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ORCIDSatoru 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:
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