
PloS one 2010;5(6):e10910.
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 systems biology 2010;4():39.
2010: Atsushi Niida; Seiya Imoto; Masao Nagasaki; Rui Yamaguchi; Satoru Miyano
A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells.
Genome informatics. International Conference on Genome Informatics 2010;22():121-31.
2010: Kaname Kojima; Rui Yamaguchi; Seiya Imoto; Mai Yamauchi; Masao Nagasaki; Ryo Yoshida; Teppei Shimamura; Kazuko Ueno; Tomoyuki Higuchi; Noriko Gotoh; Satoru Miyano
A state space representation of VAR models with sparse learning for dynamic gene networks.
Genome informatics. International Conference on Genome Informatics 2010;22():56-68.
2009: André Fujita; João Ricardo Sato; Marcos Angelo Almeida Demasi; Mari Cleide Sogayar; Carlos Eduardo Ferreira; Satoru Miyano
Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis.
Journal of bioinformatics and computational biology 2009;7(4):663-84.
2009: Jin Hwan Do; Rui Yamaguchi; Satoru Miyano
Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model.
BMC genomics 2009;10():306.
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 systems biology 2009;3():42.
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 systems biology 2009;3():41.
2009: Yoshinori Tamada; Hiromitsu Araki; Seiya Imoto; Masao Nagasaki; Atsushi Doi; Yukiko Nakanishi; Yuki Tomiyasu; K Yasuda; Ben Dunmore; Deborah Sanders; Sally Humphreys; Cristin G Print; D Stephen Charnock-Jones; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano
Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2009;():251-63.
2009: Yoshimi Yashiro; Hideo Bannai; Takashi Minowa; Tomohide Yabiku; Satoru Miyano; Mitsujiro Osawa; Atsushi Iwama; Hiromitsu Nakauchi
Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing.
International journal of hematology 2009;89(1):24-33.
2008: André Fujita; João Ricardo Sato; Humberto Miguel Garay-Malpartida; Mari Cleide Sogayar; Carlos Eduardo Ferreira; Satoru Miyano
Modeling nonlinear gene regulatory networks from time series gene expression data.
Journal of bioinformatics and computational biology 2008;6(5):961-79.
2008: Jin Hwan Do; Satoru Miyano
The GC and window-averaged DNA curvature profile of secondary metabolite gene cluster in Aspergillus fumigatus genome.
Applied microbiology and biotechnology 2008;80(5):841-7.
2008: Kaname Kojima; Masao Nagasaki; Satoru Miyano
Fast grid layout algorithm for biological networks with sweep calculation.
Bioinformatics (Oxford, England) 2008;24(12):1433-41.
2008: Osamu Hirose; Ryo Yoshida; Seiya Imoto; Rui Yamaguchi; Tomoyuki Higuchi; D Stephen Charnock-Jones; Cristin Print; Satoru Miyano
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
Bioinformatics (Oxford, England) 2008;24(7):932-42.
2008: Rui Yamaguchi; Seiya Imoto; Mai Yamauchi; Masao Nagasaki; Ryo Yoshida; Teppei Shimamura; Yosuke Hatanaka; Kazuko Ueno; Tomoyuki Higuchi; Noriko Gotoh; Satoru Miyano
Predicting differences in gene regulatory systems by state space models.
Genome informatics. International Conference on Genome Informatics 2008;21():101-13.
2008: Yosuke Hatanaka; Masao Nagasaki; Rui Yamaguchi; Takeshi Obayashi; Kazuyuki Numata; Andrè Fujita; Teppei Shimamura; Yoshinori Tamada; Seiya Imoto; Kengo Kinoshita; Kenta Nakai; Satoru Miyano
A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human.
Genome informatics. International Conference on Genome Informatics 2008;20():212-21.
2008: Kaname Kojima; André Fujita; Teppei Shimamura; Seiya Imoto; Satoru Miyano
Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data.
Genome informatics. International Conference on Genome Informatics 2008;20():37-51.
2008: Euna Jeong; Masao Nagasaki; Satoru Miyano
Rule-based reasoning for system dynamics in cell systems.
Genome informatics. International Conference on Genome Informatics 2008;20():25-36.
2008: André Fujita; Luciana Rodrigues Gomes; João Ricardo Sato; Rui Yamaguchi; Carlos Eduardo Thomaz; Mari Cleide Sogayar; Satoru Miyano
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates.
BMC systems biology 2008;2():106.
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 2008;9():494.
2008: Masao Nagasaki; Ayumu Saito; Chen Li; Euna Jeong; Satoru Miyano
Systematic reconstruction of TRANSPATH data into cell system markup language.
BMC systems biology 2008;2():53.
2007: Muna Affara; Benjamin Dunmore; Christopher Savoie; Seiya Imoto; Yoshinori Tamada; Hiromitsu Araki; D Stephen Charnock-Jones; Satoru Miyano; Cristin G Print
Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal?
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2007;362(1484):1469-87.
2007: Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; Satoru Miyano
Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data.
Genome informatics. International Conference on Genome Informatics 2007;19():142-53.
2007: Osamu Hirose; Ryo Yoshida; Rui Yamaguchi; Seiya Imoto; Tomoyuki Higuchi; Satoru Miyano
Clustering samples characterized by time course gene expression profiles using the mixture of state space models.
Genome informatics. International Conference on Genome Informatics 2007;18():258-66.
2007: Euna Jeong; Masao Nagasaki; Satoru Miyano
Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway.
Genome informatics. International Conference on Genome Informatics 2007;18():225-36.
2007: Rui Yamaguchi; Masahiro Yamamoto; Seiya Imoto; Masao Nagasaki; Ryo Yoshida; Kenji Tsuiji; Atsushi Ishige; Hiroaki Asou; Kenji Watanabe; Satoru Miyano
Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice.
Genome informatics. International Conference on Genome Informatics 2007;18():119-29.
2007: Euna Jeong; Masao Nagasaki; Ayumu Saito; Satoru Miyano
Cell system ontology: representation for modeling, visualizing, and simulating biological pathways.
In silico biology 2007;7(6):623-38.
2007: Kaname Kojima; Masao Nagasaki; Euna Jeong; Mitsuru Kato; Satoru Miyano
An efficient grid layout algorithm for biological networks utilizing various biological attributes.
BMC bioinformatics 2007;8():76.
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 2007;8():15.
2007: Seiya Imoto; Yoshinori Tamada; Christopher J Savoie; Satoru Miyano
Analysis of gene networks for drug target discovery and validation.
Methods in molecular biology (Clifton, N.J.) 2007;360():33-56.
2006: Yoshio Takei; Akatsuki Kawakoshi; Takehiro Tsukada; Shinya Yuge; Maho Ogoshi; Koji Inoue; Susumu Hyodo; Hiroko Bannai; Satoru Miyano
Contribution of comparative fish studies to general endocrinology: structure and function of some osmoregulatory hormones.
Journal of experimental zoology. Part A, Comparative experimental biology 2006;305(9):787-98.
2006: Ryo Yoshida; Tomoyuki Higuchi; Seiya Imoto; Satoru Miyano
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.
Bioinformatics (Oxford, England) 2006;22(12):1538-9.
2006: Shinya Tasaki; Masao Nagasaki; Masaaki Oyama; Hiroko Kozuka-Hata; Kazuko Ueno; Ryo Yoshida; Tomoyuki Higuchi; Sumio Sugano; Satoru Miyano
Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data.
Genome informatics. International Conference on Genome Informatics 2006;17(2):226-38.
2006: Atsushi Doi; Masao Nagasaki; Kazuko Ueno; Hiroshi Matsuno; Satoru Miyano
A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity.
Genome informatics. International Conference on Genome Informatics 2006;17(1):112-23.
2006: Ayumu Saito; Masao Nagasaki; Atsushi Doi; Kazuko Ueno; Satoru Miyano
Cell fate simulation model of gustatory neurons with MicroRNAs double-negative feedback loop by hybrid functional Petri net with extension.
Genome informatics. International Conference on Genome Informatics 2006;17(1):100-11.
2006: Ryo Yoshida; Kazuyuki Numata; Seiya Imoto; Masao Nagasaki; Atsushi Doi; Kazuko Ueno; Satoru Miyano
A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays.
Genome informatics. International Conference on Genome Informatics 2006;17(1):88-99.
2006: Masao Nagasaki; Rui Yamaguchi; Ryo Yoshida; Seiya Imoto; Atsushi Doi; Yoshinori Tamada; Hiroshi Matsuno; Satoru Miyano; Tomoyuki Higuchi
Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data.
Genome informatics. International Conference on Genome Informatics 2006;17(1):46-61.
2006: Seiya Imoto; Yoshinori Tamada; Hiromitsu Araki; Kaori Yasuda; Cristin G Print; Stephen D Charnock-Jones; Deborah Sanders; Christopher J Savoie; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano
Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():559-71.
2006: Atsushi Doi; Masao Nagasaki; Hiroshi Matsuno; Satoru Miyano
Simulation-based validation of the p53 transcriptional activity with hybrid functional petri net.
In silico biology 2006;6(1-2):1-13.
2005: Naoki Nariai; Yoshinori Tamada; Seiya Imoto; Satoru Miyano
Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data.
Bioinformatics (Oxford, England) 2005;21 Suppl 2():ii206-12.
2005: M J L De Hoon; Yuko Makita; Kenta Nakai; Satoru Miyano
Prediction of transcriptional terminators in Bacillus subtilis and related species.
PLoS computational biology 2005;1(3):e25.
2005: S Ott; A Hansen; S-Y Kim; Satoru Miyano
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.
Bioinformatics (Oxford, England) 2005;21(2):227-38.
2005: Mitsuru Kato; Masao Nagasaki; Atsushi Doi; Satoru Miyano
Automatic drawing of biological networks using cross cost and subcomponent data.
Genome informatics. International Conference on Genome Informatics 2005;16(2):22-31.
2005: Yuko Makita; M J L De Hoon; Naotake Ogasawara; Satoru Miyano; Kenta Nakai
Bayesian joint prediction of associated transcription factors in Bacillus subtilis.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():507-18.
2005: Shigeru Ohtsubo; Aritoshi Iida; Kosaku Nitta; Toshihiro Tanaka; Ryo Yamada; Yozo Ohnishi; Shiro Maeda; Tatsuhiko Tsunoda; Takashi Takei; Wataru Obara; Fumihiro Akiyama; Kyoko Ito; Kazuho Honda; Keiko Uchida; Ken Tsuchiya; Wako Yumura; Takashi Ujiie; Yuriko Nagane; Satoru Miyano; Yasushi Suzuki; Ichiei Narita; Fumitake Gejyo; Tomoaki Fujioka; Hiroshi Nihei; Yusuke Nakamura
Association of a single-nucleotide polymorphism in the immunoglobulin mu-binding protein 2 gene with immunoglobulin A nephropathy.
Journal of human genetics 2005;50(1):30-5.
2004: Hiroko Bannai; Heikki Hyyrö; Ayumi Shinohara; Masayuki Takeda; Kenta Nakai; Satoru Miyano
An O(N2) algorithm for discovering optimal Boolean pattern pairs.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2004;1(4):159-70.
2004: M J L De Hoon; Yuko Makita; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Kenta Nakai; Satoru Miyano
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i101-8.
2004: Sunyong Kim; Seiya Imoto; Satoru Miyano
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data.
Bio Systems 2004;75(1-3):57-65.
2004: M J L De Hoon; Seiya Imoto; J Nolan; Satoru Miyano
Open source clustering software.
Bioinformatics (Oxford, England) 2004;20(9):1453-4.
2004: Hiroko Bannai; Shunsuke Inenaga; Ayumi Shinohara; Masayuki Takeda; Satoru Miyano
Efficiently finding regulatory elements using correlation with gene expression.
Journal of bioinformatics and computational biology 2004;2(2):273-88.
2004: Seiya Imoto; Tomoyuki Higuchi; Takao Goto; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano
Combining microarrays and biological knowledge for estimating gene networks via bayesian networks.
Journal of bioinformatics and computational biology 2004;2(1):77-98.
2004: Yoshio Takei; Koji Inoue; Maho Ogoshi; Tetsushi Kawahara; Hiroko Bannai; Satoru Miyano
Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator.
FEBS letters 2004;556(1-3):53-8.
2004: Masao Nagasaki; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano
A versatile petri net based architecture for modeling and simulation of complex biological processes.
Genome informatics. International Conference on Genome Informatics 2004;15(1):180-97.
2004: Euna Jeong; I-Fang Chung; Satoru Miyano
A neural network method for identification of RNA-interacting residues in protein.
Genome informatics. International Conference on Genome Informatics 2004;15(1):105-16.
2004: Tomohiro Ando; Seiya Imoto; Satoru Miyano
Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities.
Genome informatics. International Conference on Genome Informatics 2004;15(2):201-10.
2004: S Ott; Seiya Imoto; Satoru Miyano
Finding optimal models for small gene networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():557-67.
2004: N Nariai; S Kim; Seiya Imoto; Satoru Miyano
Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():336-47.
2004: M J L De Hoon; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Satoru Miyano
Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():276-87.
2003: Seiya Imoto; Christopher J Savoie; Sachiyo Aburatani; Sunyong Kim; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano
Use of gene networks for identifying and validating drug targets.
Journal of bioinformatics and computational biology 2003;1(3):459-74.
2003: Yoshinori Tamada; Sunyong Kim; Hiroko Bannai; Seiya Imoto; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii227-36.
2003: Sun Yong Kim; Seiya Imoto; Satoru Miyano
Inferring gene networks from time series microarray data using dynamic Bayesian networks.
Briefings in bioinformatics 2003;4(3):228-35.
2003: Seiya Imoto; Sunyong Kim; Takao Goto; Satoru Miyano; Sachiyo Aburatani; Kousuke Tashiro; Satoru Kuhara
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network.
Journal of bioinformatics and computational biology 2003;1(2):231-52.
2003: Christopher J Savoie; Sachiyo Aburatani; Shouji Watanabe; Yoshihiro Eguchi; Shigeru Muta; Seiya Imoto; Satoru Miyano; Satoru Kuhara; Kosuke Tashiro
Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades.
DNA research : an international journal for rapid publication of reports on genes and genomes 2003;10(1):19-25.
2003: Seiya Imoto; Tomoyuki Higuchi; Takao Goto; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks.
Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference 2003;2():104-13.
2003: Sascha Ott; Satoru Miyano
Finding optimal gene networks using biological constraints.
Genome informatics. International Conference on Genome Informatics 2003;14():124-33.
2003: Masao Nagasaki; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano
Genomic Object Net: I. A platform for modelling and simulating biopathways.
Applied bioinformatics 2003;2(3):181-4.
2003: Wataru Obara; Aritoshi Iida; Yasushi Suzuki; Toshihiro Tanaka; Fumihiro Akiyama; Shiro Maeda; Yozo Ohnishi; Ryo Yamada; Tatsuhiko Tsunoda; Takashi Takei; Kyoko Ito; Kazuho Honda; Keiko Uchida; Ken Tsuchiya; Wako Yumura; Takashi Ujiie; Yuriko Nagane; Kosaku Nitta; Satoru Miyano; Ichiei Narita; Fumitake Gejyo; Hiroshi Nihei; Tomoaki Fujioka; Yusuke Nakamura
Association of single-nucleotide polymorphisms in the polymeric immunoglobulin receptor gene with immunoglobulin A nephropathy (IgAN) in Japanese patients.
Journal of human genetics 2003;48(6):293-9.
2003: S Ott; Yoshinori Tamada; Hiroko Bannai; Kenta Nakai; Satoru Miyano
Intrasplicing--analysis of long intron sequences.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():339-50.
2003: M J L De Hoon; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Satoru Miyano
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():17-28.
2002: M J L De Hoon; Seiya Imoto; Satoru Miyano
Statistical analysis of a small set of time-ordered gene expression data using linear splines.
Bioinformatics (Oxford, England) 2002;18(11):1477-85.
2002: Takashi Takei; Aritoshi Iida; Kosaku Nitta; Toshihiro Tanaka; Yozo Ohnishi; Ryo Yamada; Shiro Maeda; Tatsuhiko Tsunoda; Sachiyo Takeoka; Kyoko Ito; Kazuho Honda; Keiko Uchida; Ken Tsuchiya; Yasushi Suzuki; Tomoaki Fujioka; Takashi Ujiie; Yuriko Nagane; Satoru Miyano; Ichiei Narita; Fumitake Gejyo; Hiroshi Nihei; Yusuke Nakamura
Association between single-nucleotide polymorphisms in selectin genes and immunoglobulin A nephropathy.
American journal of human genetics 2002;70(3):781-6.
2002: Hiroko Bannai; Yoshinori Tamada; Osamu Maruyama; Kenta Nakai; Satoru Miyano
Extensive feature detection of N-terminal protein sorting signals.
Bioinformatics (Oxford, England) 2002;18(2):298-305.
2002: Seiya Imoto; Kim Sunyong; Takao Goto; Sachiyo Aburatani; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network.
Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference 2002;1():219-27.
2002: Hiroko Bannai; Shunsuke Inenaga; Ayumi Shinohara; Masayuki Takeda; Satoru Miyano
A string pattern regression algorithm and its application to pattern discovery in long introns.
Genome informatics. International Conference on Genome Informatics 2002;13():3-11.
2002: Fumihiro Akiyama; Toshihiro Tanaka; Ryo Yamada; Yozo Ohnishi; Tatsuhiko Tsunoda; Shiro Maeda; Takashi Takei; Wataru Obara; Kyoko Ito; Kazuho Honda; Keiko Uchida; Ken Tsuchiya; Kosaku Nitta; Wako Yumura; Hiroshi Nihei; Takashi Ujiie; Yuriko Nagane; Satoru Miyano; Yasushi Suzuki; Tomoaki Fujioka; Ichiei Narita; Fumitake Gejyo; Yusuke Nakamura
Single-nucleotide polymorphisms in the class II region of the major histocompatibility complex in Japanese patients with immunoglobulin A nephropathy.
Journal of human genetics 2002;47(10):532-8.
2002: Seiya Imoto; Takao Goto; Satoru Miyano
Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():175-86.
2001: K L Sim; T Uchida; Satoru Miyano
ProDDO: a database of disordered proteins from the Protein Data Bank (PDB).
Bioinformatics (Oxford, England) 2001;17(4):379-80.
2000: Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara
Inferring qualitative relations in genetic networks and metabolic pathways.
Bioinformatics (Oxford, England) 2000;16(8):727-34.
2000: Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara
Algorithms for inferring qualitative models of biological networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():293-304.
1999: Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1999;():17-28.