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Satoru Miyano
Person information
- affiliation: University of Tokyo, Human Genome Center, Japan
- affiliation (former): Kyushu University, Japan
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2020 – today
- 2024
- [c99]Satoshi Ito, Kenji Ono, Satoru Miyano:
Large-scaleWGS Analysis on the supercomputer Fugaku. ICBBB 2024: 14-20 - 2023
- [j144]Heewon Park, Seiya Imoto, Satoru Miyano:
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. J. Comput. Biol. 30(2): 223-243 (2023) - [c98]Satoshi Ito, Satoru Miyano, Kenji Ono:
Acceleration of BAM I/O on distributed file systems. BIBM 2023: 3299-3304 - 2022
- [j143]Yusuke Matsui, Yuichi Abe, Kohei Uno, Satoru Miyano:
RoDiCE: robust differential protein co-expression analysis for cancer complexome. Bioinform. 38(5): 1269-1276 (2022) - [j142]Zeheng Bai, Yao-zhong Zhang, Satoru Miyano, Rui Yamaguchi, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto:
Identification of bacteriophage genome sequences with representation learning. Bioinform. 38(18): 4264-4270 (2022) - [j141]Heewon Park, Seiya Imoto, Satoru Miyano:
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. BMC Bioinform. 23(1): 342 (2022) - [j140]Heewon Park, Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. J. Comput. Biol. 29(3): 257-275 (2022) - 2021
- [j139]Chen Li, Jiale Qin, Keisuke Kuroyanagi, Lu Lu, Masao Nagasaki, Satoru Miyano:
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net. Biosyst. 201: 104332 (2021) - [j138]Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers. PLoS Comput. Biol. 17(10) (2021) - [c97]Yao-Zhong Zhang, Kiyoshi Yamaguchi, Sera Hatakeyama, Yoichi Furukawa, Satoru Miyano, Rui Yamaguchi, Seiya Imoto:
On the application of BERT models for nanopore methylation detection. BIBM 2021: 320-327 - 2020
- [j137]Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto:
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens. Bioinform. 36(18): 4813-4816 (2020) - [j136]Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi:
Nanopore basecalling from a perspective of instance segmentation. BMC Bioinform. 21-S(3): 136 (2020) - [j135]Takanori Hasegawa, Rui Yamaguchi, Atsushi Niida, Satoru Miyano, Seiya Imoto:
Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model. J. Frankl. Inst. 357(5): 2916-2933 (2020) - [j134]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 Gonzalez-Perez, 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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [c96]Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection. ISMCO 2020: 87-101 - [i1]Koji Maruhashi, Heewon Park, Rui Yamaguchi, Satoru Miyano:
Linear Tensor Projection Revealing Nonlinearity. CoRR abs/2007.03912 (2020)
2010 – 2019
- 2019
- [j133]Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi:
A Bayesian model integration for mutation calling through data partitioning. Bioinform. 35(21): 4247-4254 (2019) - [j132]Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano:
Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers. BMC Bioinform. 20-S(16): 591:1-591:10 (2019) - [j131]Heewon Park, Makoto Yamada, Seiya Imoto, Satoru Miyano:
Robust Sample-Specific Stability Selection with Effective Error Control. J. Comput. Biol. 26(3): 202-217 (2019) - [j130]Shuto Hayashi, Takuya Moriyama, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto:
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. 26(9): 923-937 (2019) - [c95]Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples. ISMCO 2019: 47-61 - 2018
- [j129]Heewon Park, Teppei Shimamura, Seiya Imoto, Satoru Miyano:
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks. J. Comput. Biol. 25(2): 130-145 (2018) - [c94]Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano:
Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers. BIBM 2018: 387-392 - 2017
- [j128]Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano:
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level. J. Comput. Biol. 24(2): 138-152 (2017) - [j127]Ai Okada, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Yuichi Shiraishi:
A framework for generating interactive reports for cancer genome analysis. J. Open Source Softw. 2(20): 457 (2017) - [j126]Yusuke Matsui, Atsushi Niida, Ryutaro Uchi, Koshi Mimori, Satoru Miyano, Teppei Shimamura:
phyC: Clustering cancer evolutionary trees. PLoS Comput. Biol. 13(5) (2017) - [j125]Heewon Park, Yuichi Shiraishi, Seiya Imoto, Satoru Miyano:
A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity. IEEE ACM Trans. Comput. Biol. Bioinform. 14(4): 771-782 (2017) - [c93]Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning. BIBM 2017: 1227-1232 - [c92]Yusuke Matsui, Satoru Miyano, Teppei Shimamura:
Tumor Subclonal Progression Model for Cancer Hallmark Acquisition. CIBB 2017: 115-123 - [c91]Teppei Shimamura, Yusuke Matsui, Taisuke Kajino, Satoshi Ito, Takashi Takahashi, Satoru Miyano:
GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics. CIBB 2017: 124-137 - 2016
- [j124]Yusuke Matsui, Masahiro Mizuta, Satoshi Ito, Satoru Miyano, Teppei Shimamura:
D3M: detection of differential distributions of methylation levels. Bioinform. 32(15): 2248-2255 (2016) - [j123]Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto:
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. Comput. Stat. Data Anal. 94: 63-74 (2016) - [j122]Emi Ayada, Takanori Hasegawa, Atsushi Niida, Satoru Miyano, Seiya Imoto:
Binary contingency table method for analysing gene mutation in cancer genome. Int. J. Bioinform. Res. Appl. 12(3): 211-226 (2016) - [j121]Tetsuhiro Yoshino, Kotoe Katayama, Yuko Horiba, Kaori Munakata, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Hideki Mima, Kenji Watanabe:
Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study. BMC Medical Informatics Decis. Mak. 16: 118 (2016) - [c90]Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. ISBRA 2016: 40-51 - [p3]Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano:
Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. Modeling in Systems Biology, The Petri Net Approach 2016: 101-120 - [p2]Natsumi Mitou, Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye:
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 2016: 281-306 - 2015
- [j120]Kenichi Chiba, Yuichi Shiraishi, Yasunobu Nagata, Kenichi Yoshida, Seiya Imoto, Seishi Ogawa, Satoru Miyano:
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinform. 31(1): 116-118 (2015) - [j119]Tomohiro Yasuda, Satoru Miyano:
Inferring the global structure of chromosomes from structural variations. BMC Genom. 16(S-2): S13 (2015) - [j118]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu:
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. BMC Syst. Biol. 9: 14 (2015) - [j117]Heewon Park, Atsushi Niida, Satoru Miyano, Seiya Imoto:
Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis. J. Comput. Biol. 22(2): 73-84 (2015) - [c89]Satoshi Ito, Yuichi Shiraishi, Teppei Shimamura, Kenichi Chiba, Satoru Miyano:
High performance computing of a fusion gene detection pipeline on the K computer. BIBM 2015: 1441-1447 - [c88]Emi Ayada, Atsushi Niida, Takanori Hasegawa, Satoru Miyano, Seiya Imoto:
Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome. ISBRA 2015: 12-23 - [e7]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 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, DC, USA, November 9-12, 2015. IEEE Computer Society 2015, ISBN 978-1-4673-6799-8 [contents] - 2014
- [j116]Naoto Usuyama, Yuichi Shiraishi, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Satoru Miyano, Seiya Imoto:
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. Bioinform. 30(23): 3302-3309 (2014) - [j115]Chen Li, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Satoru Miyano:
CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML. Biosyst. 121: 22-28 (2014) - [j114]Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
An efficient method of exploring simulation models by assimilating literature and biological observational data. Biosyst. 121: 54-66 (2014) - [j113]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu:
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data. J. Comput. Biol. 21(11): 785-798 (2014) - [j112]Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano, Vandana Sharma, Rajeshkannan Ananthanarayanan:
A feature selection method using fixed-point algorithm for DNA microarray gene expression data. Int. J. Knowl. Based Intell. Eng. Syst. 18(1): 55-59 (2014) - [j111]Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano:
A feature selection method using improved regularized linear discriminant analysis. Mach. Vis. Appl. 25(3): 775-786 (2014) - [c87]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Parameter estimation in multi-compartment SIR model. FUSION 2014: 1-5 - 2013
- [j110]Masao Nagasaki, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li, Satoru Miyano:
XiP: a computational environment to create, extend and share workflows. Bioinform. 29(1): 137-139 (2013) - [j109]Alok Sharma, Kuldip K. Paliwal, Abdollah Dehzangi, James G. Lyons, Seiya Imoto, Satoru Miyano:
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. BMC Bioinform. 14: 233 (2013) - [j108]Mitsunori Kayano, Seiya Imoto, Rui Yamaguchi, Satoru Miyano:
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations. J. Comput. Biol. 20(8): 571-582 (2013) - [j107]Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano:
Principal component analysis using QR decomposition. Int. J. Mach. Learn. Cybern. 4(6): 679-683 (2013) - [c86]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan. FUSION 2013: 1385-1390 - [c85]Atsushi Niida, Georg Tremmel, Seiya Imoto, Satoru Miyano:
Multilayer Cluster Heat Map Visualizing Biological Tensor Data. BSB 2013: 116-125 - 2012
- [j106]Atsushi Niida, Seiya Imoto, Teppei Shimamura, Satoru Miyano:
Statistical model-based testing to evaluate the recurrence of genomic aberrations. Bioinform. 28(12): 115-120 (2012) - [j105]Shigeo Fujimori, Naoya Hirai, Kazuyo Masuoka, Tomohiro Oshikubo, Tatsuhiro Yamashita, Takanori Washio, Ayumu Saito, Masao Nagasaki, Satoru Miyano, Etsuko Miyamoto-Sato:
IRView: a database and viewer for protein interacting regions. Bioinform. 28(14): 1949-1950 (2012) - [j104]Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki, Satoru Miyano:
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinform. 13: 279 (2012) - [j103]Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh, Satoru Miyano:
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. BMC Genom. 13(S-1): S6 (2012) - [j102]André Fujita, Patricia Severino, Kaname Kojima, João Ricardo Sato, Alexandre Galvão Patriota, Satoru Miyano:
Functional clustering of time series gene expression data by Granger causality. BMC Syst. Biol. 6: 137 (2012) - [j101]Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano:
Computational gene network analysis reveals TNF-induced angiogenesis. BMC Syst. Biol. 6(S-2): S12 (2012) - [j100]Alok Sharma, Seiya Imoto, Satoru Miyano:
A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis. J. Bioinform. Comput. Biol. 10(5) (2012) - [j99]Alok Sharma, Seiya Imoto, Satoru Miyano, Vandana Sharma:
Null space based feature selection method for gene expression data. Int. J. Mach. Learn. Cybern. 3(4): 269-276 (2012) - [j98]Alok Sharma, Seiya Imoto, Satoru Miyano:
A Top-r Feature Selection Algorithm for Microarray Gene Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 754-764 (2012) - [j97]Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano:
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 966-972 (2012) - [c84]Kotoe Katayama, Seiya Imoto, Kenji Watanabe, Rui Yamaguchi, Keiko Matsuura, Satoru Miyano:
Analysis of questionnaire for traditional medical and develop decision support system. BIBM Workshops 2012: 762-763 - [c83]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Identifiability of local transmissibility parameters in agent-based pandemic simulation. FUSION 2012: 2466-2471 - 2011
- [j96]Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano:
MIRACH: efficient model checker for quantitative biological pathway models. Bioinform. 27(5): 734-735 (2011) - [j95]Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano:
SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinform. 27(8): 1172-1173 (2011) - [j94]Masao Nagasaki, Ayumu Saito, André Fujita, Georg Tremmel, Kazuko Ueno, Emi Ikeda, Euna Jeong, Satoru Miyano:
Systems biology model repository for macrophage pathway simulation. Bioinform. 27(11): 1591-1593 (2011) - [j93]Yuichi Shiraishi, Mariko Okada-Hatakeyama, Satoru Miyano:
A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinform. 27(17): 2399-2405 (2011) - [j92]Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano:
CSO validator: improving manual curation workflow for biological pathways. Bioinform. 27(17): 2471-2472 (2011) - [j91]Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano:
Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinform. 12(S-1): S8 (2011) - [j90]Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki:
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinform. 12(S-14): S7 (2011) - [j89]Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano:
Transform of visual analogue scale data and their clustering. Int. J. Knowl. Eng. Soft Data Paradigms 3(2): 143-151 (2011) - [j88]Xue-Wen Chen, Satoru Miyano:
INTRODUCTION - The First IEEE Conference on Healthcare Informatics, Imaging, and Systems biology HISB'11. J. Bioinform. Comput. Biol. 9(5) (2011) - [j87]Tsutomu Osoda, Satoru Miyano:
2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. J. Cheminformatics 3: 50 (2011) - [j86]Yoshinori Tamada, Seiya Imoto, Satoru Miyano:
Parallel Algorithm for Learning Optimal Bayesian Network Structure. J. Mach. Learn. Res. 12: 2437-2459 (2011) - [j85]Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano:
Hybrid Petri net based modeling for biological pathway simulation. Nat. Comput. 10(3): 1099-1120 (2011) - [j84]André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Rui Yamaguchi, Teppei Shimamura, Carlos Eduardo Ferreira, Mari Cleide Sogayar, Satoru Miyano:
Inferring Contagion in Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 8(2): 570-576 (2011) - [j83]Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin G. Print, Stephen D. Charnock-Jones, Satoru Miyano:
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. IEEE ACM Trans. Comput. Biol. Bioinform. 8(3): 683-697 (2011) - [j82]Georgios Chalkidis, Masao Nagasaki, Satoru Miyano:
High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA. IEEE ACM Trans. Comput. Biol. Bioinform. 8(6): 1545-1556 (2011) - [c82]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Parallel Agent-Based Simulator for Influenza Pandemic. AAMAS Workshops 2011: 361-370 - [c81]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Estimation of macroscopic parameter in agent-based pandemic simulation. FUSION 2011: 1-6 - [c80]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. ICCABS 2011: 246 - [c79]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. ISBRA 2011: 160-171 - [c78]Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano:
Clustering for Visual Analogue Scale Data in Symbolic Data Analysis. Complex Adaptive Systems 2011: 370-374 - [p1]Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Satoru Miyano:
Computational Drug Target Pathway Discovery: A Bayesian Network Approach. Handbook of Statistical Bioinformatics 2011: 501-532 - [e6]Ion I. Mandoiu, Satoru Miyano, Teresa M. Przytycka, Sanguthevar Rajasekaran:
IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, USA, February 3-5, 2011. IEEE Computer Society 2011, ISBN 978-1-61284-851-8 [contents] - 2010
- [j81]Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano:
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinform. 26(8): 1064-1072 (2010) - [j80]Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Limsoon Wong, Satoru Miyano:
DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinform. 26(14): 1794-1796 (2010) - [j79]André Fujita, Kaname Kojima, Alexandre Galvão Patriota, João Ricardo Sato, Patricia Severino, Satoru Miyano:
A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinform. 26(18): 2349-2351 (2010) - [j78]Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano:
Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinform. 26(24): 3090-3097 (2010) - [j77]Jin Hwan Do, Masao Nagasaki, Satoru Miyano:
The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosyst. 100(3): 178-184 (2010) - [j76]Kaname Kojima, Masao Nagasaki, Satoru Miyano:
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinform. 11: 335 (2010) - [j75]Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano:
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Syst. Biol. 4: 39 (2010) - [j74]Yoshimasa Miwa, Yuki Murakami, Qi-Wei Ge, Chen Li, Hiroshi Matsuno, Satoru Miyano:
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. 93-A(12): 2717-2729 (2010) - [j73]Masao Nagasaki, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda, Satoru Miyano:
Cell Illustrator 4.0: A Computational Platform for Systems Biology. Silico Biol. 10(1-2): 5-26 (2010) - [j72]Yoshimasa Miwa, Chen Li, Qi-Wei Ge, Hiroshi Matsuno, Satoru Miyano:
On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules. Silico Biol. 10(1-2): 49-66 (2010) - [j71]André Fujita, João Ricardo Sato, Kaname Kojima, Luciana Rodrigues Gomes, Masao Nagasaki, Mari Cleide Sogayar, Satoru Miyano:
Identification of Granger Causality between Gene Sets. J. Bioinform. Comput. Biol. 8(4): 679-701 (2010) - [j70]Kaname Kojima, Eric Perrier, Seiya Imoto, Satoru Miyano:
Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure. J. Mach. Learn. Res. 11: 285-310 (2010) - [c77]Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano:
Identifying Hidden Confounders in Gene Networks by Bayesian Networks. BIBE 2010: 168-173 - [c76]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 - [c75]Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano:
Network profiling analysis for generating modulator-dependent gene networks. BIBM Workshops 2010: 836 - [c74]Seiya Imoto, Kaname Kojima, Eric Perrier, Yoshinori Tamada, Satoru Miyano:
Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach. JSAI-isAI Workshops 2010: 210-218 - [c73]André Fujita, Patricia Severino, João Ricardo Sato, Satoru Miyano:
Granger Causality in Systems Biology: Modeling Gene Networks in Time Series Microarray Data Using Vector Autoregressive Models. BSB 2010: 13-24 - [e5]Carlos Eduardo Ferreira, Satoru Miyano, Peter F. Stadler:
Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings. Lecture Notes in Computer Science 6268, Springer 2010, ISBN 978-3-642-15059-3 [contents]
2000 – 2009
- 2009
- [b1]Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano:
Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases. Computational Biology 13, Springer 2009, ISBN 978-1-84882-022-7, pp. I-XII, 1-155 - [j69]André Fujita, Alexandre Galvão Patriota, João Ricardo Sato, Satoru Miyano:
The impact of measurement errors in the identification of regulatory networks. BMC Bioinform. 10: 412 (2009) - [j68]Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano:
BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinform. 10 (2009) - [j67]Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano:
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst. Biol. 3: 41 (2009) - [j66]Chen Li, Masao Nagasaki, Kazuko Ueno, Satoru Miyano:
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst. Biol. 3: 42 (2009) - [j65]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. J. Bioinform. Comput. Biol. 7(4): 663-684 (2009) - [j64]Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action. J. Comput. Sci. Technol. 25(1): 131-153 (2009) - [c72]Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto:
Gene Networks Viewed through Two Models. BICoB 2009: 54-66 - [c71]Chigusa Miyakawa, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano:
Computational Predictions for Functional Proteins Working after Cleaved in Apoptotic Pathway. CISIS 2009: 807-812 - [c70]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 - [c69]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 - [c68]Yoshinori Tamada, Hiromitsu Araki, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Yukiko Nakanishi, Yuki Tomiyasu, Kaori Yasuda, Ben Dunmore, Deborah Sanders, Sally Humphreys, Cristin G. Print, Stephen D. Charnock-Jones, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks. Pacific Symposium on Biocomputing 2009: 251-263 - 2008
- [j63]Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano:
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinform. 24(7): 932-942 (2008) - [j62]Kaname Kojima, Masao Nagasaki, Satoru Miyano:
Fast grid layout algorithm for biological networks with sweep calculation. Bioinform. 24(12): 1433-1441 (2008) - [j61]Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi:
Bayesian learning of biological pathways on genomic data assimilation. Bioinform. 24(22): 2592-2601 (2008) - [j60]Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano:
ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinform. 9 (2008) - [j59]Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano:
Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Syst. Biol. 2: 53 (2008) - [j58]André Fujita, Luciana Rodrigues Gomes, João Ricardo Sato, Rui Yamaguchi, Carlos E. Thomaz, Mari Cleide Sogayar, Satoru Miyano:
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Syst. Biol. 2: 106 (2008) - [j57]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. J. Bioinform. Comput. Biol. 6(5): 961-979 (2008) - [c67]Alvis Brazma, Satoru Miyano, Tatsuya Akutsu:
Preface. APBC 2008 - [c66]Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano:
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 2008: 940-946 - [c65]Kazuyuki Numata, Seiya Imoto, Satoru Miyano:
Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks. BIBM 2008: 357-360 - [c64]Kanji Hioka, Yoshimasa Miwa, Chen Li, Qi-Wei Ge, Hiroshi Matsuno, Satoru Miyano:
An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data. BIONETICS 2008: 1 - [e4]Alvis Brazma, Satoru Miyano, Tatsuya Akutsu:
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan. Advances in Bioinformatics and Computational Biology 6, Imperial College Press 2008, ISBN 978-1-84816-108-5 [contents] - 2007
- [j56]Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano:
An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinform. 8 (2007) - [j55]Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto, Satoru Miyano:
AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinform. 8 (2007) - [j54]André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari Cleide Sogayar, Carlos Eduardo Ferreira:
Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst. Biol. 1: 39 (2007) - [j53]Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott:
On the complexity of deriving position specific score matrices from positive and negative sequences. Discret. Appl. Math. 155(6-7): 676-685 (2007) - [j52]Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano:
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways. Silico Biol. 7(6): 623-638 (2007) - [j51]Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano:
Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data. IEEE Signal Process. Mag. 24(1): 37-46 (2007) - [c63]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 - [c62]Kazuyuki Numata, Seiya Imoto, Satoru Miyano:
A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks. BIBE 2007: 1280-1284 - [c61]Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano:
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data. ISBRA 2007: 146-157 - 2006
- [j50]Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, Satoru Miyano:
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. Bioinform. 22(12): 1538-1539 (2006) - [j49]Hiroshi Matsuno, Chen Li, Satoru Miyano:
Petri Net Based Descriptions for Systematic Understanding of Biological Pathways. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 89-A(11): 3166-3174 (2006) - [j48]Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano:
Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease. Int. J. Artif. Intell. Tools 15(5): 711-724 (2006) - [j47]Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano:
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net. Silico Biol. 6(1-2): 1-13 (2006) - [j46]Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano:
A New Regulatory Interaction Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals. J. Bioinform. Comput. Biol. 4(1): 139-154 (2006) - [j45]Chen Li, Shunichi Suzuki, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano:
Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets. J. Bioinform. Comput. Biol. 4(5): 1119-1140 (2006) - [j44]Satoru Miyano:
Preface: Special RECOMB 2005 Issue. J. Comput. Biol. 13(2): 131-132 (2006) - [j43]Euna Jeong, Satoru Miyano:
A Weighted Profile Based Method for Protein-RNA Interacting Residue Prediction. Trans. Comp. Sys. Biology 4: 123-139 (2006) - [c60]Ryo Okada, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano:
Machine Learning Prediction of Amino Acid Patterns in Protein N-myristoylation. PRIB 2006: 4-14 - [c59]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 2006: 559-571 - 2005
- [j42]Sascha Ott, Annika Hansen, SunYong Kim, Satoru Miyano:
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. Bioinform. 21(2): 227-238 (2005) - [j41]Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano:
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models. J. Bioinform. Comput. Biol. 3(6): 1295-1314 (2005) - [j40]Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano:
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. PLoS Comput. Biol. 1(3) (2005) - [c58]Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano:
A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. APBC 2005: 171-180 - [c57]Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano:
Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. ECCB/JBI 2005: 212 - [c56]Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano:
Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks. ICCSA (3) 2005: 349-356 - [c55]Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai:
Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. Pacific Symposium on Biocomputing 2005 - [e3]Satoru Miyano, Jill P. Mesirov, Simon Kasif, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman:
Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings. Lecture Notes in Computer Science 3500, Springer 2005, ISBN 3-540-25866-3 [contents] - 2004
- [j39]Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano:
Constructing biological pathway models with hybrid functional Petri net. Silico Biol. 4(3): 271-291 (2004) - [j38]Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. J. Bioinform. Comput. Biol. 2(1): 77-98 (2004) - [j37]Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano:
Efficiently Finding Regulatory Elements Using Correlation with Gene Expression. J. Bioinform. Comput. Biol. 2(2): 273-288 (2004) - [j36]Mika Matsui, Sachie Fujita, Shunichi Suzuki, Hiroshi Matsuno, Satoru Miyano:
Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net. J. Integr. Bioinform. 1(1) (2004) - [j35]Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano:
An O(N2) Algorithm for Discovering Optimal Boolean Pattern Pairs. IEEE ACM Trans. Comput. Biol. Bioinform. 1(4): 159-170 (2004) - [c54]Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano:
Integrating Biopathway Databases for Large-scale Modeling and Simulation. APBC 2004: 43-52 - [c53]Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano:
Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression. BIBE 2004: 73-78 - [c52]Seiya Imoto, Tomoyuki Higuchi, SunYong Kim, Euna Jeong, Satoru Miyano:
Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data. CMSB 2004: 149-160 - [c51]Shunsuke Inenaga, Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano:
Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. Discovery Science 2004: 32-46 - [c50]Michiel 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. ISMB/ECCB (Supplement of Bioinformatics) 2004: 101-108 - [c49]Tomohiro Ando, Seiya Imoto, Satoru Miyano:
Functional Data Analysis of the Dynamics of Gene Regulatory Networks. KELSI 2004: 69-83 - [c48]Michiel 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 2004: 276-287 - [c47]Naoki Nariai, SunYong Kim, Seiya Imoto, Satoru Miyano:
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks. Pacific Symposium on Biocomputing 2004: 336-347 - [c46]Sascha Ott, Seiya Imoto, Satoru Miyano:
Finding Optimal Models for Small Gene Networks. Pacific Symposium on Biocomputing 2004: 557-567 - [c45]Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano:
Finding Optimal Pairs of Patterns. WABI 2004: 450-462 - 2003
- [j34]SunYong Kim, Seiya Imoto, Satoru Miyano:
Inferring gene networks from time series microarray data using dynamic Bayesian networks. Briefings Bioinform. 4(3): 228 (2003) - [j33]Hiroshi Matsuno, Yukiko Tanaka, Hitoshi Aoshima, Atsushi Doi, Mika Matsui, Satoru Miyano:
Biopathways representation and simulation on hybrid functional Petri net. Silico Biol. 3(3): 389-404 (2003) - [j32]Seiya Imoto, SunYong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. J. Bioinform. Comput. Biol. 1(2): 231-252 (2003) - [j31]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. J. Bioinform. Comput. Biol. 1(3): 459-474 (2003) - [j30]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis. Theor. Comput. Sci. 292(2): 481-495 (2003) - [j29]Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano:
Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model. Theor. Comput. Sci. 298(1): 235-251 (2003) - [c44]Hiroshi Matsuno, Sachie Fujita, Atsushi Doi, Masao Nagasaki, Satoru Miyano:
Towards Biopathway Modeling and Simulation. ICATPN 2003: 3-22 - [c43]SunYong Kim, Seiya Imoto, Satoru Miyano:
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data. CMSB 2003: 104-113 - [c42]Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano:
Recreating Biopathway Databases towards Simulation. CMSB 2003: 168-169 - [c41]Satoru Miyano:
Inference, Modeling and Simulation of Gene Networks. CMSB 2003: 207-211 - [c40]Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. CSB 2003: 104-113 - [c39]Yoshinori Tamada, SunYong Kim, Hideo 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. ECCB 2003: 227-236 - [c38]Michiel 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 2003: 17-28 - [c37]Hiroshi Matsuno, Ryutaro Murakani, Rie Yamane, Naoyuki Yamasaki, Sachie Fujita, Haruka Yoshimori, Satoru Miyano:
Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net. Pacific Symposium on Biocomputing 2003: 152-163 - [c36]Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano:
Intrasplicing - Analysis of Long Intron Sequences. Pacific Symposium on Biocomputing 2003: 339-350 - 2002
- [j28]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
Extensive feature detection of N-terminal protein sorting signals. Bioinform. 18(2): 298-305 (2002) - [j27]Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano:
Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinform. 18(11): 1477-1485 (2002) - [j26]Osamu Maruyama, Hideo Bannai, Yoshinori Tamada, Satoru Kuhara, Satoru Miyano:
Fast algorithm for extracting multiple unordered short motifs using bit operations. Inf. Sci. 146(1-4): 115-126 (2002) - [c35]Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott:
On the Complexity of Deriving Position Specific Score Matrices from Examples. CPM 2002: 168-177 - [c34]Seiya Imoto, SunYong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. CSB 2002: 219-227 - [c33]Osamu Maruyama, Takayoshi Shoudai, Satoru Miyano:
Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model. Discovery Science 2002: 220-232 - [c32]Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano:
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations. Discovery Science 2002: 267-274 - [c31]Yoshinori Tamada, Hideo Bannai, Osamu Maruyama, Satoru Miyano:
Foundations of Designing Computational Knowledge Discovery Processes. Progress in Discovery Science 2002: 459-470 - [c30]Osamu Maruyama, Satoru Kuhara, Hideo Bannai, Satoru Miyano, Yoshinori Tamada:
Fast Algorithm for Extracting Multiple Unordered Short Motifs Using Bit Operations. JCIS 2002: 1180-1185 - [c29]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 2002: 175-186 - 2001
- [j25]Kim Lan Sim, Tomoyuki Uchida, Satoru Miyano:
ProDDO: a database of disordered proteins from the Protein Data Bank (PDB). Bioinform. 17(4): 379-380 (2001) - [j24]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Satoru Miyano:
HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process. Electron. Trans. Artif. Intell. 5(B): 73-83 (2001) - [j23]Russ B. Altman, Alfonso Valencia, Satoru Miyano, Shoba Ranganathan:
Challenges for Intelligent Systems in Biology. IEEE Intell. Syst. 16(6): 14-20 (2001) - [c28]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Satoru Miyano:
VML: A View Modeling Language for Computational Knowledge Discovery. Discovery Science 2001: 30-44 - [c27]Osamu Maruyama, Takayoshi Shoudai, Emiko Furuichi, Satoru Kuhara, Satoru Miyano:
Learning Conformation Rules. Discovery Science 2001: 243-257 - [c26]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
Views: Fundamental Building Blocks in the Process of Knowledge Discovery. FLAIRS 2001: 233-238 - 2000
- [j22]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Inferring qualitative relations in genetic networks and metabolic pathways. Bioinform. 16(8): 727-734 (2000) - [j21]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function. J. Comput. Biol. 7(3-4): 331-343 (2000) - [j20]Satoru Miyano, Ayumi Shinohara, Takeshi Shinohara:
Polynomial-time Learning of Elementary Formal Systems. New Gener. Comput. 18(3): 217-242 (2000) - [c25]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis. Discovery Science 2000: 86-98 - [c24]Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. RECOMB 2000: 8-14 - [e2]Ron Shamir, Satoru Miyano, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman:
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000. ACM 2000, ISBN 1-58113-186-0 [contents]
1990 – 1999
- 1999
- [j19]Ying Xu, Satoru Miyano, Tom Head:
Foreword. J. Comb. Optim. 3(2-3): 147-148 (1999) - [j18]Satoru Miyano:
Foreword: Genome Informatics. Theor. Comput. Sci. 210(2): 225-226 (1999) - [j17]Tatsuya Akutsu, Satoru Miyano:
On the Approximation of Protein Threading. Theor. Comput. Sci. 210(2): 261-275 (1999) - [c23]Osamu Maruyama, Tomoyuki Uchida, Kim Lan Sim, Satoru Miyano:
Designing Views in HypothesisCreator: System for Assisting in Discovery. Discovery Science 1999: 115-127 - [c22]Hideo Bannai, Satoru Miyano:
A Definition of Discovery in Terms of Generalized Descriptional Complexity. Discovery Science 1999: 316-318 - [c21]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 1999: 17-28 - 1998
- [c20]Osamu Maruyama, Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano:
Toward Genomic Hypothesis Creator: View Designer for Discovery. Discovery Science 1998: 105-116 - [c19]Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano:
Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. SODA 1998: 695-702 - 1997
- [j16]Atsuko Yamaguchi, Koji Nakano, Satoru Miyano:
An Approximation Algorithm for the Minimum Common Supertree Problem. Nord. J. Comput. 4(2): 303-316 (1997) - [c18]Tatsuya Akutsu, Satoru Miyano:
On the approximation of protein threading. RECOMB 1997: 3-8 - 1996
- [j15]Osamu Maruyama, Satoru Miyano:
Inferring a Tree from Walks. Theor. Comput. Sci. 161(1&2): 289-300 (1996) - [c17]Satoru Miyano:
Genome Informatics: New Frontiers of Computer Science and Biosciences. CODAS 1996: 12-21 - [c16]Erika Tateishi, Osamu Maruyama, Satoru Miyano:
Extracting Best Consensus Motifs from Positive and Negative Examples. STACS 1996: 219-230 - [e1]Tetsuo Asano, Yoshihide Igarashi, Hiroshi Nagamochi, Satoru Miyano, Subhash Suri:
Algorithms and Computation, 7th International Symposium, ISAAC '96, Osaka, Japan, December 16-18, 1996, Proceedings. Lecture Notes in Computer Science 1178, Springer 1996, ISBN 3-540-62048-6 [contents] - 1995
- [j14]Shinichi Shimozono, Satoru Miyano:
Complexity of Finding Alphabet Indexing. IEICE Trans. Inf. Syst. 78-D(1): 13-18 (1995) - [j13]Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano:
Parallel Algorithms for Refutation Tree Problem on Formal Graph Systems. IEICE Trans. Inf. Syst. 78-D(2): 99-112 (1995) - [j12]Satoru Miyano:
Learning Theory Toward Genome Informatics. IEICE Trans. Inf. Syst. 78-D(5): 560-567 (1995) - [j11]Takayoshi Shoudai, Satoru Miyano:
Using Maximal Independent Sets to Solve Problems in Parallel. Theor. Comput. Sci. 148(1): 57-65 (1995) - [c15]Satoru Miyano:
Algorithmic Problems Arising from Genome Informatics (Abstract). ISAAC 1995: 1 - [c14]Takayoshi Shoudai, Michael Lappe, Satoru Miyano, Ayumi Shinohara, Takeo Okazaki, Setsuo Arikawa, Tomoyuki Uchida, Shinichi Shimozono, Takeshi Shinohara, Satoru Kuhara:
BONSAI Garden: Parallel Knowledge Discovery System for Amino Acid Sequences. ISMB 1995: 359-366 - [c13]Osamu Maruyama, Satoru Miyano:
Graph Inference from a Walk for TRees of Bounded Degree 3 is NP-Complete. MFCS 1995: 257-266 - 1994
- [c12]Satoru Miyano, Ayumi Shinohara:
Machine Learning and Discovery for Bloinformatics: Introduction. HICSS (5) 1994: 111-112 - 1993
- [j10]Setsuo Arikawa, Satoru Miyano, Ayumi Shinohara, Satoru Kuhara, Yasuhito Mukouchi, Takeshi Shinohara:
A Machine Discovery from Amino Acid Sequences by Decision Trees over Regular Patterns. New Gener. Comput. 11(3): 361-375 (1993) - [c11]Satoru Miyano:
Learning Theory Toward Genome Informatics. ALT 1993: 19-36 - 1992
- [c10]Setsuo Arikawa, Satoru Kuhara, Satoru Miyano, Yasuhito Mukouchi, Ayumi Shinohara, Takeshi Shinohara:
A Machine Discovery from Amino Acid Sequences by Decision Trees over Regular Patterns. FGCS 1992: 618-625 - [c9]Osamu Maruyama, Satoru Miyano:
Inferring a Tree from Walks. MFCS 1992: 383-391 - 1991
- [j9]Satoru Miyano:
Delta_2^P-Complete Lexicographically First Maximal Subgraph Problems. Theor. Comput. Sci. 88(1): 33-57 (1991) - [c8]Satoru Miyano, Ayumi Shinohara, Takeshi Shinohara:
Which classes of elementary formal systems are polynomial-time learnable. ALT 1991: 139-150 - [c7]Shinji Furuya, Satoru Miyano:
Analogy is NP-hard. ALT 1991: 207-212 - [c6]Setsuo Arikawa, Takeshi Shinohara, Satoru Miyano, Ayumi Shinohara:
More About Learning Elementary Formal Systems. Nonmonotonic and Inductive Logic 1991: 107-117 - 1990
- [c5]Ayumi Shinohara, Satoru Miyano:
Teachability in Computational Learning. ALT 1990: 247-255
1980 – 1989
- 1989
- [j8]Satoru Miyano:
The Lexicographically First Maximum Subgraph Problems: P-Completeness and NC Algorithms. Math. Syst. Theory 22(1): 47-73 (1989) - 1988
- [j7]Satoru Miyano:
A Parallelizable Lexicographically First Maximal Edge-Induced Subgraph Problem. Inf. Process. Lett. 27(2): 75-78 (1988) - [c4]Satoru Miyano:
Parallel Complexity and P-Complete Problems. FGCS 1988: 532-541 - [c3]Satoru Miyano:
Δ2p-Complete Lexicographically First Maximal Subgraph Problems. MFCS 1988: 454-462 - 1987
- [c2]Satoru Miyano:
The Lexicographically First Maximal Subgraph Problems: P-Completeness and NC Algorithms. ICALP 1987: 425-434 - 1984
- [j6]Satoru Miyano:
Remarks on Two-Way Automata with Weak-Counters. Inf. Process. Lett. 18(2): 105-107 (1984) - [j5]Satoru Miyano, Takeshi Hayashi:
Alternating Finite Automata on omega-Words. Theor. Comput. Sci. 32: 321-330 (1984) - [c1]Satoru Miyano, Takeshi Hayashi:
Alternating Finite Automata on omega-Words. CAAP 1984: 195-210 - 1983
- [j4]Satoru Miyano:
Remarks on Multihead Pushdown Automata and Multihead Stack Automata. J. Comput. Syst. Sci. 27(1): 116-124 (1983) - 1982
- [j3]Satoru Miyano:
A Hierarchy Theorem for Multihead Stack-Counter Automata. Acta Informatica 17: 63-67 (1982) - [j2]Satoru Miyano:
Two-Way Deterministic Multi-Weak-Counter Machines. Theor. Comput. Sci. 21: 27-37 (1982) - 1980
- [j1]Satoru Miyano:
One-Way Weak-Stack-Counter Automata. J. Comput. Syst. Sci. 20(1): 59-76 (1980)
Coauthor Index
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