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 Satoru Miyano

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Average citations per article4.21
Citation Count341
Publication count81
Publication years1991-2017
Available for download14
Average downloads per article243.86
Downloads (cumulative)3,414
Downloads (12 Months)70
Downloads (6 Weeks)9
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81 results found Export Results: bibtexendnoteacmrefcsv

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1
July 2017 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 14 Issue 4, July 2017
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 1
Downloads (6 Weeks): 1,   Downloads (12 Months): 8,   Downloads (Overall): 13

Full text available: PDFPDF
We propose a novel adaptive penalized logistic regression modeling strategy based on Wilcoxon rank sum test WRST to effectively uncover driver genes in classification. In order to incorporate significance of gene in classification, we first measure significance of each gene by gene ranking method based on WRST, and then the ...

2
February 2016 Computational Statistics & Data Analysis: Volume 94 Issue C, February 2016
Publisher: Elsevier Science Publishers B. V.
Bibliometrics:
Citation Count: 0

For the evaluation of the dynamic behavior of biological processes, e.g., gene regulatory sequences, we typically utilize nonlinear differential equations within a state space model in the context of genomic data assimilation. For the estimation of the parameter values for such systems, the particle filter can be a strong approach ...
Keywords: Gene expression, Approximate Bayesian computation, Biological simulation, Nonlinear state space model

3
January 2016 International Journal of Bioinformatics Research and Applications: Volume 12 Issue 3, January 2016
Publisher: Inderscience Publishers
Bibliometrics:
Citation Count: 0

Somatic mutations are considered to initiate several disorders such as cancer and neurological disease. Hence, a number of computational methods have been developed to find loci subject to frequent mutations in cancer cells. Since normal cells turn into cancer cells through the accumulation of gene mutations, the elucidation of interactive ...
Keywords: Markov chain Monte Carlo, binary contingency tables, cancer cells, cancer genome, bioinformatics, MCMC, colon cancer, gene mutation, somatic mutations

4
November 2013 BSB 2013: 8th Brazilian Symposium on Advances in Bioinformatics and Computational Biology - Volume 8213
Publisher: Springer-Verlag New York, Inc.
Bibliometrics:
Citation Count: 0

Recent advances in biological high-throughput technology are generating a broad range of omics data. Facing a torrent of massive biological data, visual data mining can be considered an intuitive and powerful approach for hypothesis generation. The cluster heat map approach has been popularly used to visualize the matrix types of ...

5
October 2012 BIBMW '12: Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
Publisher: IEEE Computer Society
Bibliometrics:
Citation Count: 0

In Japanese traditional medicine, "Monshin" plays an important role. "Monshin" is a questionnaire that asked the patient's lifestyle and subjective symptoms. Specialists decide traditional herbal medicine by using of "Monshin". In this research, we analyze "Monshin" and predict "Sho" which is the name of a disease.
Keywords: machine learning,Traditional medicine,random forest

6
July 2012 Bioinformatics: Volume 28 Issue 14, July 2012
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 0

Summary: Protein–protein interactions (PPIs) are mediated through specific regions on proteins. Some proteins have two or more protein interacting regions (IRs) and some IRs are competitively used for interactions with different proteins. IRView currently contains data for 3417 IRs in human and mouse proteins. The data were obtained from different ...

7
July 2012 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 9 Issue 4, July 2012
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 0,   Downloads (12 Months): 2,   Downloads (Overall): 136

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We propose a statistical method for uncovering gene pathways that characterize cancer heterogeneity. To incorporate knowledge of the pathways into the model, we define a set of activities of pathways from microarray gene expression data based on the Sparse Probabilistic Principal Component Analysis (SPPCA). A pathway activity logistic regression model ...
Keywords: Cancer heterogeneity, gene network, microarray, pathway activity, sparse supervised learning.

8
June 2012 Bioinformatics: Volume 28 Issue 12, June 2012
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 3

Motivation: In cancer genomes, chromosomal regions harboring cancer genes are often subjected to genomic aberrations like copy number alteration and loss of heterozygosity. Given this, finding recurrent genomic aberrations is considered an apt approach for screening cancer genes. Although several permutation-based tests have been proposed for this purpose, none of ...

9
May 2012 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 9 Issue 3, May 2012
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 23
Downloads (6 Weeks): 4,   Downloads (12 Months): 29,   Downloads (Overall): 333

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Most of the conventional feature selection algorithms have a drawback whereby a weakly ranked gene that could perform well in terms of classification accuracy with an appropriate subset of genes will be left out of the selection. Considering this shortcoming, we propose a feature selection algorithm in gene expression data ...
Keywords: Feature selection, classification accuracy, top-r features, DNA microarray gene expression data.

10
November 2011 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 8 Issue 6, November 2011
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 1
Downloads (6 Weeks): 3,   Downloads (12 Months): 6,   Downloads (Overall): 149

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Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand ...
Keywords: CUDA, GPGPU, hybrid functional Petri nets, biological pathway modeling, delta-notch signaling.

11
September 2011 Natural Computing: an international journal: Volume 10 Issue 3, September 2011
Publisher: Kluwer Academic Publishers
Bibliometrics:
Citation Count: 0

Hybrid Petri net (HPN) is an extension of the Petri net formalism, which enables us to handle continuous information in addition to discrete information. Firstly, this paper demonstrates how biological pathways can be modeled by the integration of discrete and continuous elements, with an example of the � phage genetic ...
Keywords: Cell Illustrator, Hybrid Petri net, Pathway simulation

12
September 2011 Bioinformatics: Volume 27 Issue 17, September 2011
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 0

Summary: Manual curation and validation of large-scale biological pathways are required to obtain high-quality pathway databases. In a typical curation process, model validation and model update based on appropriate feedback are repeated and requires considerable cooperation of scientists. We have developed a CSO (Cell System Ontology) validator to reduce the ...

13
July 2011 The Journal of Machine Learning Research: Volume 12, 2/1/2011
Publisher: JMLR.org
Bibliometrics:
Citation Count: 8
Downloads (6 Weeks): 1,   Downloads (12 Months): 5,   Downloads (Overall): 133

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We present a parallel algorithm for the score-based optimal structure search of Bayesian networks. This algorithm is based on a dynamic programming (DP) algorithm having O(n ⋅ 2 n ) time and space complexity, which is known to be the fastest algorithm for the optimal structure search of networks with ...

14
June 2011 Bioinformatics: Volume 27 Issue 11, June 2011
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 0

Summary: The Macrophage Pathway Knowledgebase (MACPAK) is a computational system that allows biomedical researchers to query and study the dynamic behaviors of macrophage molecular pathways. It integrates the knowledge of 230 reviews that were carefully checked by specialists for their accuracy and then converted to 230 dynamic mathematical pathway models. ...

15
May 2011 ISBRA'11: Proceedings of the 7th international conference on Bioinformatics research and applications
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 1

We propose a computational method to comprehensively screen for pharmacogenomic pathway simulation models. A systematic model generation strategy is developed; candidate pharmacogenomic models are automatically generated from some prototype models constructed from existing literature. The parameters in the model are automatically estimated based on time-course observed gene expression data by ...

16
May 2011 AAMAS'11: Proceedings of the 10th international conference on Advanced Agent Technology
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 0

We have developed a parallel agent-based influenza pandemic simulator, in order to study the influenza spread in a city. In the simulator, the city consists of several towns connected tightly by trains. Residents of the towns walk around places such as corporations and schools using trains by need, following to ...
Keywords: agent-based simulation, influenza pandemic, parallel computing

17
May 2011 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 8 Issue 3, May 2011
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 7
Downloads (6 Weeks): 0,   Downloads (12 Months): 4,   Downloads (Overall): 171

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We present a novel algorithm to estimate genome-wide gene networks consisting of more than 20,000 genes from gene expression data using nonparametric Bayesian networks. Due to the difficulty of learning Bayesian network structures, existing algorithms cannot be applied to more than a few thousand genes. Our algorithm overcomes this limitation ...
Keywords: Biology and genetics, gene networks, Bayesian network structure learning, gene expression data analysis.

18
April 2011 Bioinformatics: Volume 27 Issue 8, April 2011
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 0

Summary: SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel ...

19
March 2011 Bioinformatics: Volume 27 Issue 5, March 2011
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 0

Summary: Model checking is playing an increasingly important role in systems biology as larger and more complex biological pathways are being modeled. In this article we report the release of an efficient model checker MIRACH 1.0, which supports any model written in popular formats such as CSML and SBML. MIRACH ...

20
March 2011 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 8 Issue 2, March 2011
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 0,   Downloads (12 Months): 1,   Downloads (Overall): 79

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Several gene regulatory network models containing concepts of directionality at the edges have been proposed. However, only a few reports have an interpretable definition of directionality. Here, differently from the standard causality concept defined by Pearl, we introduce the concept of contagion in order to infer directionality at the edges, ...
Keywords: Contagion, local correlation, regulatory network.



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