Satoru Miyano

257 papers A* 2A 2B 28C 10Misc 14Journal 147Unranked 47
YearRankTypeTitle / Venue / Authors
2025 J jnl
Powerful gene network enrichment analysis and its application to severe COVID-19 gene network.
Briefings Bioinform.
Heewon Park, Seiya Imoto, Satoru Miyano
2024 — conf
Large-scaleWGS Analysis on the supercomputer Fugaku.
ICBBB
Satoshi Ito, Kenji Ono, Satoru Miyano
2024 J jnl
Network-Constrained Eigen-Single-Cell Profile Estimation for Uncovering Crucial Immunogene Regulatory Systems in Human Bone Marrow.
J. Comput. Biol.
Heewon Park, Satoru Miyano
2023 — conf
Acceleration of BAM I/O on distributed file systems.
BIBM
Satoshi Ito, Satoru Miyano, Kenji Ono
2023 J jnl
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification.
J. Comput. Biol.
Heewon Park, Seiya Imoto, Satoru Miyano
2022 J jnl
Identification of bacteriophage genome sequences with representation learning.
Bioinform.
Zeheng Bai, Yao-Zhong Zhang, Satoru Miyano, Rui Yamaguchi, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto
2022 J jnl
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis.
BMC Bioinform.
Heewon Park, Seiya Imoto, Satoru Miyano
2022 J jnl
RoDiCE: robust differential protein co-expression analysis for cancer complexome.
Bioinform.
Yusuke Matsui, Yuichi Abe, Kohei Uno, Satoru Miyano
2022 J jnl
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification.
J. Comput. Biol.
Heewon Park, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2021 J jnl
Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.
PLoS Comput. Biol.
Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2021 J jnl
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net.
Biosyst.
Chen Li, Jiale Qin, Keisuke Kuroyanagi, Lu Lu, Masao Nagasaki, Satoru Miyano
2021 — conf
On the application of BERT models for nanopore methylation detection.
BIBM
Yao-Zhong Zhang, Kiyoshi Yamaguchi, Sera Hatakeyama, Yoichi Furukawa, Satoru Miyano, Rui Yamaguchi, Seiya Imoto
2020 J jnl
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Nat.
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel González-Pérez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora
2020 J jnl
Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model.
J. Frankl. Inst.
Takanori Hasegawa, Rui Yamaguchi, Atsushi Niida, Satoru Miyano, Seiya Imoto
2020 J jnl
Linear Tensor Projection Revealing Nonlinearity.
CoRR
Koji Maruhashi, Heewon Park, Rui Yamaguchi, Satoru Miyano
2020 J jnl
Nanopore basecalling from a perspective of instance segmentation.
BMC Bioinform.
Yao-Zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi
2020 J jnl
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens.
Bioinform.
Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto
2020 — conf
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection.
ISMCO
Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2019 J jnl
A Bayesian model integration for mutation calling through data partitioning.
Bioinform.
Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi
2019 J jnl
ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data.
J. Comput. Biol.
Shuto Hayashi, Takuya Moriyama, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto
2019 — conf
Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples.
ISMCO
Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2019 J jnl
Robust Sample-Specific Stability Selection with Effective Error Control.
J. Comput. Biol.
Heewon Park, Makoto Yamada, Seiya Imoto, Satoru Miyano
2019 J jnl
Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers.
BMC Bioinform.
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano
2018 J jnl
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks.
J. Comput. Biol.
Heewon Park, Teppei Shimamura, Seiya Imoto, Satoru Miyano
2018 — conf
Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers.
BIBM
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano
2017 J jnl
A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity.
IEEE ACM Trans. Comput. Biol. Bioinform.
Heewon Park, Yuichi Shiraishi, Seiya Imoto, Satoru Miyano
2017 J jnl
A framework for generating interactive reports for cancer genome analysis.
J. Open Source Softw.
Ai Okada, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Yuichi Shiraishi
2017 — conf
GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics.
CIBB
Teppei Shimamura, Yusuke Matsui, Taisuke Kajino, Satoshi Ito, Takashi Takahashi, Satoru Miyano
2017 J jnl
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level.
J. Comput. Biol.
Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano
2017 — conf
Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning.
BIBM
Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2017 — conf
Tumor Subclonal Progression Model for Cancer Hallmark Acquisition.
CIBB
Yusuke Matsui, Satoru Miyano, Teppei Shimamura
2017 J jnl
phyC: Clustering cancer evolutionary trees.
PLoS Comput. Biol.
Yusuke Matsui, Atsushi Niida, Ryutaro Uchi, Koshi Mimori, Satoru Miyano, Teppei Shimamura
2016 — ch.
A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock.
Modeling in Systems Biology, The Petri Net Approach
Natsumi Mitou, Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye
2016 J jnl
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models.
Comput. Stat. Data Anal.
Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto
2016 J jnl
Binary contingency table method for analysing gene mutation in cancer genome.
Int. J. Bioinform. Res. Appl.
Emi Ayada, Takanori Hasegawa, Atsushi Niida, Satoru Miyano, Seiya Imoto
2016 J jnl
D
Bioinform.
Yusuke Matsui, Masahiro Mizuta, Satoshi Ito, Satoru Miyano, Teppei Shimamura
2016 — ch.
Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling.
Modeling in Systems Biology, The Petri Net Approach
Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano
2016 — conf
OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads.
ISBRA
Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2016 J jnl
Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study.
BMC Medical Informatics Decis. Mak.
Tetsuhiro Yoshino, Kotoe Katayama, Yuko Horiba, Kaori Munakata, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Hideki Mima, Kenji Watanabe
2015 — ed.
2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, DC, USA, November 9-12, 2015
BIBM
Jun Huan, Satoru Miyano, Amarda Shehu, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Vijay K. Gombar, Matthieu-P. Schapranow, Illhoi Yoo, Jiayu Zhou, Brian Chen, Vinay Pai, Brian G. Pierce
2015 — conf
Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome.
ISBRA
Emi Ayada, Atsushi Niida, Takanori Hasegawa, Satoru Miyano, Seiya Imoto
2015 J jnl
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.
BMC Syst. Biol.
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu
2015 J jnl
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data.
Bioinform.
Kenichi Chiba, Yuichi Shiraishi, Yasunobu Nagata, Kenichi Yoshida, Seiya Imoto, Seishi Ogawa, Satoru Miyano
2015 — conf
High performance computing of a fusion gene detection pipeline on the K computer.
BIBM
Satoshi Ito, Yuichi Shiraishi, Teppei Shimamura, Kenichi Chiba, Satoru Miyano
2015 J jnl
Inferring the global structure of chromosomes from structural variations.
BMC Genom.
Tomohiro Yasuda, Satoru Miyano
2015 J jnl
Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis.
J. Comput. Biol.
Heewon Park, Atsushi Niida, Satoru Miyano, Seiya Imoto
2014 J jnl
A feature selection method using fixed-point algorithm for DNA microarray gene expression data.
Int. J. Knowl. Based Intell. Eng. Syst.
Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano, Vandana Sharma, Rajeshkannan Ananthanarayanan
2014 J jnl
A feature selection method using improved regularized linear discriminant analysis.
Mach. Vis. Appl.
Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano
2014 J jnl
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data.
J. Comput. Biol.
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu
2014 J jnl
An efficient method of exploring simulation models by assimilating literature and biological observational data.
Biosyst.
Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2014 J jnl
CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML.
Biosyst.
Chen Li, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Satoru Miyano
2014 J jnl
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.
Bioinform.
Naoto Usuyama, Yuichi Shiraishi, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Satoru Miyano, Seiya Imoto
2014 C conf
Parameter estimation in multi-compartment SIR model.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2013 J jnl
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition.
BMC Bioinform.
Alok Sharma, Kuldip K. Paliwal, Abdollah Dehzangi, James G. Lyons, Seiya Imoto, Satoru Miyano
2013 C conf
Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2013 J jnl
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations.
J. Comput. Biol.
Mitsunori Kayano, Seiya Imoto, Rui Yamaguchi, Satoru Miyano
2013 — conf
Multilayer Cluster Heat Map Visualizing Biological Tensor Data.
BSB
Atsushi Niida, Georg Tremmel, Seiya Imoto, Satoru Miyano
2013 J jnl
Principal component analysis using QR decomposition.
Int. J. Mach. Learn. Cybern.
Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano
2013 J jnl
XiP: a computational environment to create, extend and share workflows.
Bioinform.
Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li, Satoru Miyano
2012 J jnl
A Top-r Feature Selection Algorithm for Microarray Gene Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alok Sharma, Seiya Imoto, Satoru Miyano
2012 J jnl
A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis.
J. Bioinform. Comput. Biol.
Alok Sharma, Seiya Imoto, Satoru Miyano
2012 — conf
Analysis of questionnaire for traditional medical and develop decision support system.
BIBM Workshops
Kotoe Katayama, Seiya Imoto, Kenji Watanabe, Rui Yamaguchi, Keiko Matsuura, Satoru Miyano
2012 J jnl
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.
BMC Bioinform.
Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki, Satoru Miyano
2012 J jnl
Computational gene network analysis reveals TNF-induced angiogenesis.
BMC Syst. Biol.
Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano
2012 J jnl
Functional clustering of time series gene expression data by Granger causality.
BMC Syst. Biol.
André Fujita, Patricia Severino, Kaname Kojima, João Ricardo Sato, Alexandre Galvão Patriota, Satoru Miyano
2012 J jnl
IRView: a database and viewer for protein interacting regions.
Bioinform.
Shigeo Fujimori, Naoya Hirai, Kazuyo Masuoka, Tomohiro Oshikubo, Tatsuhiro Yamashita, Takanori Washio, Ayumu Saito, Masao Nagasaki, Satoru Miyano, Etsuko Miyamoto-Sato
2012 C conf
Identifiability of local transmissibility parameters in agent-based pandemic simulation.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2012 J jnl
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
2012 J jnl
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing.
BMC Genom.
Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh, Satoru Miyano
2012 J jnl
Null space based feature selection method for gene expression data.
Int. J. Mach. Learn. Cybern.
Alok Sharma, Seiya Imoto, Satoru Miyano, Vandana Sharma
2012 J jnl
Statistical model-based testing to evaluate the recurrence of genomic aberrations.
Bioinform.
Atsushi Niida, Seiya Imoto, Teppei Shimamura, Satoru Miyano
2011 J jnl
2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope.
J. Cheminformatics
Tsutomu Osoda, Satoru Miyano
2011 J jnl
A rank-based statistical test for measuring synergistic effects between two gene sets.
Bioinform.
Yuichi Shiraishi, Mariko Okada-Hatakeyama, Satoru Miyano
2011 J jnl
CSO validator: improving manual curation workflow for biological pathways.
Bioinform.
Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano
2011 J jnl
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.
BMC Bioinform.
Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki
2011 — conf
Clustering for Visual Analogue Scale Data in Symbolic Data Analysis.
Complex Adaptive Systems
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano
2011 — conf
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation.
ISBRA
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
2011 — ch.
Computational Drug Target Pathway Discovery: A Bayesian Network Approach.
Handbook of Statistical Bioinformatics
Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Satoru Miyano
2011 J jnl
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin G. Print, Stephen D. Charnock-Jones, Satoru Miyano
2011 C conf
Estimation of macroscopic parameter in agent-based pandemic simulation.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2011 J jnl
High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA.
IEEE ACM Trans. Comput. Biol. Bioinform.
Georgios Chalkidis, Masao Nagasaki, Satoru Miyano
2011 J jnl
Hybrid Petri net based modeling for biological pathway simulation.
Nat. Comput.
Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano
2011 — ed.
IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, USA, February 3-5, 2011
ICCABS
Ion I. Mandoiu, Satoru Miyano, Teresa M. Przytycka, Sanguthevar Rajasekaran
2011 J jnl
INTRODUCTION - The First IEEE Conference on Healthcare Informatics, Imaging, and Systems biology HISB'11.
J. Bioinform. Comput. Biol.
Xue-Wen Chen, Satoru Miyano
2011 J jnl
Inferring Contagion in Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Rui Yamaguchi, Teppei Shimamura, Carlos Eduardo Ferreira, Mari Cleide Sogayar, Satoru Miyano
2011 J jnl
MIRACH: efficient model checker for quantitative biological pathway models.
Bioinform.
Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano
2011 J jnl
Ontology-based instance data validation for high-quality curated biological pathways.
BMC Bioinform.
Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano
2011 — conf
Parallel Agent-Based Simulator for Influenza Pandemic.
AAMAS Workshops
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2011 J jnl
Parallel Algorithm for Learning Optimal Bayesian Network Structure.
J. Mach. Learn. Res.
Yoshinori Tamada, Seiya Imoto, Satoru Miyano
2011 — conf
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation.
ICCABS
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
2011 J jnl
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinform.
Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano
2011 J jnl
Systems biology model repository for macrophage pathway simulation.
Bioinform.
Masao Nagasaki, Ayumu Saito, André Fujita, Georg Tremmel, Kazuko Ueno, Emi Ikeda, Euna Jeong, Satoru Miyano
2011 J jnl
Transform of visual analogue scale data and their clustering.
Int. J. Knowl. Eng. Soft Data Paradigms
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano
2010 J jnl
A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets.
Bioinform.
André Fujita, Kaname Kojima, Alexandre Galvão Patriota, João Ricardo Sato, Patricia Severino, Satoru Miyano
2010 — ed.
Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings
BSB
Carlos Eduardo Ferreira, Satoru Miyano, Peter F. Stadler
2010 J jnl
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.
BMC Bioinform.
Kaname Kojima, Masao Nagasaki, Satoru Miyano
2010 J jnl
Cell Illustrator 4.0: A Computational Platform for Systems Biology.
Silico Biol.
Masao Nagasaki, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda, Satoru Miyano
2010 J jnl
DA 1.0: parameter estimation of biological pathways using data assimilation approach.
Bioinform.
Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Limsoon Wong, Satoru Miyano
2010 J jnl
Delay Time Determination for the Timed Petri Net Model of a Signaling Pathway Based on Its Structural Information.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Yoshimasa Miwa, Yuki Murakami, Qi-Wei Ge, Chen Li, Hiroshi Matsuno, Satoru Miyano
2010 — conf
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning.
BIBM
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
2010 — conf
Granger Causality in Systems Biology: Modeling Gene Networks in Time Series Microarray Data Using Vector Autoregressive Models.
BSB
André Fujita, Patricia Severino, João Ricardo Sato, Satoru Miyano
2010 J jnl
Identification of Granger Causality between Gene Sets.
J. Bioinform. Comput. Biol.
André Fujita, João Ricardo Sato, Kaname Kojima, Luciana Rodrigues Gomes, Masao Nagasaki, Mari Cleide Sogayar, Satoru Miyano
2010 C conf
Identifying Hidden Confounders in Gene Networks by Bayesian Networks.
BIBE
Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano
2010 J jnl
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
Bioinform.
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
2010 J jnl
Model-free unsupervised gene set screening based on information enrichment in expression profiles.
Bioinform.
Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano
2010 — conf
Network profiling analysis for generating modulator-dependent gene networks.
BIBM Workshops
Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano
2010 J jnl
On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules.
Silico Biol.
Yoshimasa Miwa, Chen Li, Qi-Wei Ge, Hiroshi Matsuno, Satoru Miyano
2010 J jnl
Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure.
J. Mach. Learn. Res.
Kaname Kojima, Eric Perrier, Seiya Imoto, Satoru Miyano
2010 — conf
Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach.
JSAI-isAI Workshops
Seiya Imoto, Kaname Kojima, Eric Perrier, Yoshinori Tamada, Satoru Miyano
2010 J jnl
The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis.
Biosyst.
Jin Hwan Do, Masao Nagasaki, Satoru Miyano
2010 J jnl
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram.
BMC Syst. Biol.
Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano
2009 J jnl
BFL: a node and edge betweenness based fast layout algorithm for large scale networks.
BMC Bioinform.
Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano
2009 B conf
Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality.
Discovery Science
Takanori Yamamoto, Hideo Bannai, Masao Nagasaki, Satoru Miyano
2009 J jnl
Comparing Pearson, Spearman and Hoeffding's d Measure for Gene Expression Association Analysis.
J. Bioinform. Comput. Biol.
André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Mari Cleide Sogayar, Carlos Eduardo Ferreira, Satoru Miyano
2009 Misc conf
Computational Predictions for Functional Proteins Working after Cleaved in Apoptotic Pathway.
CISIS
Chigusa Miyakawa, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano
2009 — book
Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases.
Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
2009 — conf
Gene Networks Viewed through Two Models.
BICoB
Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto
2009 J jnl
Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action.
J. Comput. Sci. Technol.
Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2009 Misc conf
Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing.
Pacific Symposium on Biocomputing
Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi
2009 J jnl
Recursive regularization for inferring gene networks from time-course gene expression profiles.
BMC Syst. Biol.
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano
2009 J jnl
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.
BMC Syst. Biol.
Chen Li, Masao Nagasaki, Kazuko Ueno, Satoru Miyano
2009 J jnl
The impact of measurement errors in the identification of regulatory networks.
BMC Bioinform.
André Fujita, Alexandre Galvão Patriota, João Ricardo Sato, Satoru Miyano
2009 Misc conf
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks.
Pacific Symposium on Biocomputing
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
2008 — conf
An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data.
BIONETICS
Kanji Hioka, Yoshimasa Miwa, Chen Li, Qi-Wei Ge, Hiroshi Matsuno, Satoru Miyano
2008 — conf
Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models.
Asia International Conference on Modelling and Simulation
Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
2008 J jnl
Bayesian learning of biological pathways on genomic data assimilation.
Bioinform.
Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi
2008 J jnl
ExonMiner: Web service for analysis of GeneChip Exon array data.
BMC Bioinform.
Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano
2008 J jnl
Fast grid layout algorithm for biological networks with sweep calculation.
Bioinform.
Kaname Kojima, Masao Nagasaki, Satoru Miyano
2008 J jnl
Modeling Nonlinear Gene Regulatory Networks from Time Series Gene Expression Data.
J. Bioinform. Comput. Biol.
André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Mari Cleide Sogayar, Carlos Eduardo Ferreira, Satoru Miyano
2008 J jnl
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates.
BMC Syst. Biol.
André Fujita, Luciana Rodrigues Gomes, João Ricardo Sato, Rui Yamaguchi, Carlos E. Thomaz, Mari Cleide Sogayar, Satoru Miyano
2008 — conf
Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks.
BIBM
Kazuyuki Numata, Seiya Imoto, Satoru Miyano
2008 B conf
Preface.
APBC
Alvis Brazma, Satoru Miyano, Tatsuya Akutsu
2008 B ed.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan
APBC
Alvis Brazma, Satoru Miyano, Tatsuya Akutsu
2008 J jnl
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
Bioinform.
Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano
2008 J jnl
Systematic reconstruction of TRANSPATH data into Cell System Markup Language.
BMC Syst. Biol.
Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano
2007 C conf
A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks.
BIBE
Kazuyuki Numata, Seiya Imoto, Satoru Miyano
2007 J jnl
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.
Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto, Satoru Miyano
2007 J jnl
An efficient grid layout algorithm for biological networks utilizing various biological attributes.
BMC Bioinform.
Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano
2007 J jnl
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways.
Silico Biol.
Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano
2007 C conf
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles.
BIBE
Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano
2007 J jnl
Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data.
IEEE Signal Process. Mag.
Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
2007 J jnl
Modeling gene expression regulatory networks with the sparse vector autoregressive model.
BMC Syst. Biol.
André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari Cleide Sogayar, Carlos Eduardo Ferreira
2007 J jnl
On the complexity of deriving position specific score matrices from positive and negative sequences.
Discret. Appl. Math.
Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott
2007 — conf
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data.
ISBRA
Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano
2006 J jnl
A New Regulatory Interaction Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals.
J. Bioinform. Comput. Biol.
Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano
2006 J jnl
A Weighted Profile Based Method for Protein-RNA Interacting Residue Prediction.
Trans. Comp. Sys. Biology
Euna Jeong, Satoru Miyano
2006 J jnl
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.
Bioinform.
Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, Satoru Miyano
2006 Misc conf
Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles.
Pacific Symposium on Biocomputing
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
2006 — conf
Machine Learning Prediction of Amino Acid Patterns in Protein N-myristoylation.
PRIB
Ryo Okada, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano
2006 J jnl
Petri Net Based Descriptions for Systematic Understanding of Biological Pathways.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Hiroshi Matsuno, Chen Li, Satoru Miyano
2006 J jnl
Preface: Special RECOMB 2005 Issue.
J. Comput. Biol.
Satoru Miyano
2006 J jnl
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.
Silico Biol.
Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano
2006 J jnl
Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease.
Int. J. Artif. Intell. Tools
Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano
2006 J jnl
Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets.
J. Bioinform. Comput. Biol.
Chen Li, Shunichi Suzuki, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano
2005 B conf
A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals.
APBC
Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano
2005 Misc conf
Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis.
Pacific Symposium on Biocomputing
Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai
2005 — conf
Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks.
ICCSA (3)
Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano
2005 — conf
Estimating gene regulatory networks and protein-protein interactions of
ECCB/JBI
Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano
2005 J jnl
Prediction of Transcriptional Terminators in
PLoS Comput. Biol.
Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano
2005 B ed.
Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings
RECOMB
Satoru Miyano, Jill P. Mesirov, Simon Kasif, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman
2005 J jnl
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.
Bioinform.
Sascha Ott, Annika Hansen, Sunyong Kim, Satoru Miyano
2005 J jnl
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.
J. Bioinform. Comput. Biol.
Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano
2004 J jnl
An O(N
IEEE ACM Trans. Comput. Biol. Bioinform.
Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
2004 C conf
Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression.
BIBE
Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano
2004 J jnl
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
J. Bioinform. Comput. Biol.
Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2004 J jnl
Constructing biological pathway models with hybrid functional Petri net.
Silico Biol.
Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano
2004 J jnl
Efficiently Finding Regulatory Elements Using Correlation with Gene Expression.
J. Bioinform. Comput. Biol.
Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano
2004 Misc conf
Finding Optimal Models for Small Gene Networks.
Pacific Symposium on Biocomputing
Sascha Ott, Seiya Imoto, Satoru Miyano
2004 B conf
Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance.
Discovery Science
Shunsuke Inenaga, Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
2004 C conf
Finding Optimal Pairs of Patterns.
WABI
Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
2004 — conf
Functional Data Analysis of the Dynamics of Gene Regulatory Networks.
KELSI
Tomohiro Ando, Seiya Imoto, Satoru Miyano
2004 B conf
Integrating Biopathway Databases for Large-scale Modeling and Simulation.
APBC
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
2004 — conf
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
ISMB/ECCB (Supplement of Bioinformatics)
Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano
2004 Misc conf
Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information.
Pacific Symposium on Biocomputing
Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano
2004 — conf
Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data.
CMSB
Seiya Imoto, Tomoyuki Higuchi, Sunyong Kim, Euna Jeong, Satoru Miyano
2004 J jnl
Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net.
J. Integr. Bioinform.
Mika Matsui, Sachie Fujita, Shunichi Suzuki, Hiroshi Matsuno, Satoru Miyano
2004 Misc conf
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks.
Pacific Symposium on Biocomputing
Naoki Nariai, Sunyong Kim, Seiya Imoto, Satoru Miyano
2003 J jnl
A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis.
Theor. Comput. Sci.
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2003 J jnl
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
J. Bioinform. Comput. Biol.
Seiya Imoto, Sunyong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2003 J jnl
Biopathways representation and simulation on hybrid functional Petri net.
Silico Biol.
Hiroshi Matsuno, Yukiko Tanaka, Hitoshi Aoshima, Atsushi Doi, Mika Matsui, Satoru Miyano
2003 Misc conf
Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net.
Pacific Symposium on Biocomputing
Hiroshi Matsuno, Ryutaro Murakani, Rie Yamane, Naoyuki Yamasaki, Sachie Fujita, Haruka Yoshimori, Satoru Miyano
2003 — conf
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
CSB
Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2003 — conf
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data.
CMSB
Sunyong Kim, Seiya Imoto, Satoru Miyano
2003 C conf
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection.
ECCB
Yoshinori Tamada, Sunyong Kim, Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2003 J jnl
Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model.
Theor. Comput. Sci.
Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano
2003 — conf
Inference, Modeling and Simulation of Gene Networks.
CMSB
Satoru Miyano
2003 Misc conf
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations.
Pacific Symposium on Biocomputing
Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano
2003 J jnl
Inferring gene networks from time series microarray data using dynamic Bayesian networks.
Briefings Bioinform.
Sunyong Kim, Seiya Imoto, Satoru Miyano
2003 Misc conf
Intrasplicing - Analysis of Long Intron Sequences.
Pacific Symposium on Biocomputing
Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano
2003 — conf
Recreating Biopathway Databases towards Simulation.
CMSB
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
2003 — conf
Towards Biopathway Modeling and Simulation.
ICATPN
Hiroshi Matsuno, Sachie Fujita, Atsushi Doi, Masao Nagasaki, Satoru Miyano
2003 J jnl
Use of Gene Networks for Identifying and Validating Drug Targets.
J. Bioinform. Comput. Biol.
Seiya Imoto, Christopher J. Savoie, Sachiyo Aburatani, Sunyong Kim, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2002 — conf
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
CSB
Seiya Imoto, Sunyong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2002 Misc conf
Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression.
Pacific Symposium on Biocomputing
Seiya Imoto, Takao Goto, Satoru Miyano
2002 J jnl
Extensive feature detection of N-terminal protein sorting signals.
Bioinform.
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
2002 — conf
Fast Algorithm for Extracting Multiple Unordered Short Motifs Using Bit Operations.
JCIS
Osamu Maruyama, Satoru Kuhara, Hideo Bannai, Satoru Miyano, Yoshinori Tamada
2002 J jnl
Fast algorithm for extracting multiple unordered short motifs using bit operations.
Inf. Sci.
Osamu Maruyama, Hideo Bannai, Yoshinori Tamada, Satoru Kuhara, Satoru Miyano
2002 — conf
Foundations of Designing Computational Knowledge Discovery Processes.
Progress in Discovery Science
Yoshinori Tamada, Hideo Bannai, Osamu Maruyama, Satoru Miyano
2002 B conf
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations.
Discovery Science
Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano
2002 B conf
On the Complexity of Deriving Position Specific Score Matrices from Examples.
CPM
Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott
2002 J jnl
Statistical analysis of a small set of time-ordered gene expression data using linear splines.
Bioinform.
Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano
2002 B conf
Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model.
Discovery Science
Osamu Maruyama, Takayoshi Shoudai, Satoru Miyano
2001 J jnl
Challenges for Intelligent Systems in Biology.
IEEE Intell. Syst.
Russ B. Altman, Alfonso Valencia, Satoru Miyano, Shoba Ranganathan
2001 J jnl
HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process.
Electron. Trans. Artif. Intell.
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Satoru Miyano
2001 B conf
Learning Conformation Rules.
Discovery Science
Osamu Maruyama, Takayoshi Shoudai, Emiko Furuichi, Satoru Kuhara, Satoru Miyano
2001 J jnl
ProDDO: a database of disordered proteins from the Protein Data Bank (PDB).
Bioinform.
Kim Lan Sim, Tomoyuki Uchida, Satoru Miyano
2001 B conf
VML: A View Modeling Language for Computational Knowledge Discovery.
Discovery Science
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Satoru Miyano
2001 Misc conf
Views: Fundamental Building Blocks in the Process of Knowledge Discovery.
FLAIRS
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
2000 B conf
A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis.
Discovery Science
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 J jnl
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function.
J. Comput. Biol.
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 B conf
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function.
RECOMB
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 J jnl
Inferring qualitative relations in genetic networks and metabolic pathways.
Bioinform.
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 J jnl
Polynomial-time Learning of Elementary Formal Systems.
New Gener. Comput.
Satoru Miyano, Ayumi Shinohara, Takeshi Shinohara
2000 B ed.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000
RECOMB
Ron Shamir, Satoru Miyano, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman
1999 B conf
A Definition of Discovery in Terms of Generalized Descriptional Complexity.
Discovery Science
Hideo Bannai, Satoru Miyano
1999 B conf
Designing Views in HypothesisCreator: System for Assisting in Discovery.
Discovery Science
Osamu Maruyama, Tomoyuki Uchida, Kim Lan Sim, Satoru Miyano
1999 J jnl
Foreword.
J. Comb. Optim.
Ying Xu, Satoru Miyano, Tom Head
1999 J jnl
Foreword: Genome Informatics.
Theor. Comput. Sci.
Satoru Miyano
1999 Misc conf
Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model.
Pacific Symposium on Biocomputing
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
1999 J jnl
On the Approximation of Protein Threading.
Theor. Comput. Sci.
Tatsuya Akutsu, Satoru Miyano
1998 A* conf
Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions.
SODA
Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano
1998 B conf
Toward Genomic Hypothesis Creator: View Designer for Discovery.
Discovery Science
Osamu Maruyama, Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano
1997 J jnl
An Approximation Algorithm for the Minimum Common Supertree Problem.
Nord. J. Comput.
Atsuko Yamaguchi, Koji Nakano, Satoru Miyano
1997 B conf
On the approximation of protein threading.
RECOMB
Tatsuya Akutsu, Satoru Miyano
1996 B ed.
Algorithms and Computation, 7th International Symposium, ISAAC '96, Osaka, Japan, December 16-18, 1996, Proceedings
ISAAC
Tetsuo Asano, Yoshihide Igarashi, Hiroshi Nagamochi, Satoru Miyano, Subhash Suri
1996 A conf
Extracting Best Consensus Motifs from Positive and Negative Examples.
STACS
Erika Tateishi, Osamu Maruyama, Satoru Miyano
1996 — conf
Genome Informatics: New Frontiers of Computer Science and Biosciences.
CODAS
Satoru Miyano
1996 J jnl
Inferring a Tree from Walks.
Theor. Comput. Sci.
Osamu Maruyama, Satoru Miyano
1995 B conf
Algorithmic Problems Arising from Genome Informatics (Abstract).
ISAAC
Satoru Miyano
1995 A conf
BONSAI Garden: Parallel Knowledge Discovery System for Amino Acid Sequences.
ISMB
Takayoshi Shoudai, Michael Lappe, Satoru Miyano, Ayumi Shinohara, Takeo Okazaki, Setsuo Arikawa, Tomoyuki Uchida, Shinichi Shimozono, Takeshi Shinohara, Satoru Kuhara
1995 J jnl
Complexity of Finding Alphabet Indexing.
IEICE Trans. Inf. Syst.
Shinichi Shimozono, Satoru Miyano
1995 B conf
Graph Inference from a Walk for TRees of Bounded Degree 3 is NP-Complete.
MFCS
Osamu Maruyama, Satoru Miyano
1995 J jnl
Learning Theory Toward Genome Informatics.
IEICE Trans. Inf. Syst.
Satoru Miyano
1995 J jnl
Parallel Algorithms for Refutation Tree Problem on Formal Graph Systems.
IEICE Trans. Inf. Syst.
Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano
1995 J jnl
Using Maximal Independent Sets to Solve Problems in Parallel.
Theor. Comput. Sci.
Takayoshi Shoudai, Satoru Miyano
1994 — conf
Machine Learning and Discovery for Bloinformatics: Introduction.
HICSS (5)
Satoru Miyano, Ayumi Shinohara
1993 J jnl
A Machine Discovery from Amino Acid Sequences by Decision Trees over Regular Patterns.
New Gener. Comput.
Setsuo Arikawa, Satoru Miyano, Ayumi Shinohara, Satoru Kuhara, Yasuhito Mukouchi, Takeshi Shinohara
1993 B conf
Learning Theory Toward Genome Informatics.
ALT
Satoru Miyano
1992 — conf
A Machine Discovery from Amino Acid Sequences by Decision Trees over Regular Patterns.
FGCS
Setsuo Arikawa, Satoru Kuhara, Satoru Miyano, Yasuhito Mukouchi, Ayumi Shinohara, Takeshi Shinohara
1992 B conf
Inferring a Tree from Walks.
MFCS
Osamu Maruyama, Satoru Miyano
1991 B conf
Analogy is NP-hard.
ALT
Shinji Furuya, Satoru Miyano
1991 J jnl
Delta_2^P-Complete Lexicographically First Maximal Subgraph Problems.
Theor. Comput. Sci.
Satoru Miyano
1991 — conf
More About Learning Elementary Formal Systems.
Nonmonotonic and Inductive Logic
Setsuo Arikawa, Takeshi Shinohara, Satoru Miyano, Ayumi Shinohara
1991 B conf
Which classes of elementary formal systems are polynomial-time learnable.
ALT
Satoru Miyano, Ayumi Shinohara, Takeshi Shinohara
1990 B conf
Teachability in Computational Learning.
ALT
Ayumi Shinohara, Satoru Miyano
1989 J jnl
The Lexicographically First Maximum Subgraph Problems: P-Completeness and NC Algorithms.
Math. Syst. Theory
Satoru Miyano
1988 J jnl
A Parallelizable Lexicographically First Maximal Edge-Induced Subgraph Problem.
Inf. Process. Lett.
Satoru Miyano
1988 — conf
Parallel Complexity and P-Complete Problems.
FGCS
Satoru Miyano
1988 B conf
Δ
MFCS
Satoru Miyano
1987 A* conf
The Lexicographically First Maximal Subgraph Problems: P-Completeness and NC Algorithms.
ICALP
Satoru Miyano
1984 — conf
Alternating Finite Automata on omega-Words.
CAAP
Satoru Miyano, Takeshi Hayashi
1984 J jnl
Alternating Finite Automata on omega-Words.
Theor. Comput. Sci.
Satoru Miyano, Takeshi Hayashi
1984 J jnl
Remarks on Two-Way Automata with Weak-Counters.
Inf. Process. Lett.
Satoru Miyano
1983 J jnl
Remarks on Multihead Pushdown Automata and Multihead Stack Automata.
J. Comput. Syst. Sci.
Satoru Miyano
1982 J jnl
A Hierarchy Theorem for Multihead Stack-Counter Automata.
Acta Informatica
Satoru Miyano
1982 J jnl
Two-Way Deterministic Multi-Weak-Counter Machines.
Theor. Comput. Sci.
Satoru Miyano
1980 J jnl
One-Way Weak-Stack-Counter Automata.
J. Comput. Syst. Sci.
Satoru Miyano