BibTeX records: Seiya Imoto

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@article{DBLP:journals/bib/XuLLGLSPLIYAS23,
  author       = {Jing Xu and
                  Fuyi Li and
                  Chen Li and
                  Xudong Guo and
                  Cornelia B. Landersdorfer and
                  Hsin{-}Hui Shen and
                  Anton Y. Peleg and
                  Jian Li and
                  Seiya Imoto and
                  Jianhua Yao and
                  Tatsuya Akutsu and
                  Jiangning Song},
  title        = {iAMPCN: a deep-learning approach for identifying antimicrobial peptides
                  and their functional activities},
  journal      = {Briefings Bioinform.},
  volume       = {24},
  number       = {4},
  year         = {2023},
  url          = {https://doi.org/10.1093/bib/bbad240},
  doi          = {10.1093/BIB/BBAD240},
  timestamp    = {Fri, 22 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/XuLLGLSPLIYAS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLBFUI23,
  author       = {Yao{-}zhong Zhang and
                  Yunjie Liu and
                  Zeheng Bai and
                  Kosuke Fujimoto and
                  Satoshi Uematsu and
                  Seiya Imoto},
  title        = {Zero-shot-capable identification of phage-host relationships with
                  whole-genome sequence representation by contrastive learning},
  journal      = {Briefings Bioinform.},
  volume       = {24},
  number       = {5},
  year         = {2023},
  url          = {https://doi.org/10.1093/bib/bbad239},
  doi          = {10.1093/BIB/BBAD239},
  timestamp    = {Sat, 28 Oct 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/ZhangLBFUI23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanLBWGPAWIS23,
  author       = {Tong Pan and
                  Chen Li and
                  Yue Bi and
                  Zhikang Wang and
                  Robin B. Gasser and
                  Anthony W. Purcell and
                  Tatsuya Akutsu and
                  Geoffrey I. Webb and
                  Seiya Imoto and
                  Jiangning Song},
  title        = {PFresGO: an attention mechanism-based deep-learning approach for protein
                  annotation by integrating gene ontology inter-relationships},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {3},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad094},
  doi          = {10.1093/BIOINFORMATICS/BTAD094},
  timestamp    = {Fri, 22 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/PanLBWGPAWIS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangBPWBBIYDS23,
  author       = {Zhikang Wang and
                  Yue Bi and
                  Tong Pan and
                  Xiaoyu Wang and
                  Chris Bain and
                  Richard Bassed and
                  Seiya Imoto and
                  Jianhua Yao and
                  Roger J. Daly and
                  Jiangning Song},
  title        = {Targeting tumor heterogeneity: multiplex-detection-based multiple
                  instance learning for whole slide image classification},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {3},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad114},
  doi          = {10.1093/BIOINFORMATICS/BTAD114},
  timestamp    = {Fri, 22 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/WangBPWBBIYDS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SatoUFUI23,
  author       = {Noriaki Sato and
                  Miho Uematsu and
                  Kosuke Fujimoto and
                  Satoshi Uematsu and
                  Seiya Imoto},
  title        = {\emph{ggkegg}: analysis and visualization of {KEGG} data utilizing
                  the grammar of graphics},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {10},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad622},
  doi          = {10.1093/BIOINFORMATICS/BTAD622},
  timestamp    = {Fri, 15 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SatoUFUI23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangBI23,
  author       = {Yao{-}zhong Zhang and
                  Zeheng Bai and
                  Seiya Imoto},
  title        = {Investigation of the {BERT} model on nucleotide sequences with non-standard
                  pre-training and evaluation of different k-mer embeddings},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {10},
  year         = {2023},
  url          = {https://doi.org/10.1093/bioinformatics/btad617},
  doi          = {10.1093/BIOINFORMATICS/BTAD617},
  timestamp    = {Fri, 22 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ZhangBI23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cmpb/WangGYZZZLBBLGIYDS23,
  author       = {Zhikang Wang and
                  Qian Gao and
                  Xiaoping Yi and
                  Xinyu Zhang and
                  Yiwen Zhang and
                  Daokun Zhang and
                  Pietro Li{\`{o}} and
                  Chris Bain and
                  Richard Bassed and
                  Shanshan Li and
                  Yuming Guo and
                  Seiya Imoto and
                  Jianhua Yao and
                  Roger J. Daly and
                  Jiangning Song},
  title        = {Surformer: An interpretable pattern-perceptive survival transformer
                  for cancer survival prediction from histopathology whole slide images},
  journal      = {Comput. Methods Programs Biomed.},
  volume       = {241},
  pages        = {107733},
  year         = {2023},
  url          = {https://doi.org/10.1016/j.cmpb.2023.107733},
  doi          = {10.1016/J.CMPB.2023.107733},
  timestamp    = {Sun, 12 Nov 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/cmpb/WangGYZZZLBBLGIYDS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ParkIM23,
  author       = {Heewon Park and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Gene Regulatory Network-Classifier: Gene Regulatory Network-Based
                  Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil)
                  Marker Identification},
  journal      = {J. Comput. Biol.},
  volume       = {30},
  number       = {2},
  pages        = {223--243},
  year         = {2023},
  url          = {https://doi.org/10.1089/cmb.2022.0181},
  doi          = {10.1089/CMB.2022.0181},
  timestamp    = {Sat, 25 Feb 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcb/ParkIM23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/SekiZI23,
  author       = {Misato Seki and
                  Yao{-}Zhong Zhang and
                  Seiya Imoto},
  editor       = {Xingpeng Jiang and
                  Haiying Wang and
                  Reda Alhajj and
                  Xiaohua Hu and
                  Felix Engel and
                  Mufti Mahmud and
                  Nadia Pisanti and
                  Xuefeng Cui and
                  Hong Song},
  title        = {Imputing time-series microbiome abundance profiles with diffusion
                  model},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2023, Istanbul, Turkiye, December 5-8, 2023},
  pages        = {914--919},
  publisher    = {{IEEE}},
  year         = {2023},
  url          = {https://doi.org/10.1109/BIBM58861.2023.10385703},
  doi          = {10.1109/BIBM58861.2023.10385703},
  timestamp    = {Thu, 14 Mar 2024 16:59:09 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/SekiZI23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaiZMYFUI22,
  author       = {Zeheng Bai and
                  Yao{-}zhong Zhang and
                  Satoru Miyano and
                  Rui Yamaguchi and
                  Kosuke Fujimoto and
                  Satoshi Uematsu and
                  Seiya Imoto},
  title        = {Identification of bacteriophage genome sequences with representation
                  learning},
  journal      = {Bioinform.},
  volume       = {38},
  number       = {18},
  pages        = {4264--4270},
  year         = {2022},
  url          = {https://doi.org/10.1093/bioinformatics/btac509},
  doi          = {10.1093/BIOINFORMATICS/BTAC509},
  timestamp    = {Sat, 13 May 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/BaiZMYFUI22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ParkIM22,
  author       = {Heewon Park and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {PredictiveNetwork: predictive gene network estimation with application
                  to gastric cancer drug response-predictive network analysis},
  journal      = {{BMC} Bioinform.},
  volume       = {23},
  number       = {1},
  pages        = {342},
  year         = {2022},
  url          = {https://doi.org/10.1186/s12859-022-04871-z},
  doi          = {10.1186/S12859-022-04871-Z},
  timestamp    = {Mon, 26 Sep 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/ParkIM22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijmi/TakeshitaTIM22,
  author       = {Kohei Takeshita and
                  Hiroyuki Takao and
                  Seiya Imoto and
                  Yuichi Murayama},
  title        = {Improvement of the Japanese healthcare data system for the effective
                  management of patients with {COVID-19:} {A} national survey},
  journal      = {Int. J. Medical Informatics},
  volume       = {162},
  pages        = {104752},
  year         = {2022},
  url          = {https://doi.org/10.1016/j.ijmedinf.2022.104752},
  doi          = {10.1016/J.IJMEDINF.2022.104752},
  timestamp    = {Mon, 24 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ijmi/TakeshitaTIM22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ParkYIM22,
  author       = {Heewon Park and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained
                  Common Structure Identification},
  journal      = {J. Comput. Biol.},
  volume       = {29},
  number       = {3},
  pages        = {257--275},
  year         = {2022},
  url          = {https://doi.org/10.1089/cmb.2021.0314},
  doi          = {10.1089/CMB.2021.0314},
  timestamp    = {Fri, 01 Apr 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/ParkYIM22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2208-03526,
  author       = {Zhikang Wang and
                  Yue Bi and
                  Tong Pan and
                  Xiaoyu Wang and
                  Chris Bain and
                  Richard Bassed and
                  Seiya Imoto and
                  Jianhua Yao and
                  Jiangning Song},
  title        = {Multiplex-detection Based Multiple Instance Learning Network for Whole
                  Slide Image Classification},
  journal      = {CoRR},
  volume       = {abs/2208.03526},
  year         = {2022},
  url          = {https://doi.org/10.48550/arXiv.2208.03526},
  doi          = {10.48550/ARXIV.2208.03526},
  eprinttype    = {arXiv},
  eprint       = {2208.03526},
  timestamp    = {Tue, 11 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2208-03526.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KonishiYYFI21,
  author       = {Hiroki Konishi and
                  Rui Yamaguchi and
                  Kiyoshi Yamaguchi and
                  Yoichi Furukawa and
                  Seiya Imoto},
  title        = {Halcyon: an accurate basecaller exploiting an encoder-decoder model
                  with monotonic attention},
  journal      = {Bioinform.},
  volume       = {37},
  number       = {9},
  pages        = {1211--1217},
  year         = {2021},
  url          = {https://doi.org/10.1093/bioinformatics/btaa953},
  doi          = {10.1093/BIOINFORMATICS/BTAA953},
  timestamp    = {Tue, 12 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KonishiYYFI21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangCZLHZITWDS21,
  author       = {Yanan Wang and
                  Nicolas Coudray and
                  Yun Zhao and
                  Fuyi Li and
                  Changyuan Hu and
                  Yao{-}Zhong Zhang and
                  Seiya Imoto and
                  Aristotelis Tsirigos and
                  Geoffrey I. Webb and
                  Roger J. Daly and
                  Jiangning Song},
  title        = {{HEAL:} an automated deep learning framework for cancer histopathology
                  image analysis},
  journal      = {Bioinform.},
  volume       = {37},
  number       = {22},
  pages        = {4291--4295},
  year         = {2021},
  url          = {https://doi.org/10.1093/bioinformatics/btab380},
  doi          = {10.1093/BIOINFORMATICS/BTAB380},
  timestamp    = {Mon, 26 Jun 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/WangCZLHZITWDS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ZhangIMY21,
  author       = {Yao{-}Zhong Zhang and
                  Seiya Imoto and
                  Satoru Miyano and
                  Rui Yamaguchi},
  title        = {Enhancing breakpoint resolution with deep segmentation model: {A}
                  general refinement method for read-depth based structural variant
                  callers},
  journal      = {PLoS Comput. Biol.},
  volume       = {17},
  number       = {10},
  year         = {2021},
  url          = {https://doi.org/10.1371/journal.pcbi.1009186},
  doi          = {10.1371/JOURNAL.PCBI.1009186},
  timestamp    = {Tue, 16 Aug 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/ZhangIMY21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ZhangYHFMYI21,
  author       = {Yao{-}Zhong Zhang and
                  Kiyoshi Yamaguchi and
                  Sera Hatakeyama and
                  Yoichi Furukawa and
                  Satoru Miyano and
                  Rui Yamaguchi and
                  Seiya Imoto},
  editor       = {Yufei Huang and
                  Lukasz A. Kurgan and
                  Feng Luo and
                  Xiaohua Hu and
                  Yidong Chen and
                  Edward R. Dougherty and
                  Andrzej Kloczkowski and
                  Yaohang Li},
  title        = {On the application of {BERT} models for nanopore methylation detection},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2021, Houston, TX, USA, December 9-12, 2021},
  pages        = {320--327},
  publisher    = {{IEEE}},
  year         = {2021},
  url          = {https://doi.org/10.1109/BIBM52615.2021.9669841},
  doi          = {10.1109/BIBM52615.2021.9669841},
  timestamp    = {Tue, 18 Jan 2022 09:39:01 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/ZhangYHFMYI21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/LiuZI21,
  author       = {Yunjie Liu and
                  Yaozhong Zhang and
                  Seiya Imoto},
  editor       = {Yufei Huang and
                  Lukasz A. Kurgan and
                  Feng Luo and
                  Xiaohua Hu and
                  Yidong Chen and
                  Edward R. Dougherty and
                  Andrzej Kloczkowski and
                  Yaohang Li},
  title        = {Discovering microbe functionality in human disease with a gene-ontology-aware
                  model},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2021, Houston, TX, USA, December 9-12, 2021},
  pages        = {1873--1880},
  publisher    = {{IEEE}},
  year         = {2021},
  url          = {https://doi.org/10.1109/BIBM52615.2021.9669492},
  doi          = {10.1109/BIBM52615.2021.9669492},
  timestamp    = {Tue, 18 Jan 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/LiuZI21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HasegawaHSMNYMN20,
  author       = {Takanori Hasegawa and
                  Shuto Hayashi and
                  Eigo Shimizu and
                  Shinichi Mizuno and
                  Atsushi Niida and
                  Rui Yamaguchi and
                  Satoru Miyano and
                  Hidewaki Nakagawa and
                  Seiya Imoto},
  title        = {Neoantimon: a multifunctional {R} package for identification of tumor-specific
                  neoantigens},
  journal      = {Bioinform.},
  volume       = {36},
  number       = {18},
  pages        = {4813--4816},
  year         = {2020},
  url          = {https://doi.org/10.1093/bioinformatics/btaa616},
  doi          = {10.1093/BIOINFORMATICS/BTAA616},
  timestamp    = {Tue, 21 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HasegawaHSMNYMN20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangATIMSY20,
  author       = {Yao{-}zhong Zhang and
                  Arda Akdemir and
                  Georg Tremmel and
                  Seiya Imoto and
                  Satoru Miyano and
                  Tetsuo Shibuya and
                  Rui Yamaguchi},
  title        = {Nanopore basecalling from a perspective of instance segmentation},
  journal      = {{BMC} Bioinform.},
  volume       = {21-S},
  number       = {3},
  pages        = {136},
  year         = {2020},
  url          = {https://doi.org/10.1186/s12859-020-3459-0},
  doi          = {10.1186/S12859-020-3459-0},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/ZhangATIMSY20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jfi/HasegawaYNMI20,
  author       = {Takanori Hasegawa and
                  Rui Yamaguchi and
                  Atsushi Niida and
                  Satoru Miyano and
                  Seiya Imoto},
  title        = {Ensemble smoothers for inference of hidden states and parameters in
                  combinatorial regulatory model},
  journal      = {J. Frankl. Inst.},
  volume       = {357},
  number       = {5},
  pages        = {2916--2933},
  year         = {2020},
  url          = {https://doi.org/10.1016/j.jfranklin.2019.10.015},
  doi          = {10.1016/J.JFRANKLIN.2019.10.015},
  timestamp    = {Mon, 11 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jfi/HasegawaYNMI20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismco/MoriyamaIMY20,
  author       = {Takuya Moriyama and
                  Seiya Imoto and
                  Satoru Miyano and
                  Rui Yamaguchi},
  editor       = {George Bebis and
                  Max A. Alekseyev and
                  Heyrim Cho and
                  Jana Gevertz and
                  Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez},
  title        = {Theoretical Foundation of the Performance of Phylogeny-Based Somatic
                  Variant Detection},
  booktitle    = {Mathematical and Computational Oncology - Second International Symposium,
                  {ISMCO} 2020, San Diego, CA, USA, October 8-10, 2020, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {12508},
  pages        = {87--101},
  publisher    = {Springer},
  year         = {2020},
  url          = {https://doi.org/10.1007/978-3-030-64511-3\_9},
  doi          = {10.1007/978-3-030-64511-3\_9},
  timestamp    = {Tue, 21 Dec 2021 17:15:56 +0100},
  biburl       = {https://dblp.org/rec/conf/ismco/MoriyamaIMY20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MoriyamaIHSMY19,
  author       = {Takuya Moriyama and
                  Seiya Imoto and
                  Shuto Hayashi and
                  Yuichi Shiraishi and
                  Satoru Miyano and
                  Rui Yamaguchi},
  title        = {A Bayesian model integration for mutation calling through data partitioning},
  journal      = {Bioinform.},
  volume       = {35},
  number       = {21},
  pages        = {4247--4254},
  year         = {2019},
  url          = {https://doi.org/10.1093/bioinformatics/btz233},
  doi          = {10.1093/BIOINFORMATICS/BTZ233},
  timestamp    = {Sat, 30 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MoriyamaIHSMY19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KonishiKKAKYSFY19,
  author       = {Hiroki Konishi and
                  Daisuke Komura and
                  Hiroto Katoh and
                  Shinichiro Atsumi and
                  Hirotomo Koda and
                  Asami Yamamoto and
                  Yasuyuki Seto and
                  Masashi Fukayama and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Shumpei Ishikawa},
  title        = {Capturing the differences between humoral immunity in the normal and
                  tumor environments from repertoire-seq of B-cell receptors using supervised
                  machine learning},
  journal      = {{BMC} Bioinform.},
  volume       = {20},
  number       = {1},
  pages        = {267:1--267:11},
  year         = {2019},
  url          = {https://doi.org/10.1186/s12859-019-2853-y},
  doi          = {10.1186/S12859-019-2853-Y},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/KonishiKKAKYSFY19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ParkYIM19,
  author       = {Heewon Park and
                  Makoto Yamada and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Robust Sample-Specific Stability Selection with Effective Error Control},
  journal      = {J. Comput. Biol.},
  volume       = {26},
  number       = {3},
  pages        = {202--217},
  year         = {2019},
  url          = {https://doi.org/10.1089/cmb.2018.0180},
  doi          = {10.1089/CMB.2018.0180},
  timestamp    = {Mon, 26 Jun 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/ParkYIM19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HayashiMYMKMNI19,
  author       = {Shuto Hayashi and
                  Takuya Moriyama and
                  Rui Yamaguchi and
                  Shinichi Mizuno and
                  Mitsuhiro Komura and
                  Satoru Miyano and
                  Hidewaki Nakagawa and
                  Seiya Imoto},
  title        = {{ALPHLARD-NT:} Bayesian Method for Human Leukocyte Antigen Genotyping
                  and Mutation Calling through Simultaneous Analysis of Normal and Tumor
                  Whole-Genome Sequence Data},
  journal      = {J. Comput. Biol.},
  volume       = {26},
  number       = {9},
  pages        = {923--937},
  year         = {2019},
  url          = {https://doi.org/10.1089/cmb.2018.0224},
  doi          = {10.1089/CMB.2018.0224},
  timestamp    = {Tue, 21 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcb/HayashiMYMKMNI19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismco/MoriyamaIMY19,
  author       = {Takuya Moriyama and
                  Seiya Imoto and
                  Satoru Miyano and
                  Rui Yamaguchi},
  editor       = {George Bebis and
                  Takis Benos and
                  Ken Chen and
                  Katharina Jahn and
                  Ernesto Lima},
  title        = {Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor
                  Samples},
  booktitle    = {Mathematical and Computational Oncology - First International Symposium,
                  {ISMCO} 2019, Lake Tahoe, NV, USA, October 14-16, 2019, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {11826},
  pages        = {47--61},
  publisher    = {Springer},
  year         = {2019},
  url          = {https://doi.org/10.1007/978-3-030-35210-3\_4},
  doi          = {10.1007/978-3-030-35210-3\_4},
  timestamp    = {Thu, 09 Jun 2022 16:00:23 +0200},
  biburl       = {https://dblp.org/rec/conf/ismco/MoriyamaIMY19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ParkSIM18,
  author       = {Heewon Park and
                  Teppei Shimamura and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific
                  Gene Regulatory Networks},
  journal      = {J. Comput. Biol.},
  volume       = {25},
  number       = {2},
  pages        = {130--145},
  year         = {2018},
  url          = {https://doi.org/10.1089/cmb.2017.0120},
  doi          = {10.1089/CMB.2017.0120},
  timestamp    = {Mon, 26 Jun 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/ParkSIM18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ParkNIM17,
  author       = {Heewon Park and
                  Atsushi Niida and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Interaction-Based Feature Selection for Uncovering Cancer Driver Genes
                  Through Copy Number-Driven Expression Level},
  journal      = {J. Comput. Biol.},
  volume       = {24},
  number       = {2},
  pages        = {138--152},
  year         = {2017},
  url          = {https://doi.org/10.1089/cmb.2016.0140},
  doi          = {10.1089/CMB.2016.0140},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/ParkNIM17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ParkSIM17,
  author       = {Heewon Park and
                  Yuichi Shiraishi and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker
                  Associated with Anti-Cancer Drug Sensitivity},
  journal      = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
  volume       = {14},
  number       = {4},
  pages        = {771--782},
  year         = {2017},
  url          = {https://doi.org/10.1109/TCBB.2016.2561937},
  doi          = {10.1109/TCBB.2016.2561937},
  timestamp    = {Mon, 03 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcbb/ParkSIM17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ZhangIMY17,
  author       = {Yao{-}Zhong Zhang and
                  Seiya Imoto and
                  Satoru Miyano and
                  Rui Yamaguchi},
  editor       = {Xiaohua Hu and
                  Chi{-}Ren Shyu and
                  Yana Bromberg and
                  Jean Gao and
                  Yang Gong and
                  Dmitry Korkin and
                  Illhoi Yoo and
                  Huiru Jane Zheng},
  title        = {Reconstruction of high read-depth signals from low-depth whole genome
                  sequencing data using deep learning},
  booktitle    = {2017 {IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2017, Kansas City, MO, USA, November 13-16, 2017},
  pages        = {1227--1232},
  publisher    = {{IEEE} Computer Society},
  year         = {2017},
  url          = {https://doi.org/10.1109/BIBM.2017.8217832},
  doi          = {10.1109/BIBM.2017.8217832},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/ZhangIMY17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/csda/HasegawaNMSYMAI16,
  author       = {Takanori Hasegawa and
                  Atsushi Niida and
                  Tomoya Mori and
                  Teppei Shimamura and
                  Rui Yamaguchi and
                  Satoru Miyano and
                  Tatsuya Akutsu and
                  Seiya Imoto},
  title        = {A likelihood-free filtering method via approximate Bayesian computation
                  in evaluating biological simulation models},
  journal      = {Comput. Stat. Data Anal.},
  volume       = {94},
  pages        = {63--74},
  year         = {2016},
  url          = {https://doi.org/10.1016/j.csda.2015.08.003},
  doi          = {10.1016/J.CSDA.2015.08.003},
  timestamp    = {Fri, 09 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/csda/HasegawaNMSYMAI16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/AyadaHNMI16,
  author       = {Emi Ayada and
                  Takanori Hasegawa and
                  Atsushi Niida and
                  Satoru Miyano and
                  Seiya Imoto},
  title        = {Binary contingency table method for analysing gene mutation in cancer
                  genome},
  journal      = {Int. J. Bioinform. Res. Appl.},
  volume       = {12},
  number       = {3},
  pages        = {211--226},
  year         = {2016},
  url          = {https://doi.org/10.1504/IJBRA.2016.078231},
  doi          = {10.1504/IJBRA.2016.078231},
  timestamp    = {Fri, 11 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ijbra/AyadaHNMI16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jsw/SainiRLDIS16,
  author       = {Harsh Saini and
                  Gaurav Raicar and
                  Sunil Pranit Lal and
                  Abdollah Dehzangi and
                  Seiya Imoto and
                  Alok Sharma},
  title        = {Protein Fold Recognition Using Genetic Algorithm Optimized Voting
                  Scheme and Profile Bigram},
  journal      = {J. Softw.},
  volume       = {11},
  number       = {8},
  pages        = {756--767},
  year         = {2016},
  url          = {https://doi.org/10.17706/jsw.11.8.756-767},
  doi          = {10.17706/JSW.11.8.756-767},
  timestamp    = {Fri, 07 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jsw/SainiRLDIS16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/YoshinoKHMYIMMW16,
  author       = {Tetsuhiro Yoshino and
                  Kotoe Katayama and
                  Yuko Horiba and
                  Kaori Munakata and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Satoru Miyano and
                  Hideki Mima and
                  Kenji Watanabe},
  title        = {Predicting Japanese Kampo formulas by analyzing database of medical
                  records: a preliminary observational study},
  journal      = {{BMC} Medical Informatics Decis. Mak.},
  volume       = {16},
  pages        = {118},
  year         = {2016},
  url          = {https://doi.org/10.1186/s12911-016-0361-9},
  doi          = {10.1186/S12911-016-0361-9},
  timestamp    = {Wed, 07 Dec 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/midm/YoshinoKHMYIMMW16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/MoriyamaSCYIM16,
  author       = {Takuya Moriyama and
                  Yuichi Shiraishi and
                  Kenichi Chiba and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Anu G. Bourgeois and
                  Pavel Skums and
                  Xiang Wan and
                  Alex Zelikovsky},
  title        = {OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End
                  Reads},
  booktitle    = {Bioinformatics Research and Applications - 12th International Symposium,
                  {ISBRA} 2016, Minsk, Belarus, June 5-8, 2016, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {9683},
  pages        = {40--51},
  publisher    = {Springer},
  year         = {2016},
  url          = {https://doi.org/10.1007/978-3-319-38782-6\_4},
  doi          = {10.1007/978-3-319-38782-6\_4},
  timestamp    = {Tue, 14 May 2019 10:00:51 +0200},
  biburl       = {https://dblp.org/rec/conf/isbra/MoriyamaSCYIM16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChibaSNYIOM15,
  author       = {Kenichi Chiba and
                  Yuichi Shiraishi and
                  Yasunobu Nagata and
                  Kenichi Yoshida and
                  Seiya Imoto and
                  Seishi Ogawa and
                  Satoru Miyano},
  title        = {Genomon ITDetector: a tool for somatic internal tandem duplication
                  detection from cancer genome sequencing data},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {1},
  pages        = {116--118},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btu593},
  doi          = {10.1093/BIOINFORMATICS/BTU593},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ChibaSNYIOM15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/HasegawaMYSMIA15,
  author       = {Takanori Hasegawa and
                  Tomoya Mori and
                  Rui Yamaguchi and
                  Teppei Shimamura and
                  Satoru Miyano and
                  Seiya Imoto and
                  Tatsuya Akutsu},
  title        = {Genomic data assimilation using a higher moment filtering technique
                  for restoration of gene regulatory networks},
  journal      = {{BMC} Syst. Biol.},
  volume       = {9},
  pages        = {14},
  year         = {2015},
  url          = {https://doi.org/10.1186/s12918-015-0154-2},
  doi          = {10.1186/S12918-015-0154-2},
  timestamp    = {Fri, 09 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/HasegawaMYSMIA15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ParkNMI15,
  author       = {Heewon Park and
                  Atsushi Niida and
                  Satoru Miyano and
                  Seiya Imoto},
  title        = {Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis},
  journal      = {J. Comput. Biol.},
  volume       = {22},
  number       = {2},
  pages        = {73--84},
  year         = {2015},
  url          = {https://doi.org/10.1089/cmb.2014.0197},
  doi          = {10.1089/CMB.2014.0197},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/ParkNMI15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AyadaNHMI15,
  author       = {Emi Ayada and
                  Atsushi Niida and
                  Takanori Hasegawa and
                  Satoru Miyano and
                  Seiya Imoto},
  editor       = {Robert W. Harrison and
                  Yaohang Li and
                  Ion I. Mandoiu},
  title        = {Binary Contingency Table Method for Analyzing Gene Mutation in Cancer
                  Genome},
  booktitle    = {Bioinformatics Research and Applications - 11th International Symposium,
                  {ISBRA} 2015, Norfolk, VA, USA, June 7-10, 2015 Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {9096},
  pages        = {12--23},
  publisher    = {Springer},
  year         = {2015},
  url          = {https://doi.org/10.1007/978-3-319-19048-8\_2},
  doi          = {10.1007/978-3-319-19048-8\_2},
  timestamp    = {Tue, 14 May 2019 10:00:51 +0200},
  biburl       = {https://dblp.org/rec/conf/isbra/AyadaNHMI15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UsuyamaSSKHOMI14,
  author       = {Naoto Usuyama and
                  Yuichi Shiraishi and
                  Yusuke Sato and
                  Haruki Kume and
                  Yukio Homma and
                  Seishi Ogawa and
                  Satoru Miyano and
                  Seiya Imoto},
  title        = {HapMuC: somatic mutation calling using heterozygous germ line variants
                  near candidate mutations},
  journal      = {Bioinform.},
  volume       = {30},
  number       = {23},
  pages        = {3302--3309},
  year         = {2014},
  url          = {https://doi.org/10.1093/bioinformatics/btu537},
  doi          = {10.1093/BIOINFORMATICS/BTU537},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/UsuyamaSSKHOMI14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/HasegawaNYIM14,
  author       = {Takanori Hasegawa and
                  Masao Nagasaki and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {An efficient method of exploring simulation models by assimilating
                  literature and biological observational data},
  journal      = {Biosyst.},
  volume       = {121},
  pages        = {54--66},
  year         = {2014},
  url          = {https://doi.org/10.1016/j.biosystems.2014.06.001},
  doi          = {10.1016/J.BIOSYSTEMS.2014.06.001},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/biosystems/HasegawaNYIM14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HasegawaMYIMA14,
  author       = {Takanori Hasegawa and
                  Tomoya Mori and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Satoru Miyano and
                  Tatsuya Akutsu},
  title        = {An Efficient Data Assimilation Schema for Restoration and Extension
                  of Gene Regulatory Networks Using Time-Course Observation Data},
  journal      = {J. Comput. Biol.},
  volume       = {21},
  number       = {11},
  pages        = {785--798},
  year         = {2014},
  url          = {https://doi.org/10.1089/cmb.2014.0171},
  doi          = {10.1089/CMB.2014.0171},
  timestamp    = {Fri, 09 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/HasegawaMYIMA14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/kes/SharmaPIMSA14,
  author       = {Alok Sharma and
                  Kuldip K. Paliwal and
                  Seiya Imoto and
                  Satoru Miyano and
                  Vandana Sharma and
                  Rajeshkannan Ananthanarayanan},
  title        = {A feature selection method using fixed-point algorithm for {DNA} microarray
                  gene expression data},
  journal      = {Int. J. Knowl. Based Intell. Eng. Syst.},
  volume       = {18},
  number       = {1},
  pages        = {55--59},
  year         = {2014},
  url          = {https://doi.org/10.3233/KES-140285},
  doi          = {10.3233/KES-140285},
  timestamp    = {Thu, 20 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/kes/SharmaPIMSA14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mva/SharmaPIM14,
  author       = {Alok Sharma and
                  Kuldip K. Paliwal and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {A feature selection method using improved regularized linear discriminant
                  analysis},
  journal      = {Mach. Vis. Appl.},
  volume       = {25},
  number       = {3},
  pages        = {775--786},
  year         = {2014},
  url          = {https://doi.org/10.1007/s00138-013-0577-y},
  doi          = {10.1007/S00138-013-0577-Y},
  timestamp    = {Thu, 08 Jun 2017 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/mva/SharmaPIM14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fusion/SaitoIYMH14,
  author       = {Masaya M. Saito and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Satoru Miyano and
                  Tomoyuki Higuchi},
  title        = {Parameter estimation in multi-compartment {SIR} model},
  booktitle    = {17th International Conference on Information Fusion, {FUSION} 2014,
                  Salamanca, Spain, July 7-10, 2014},
  pages        = {1--5},
  publisher    = {{IEEE}},
  year         = {2014},
  url          = {https://ieeexplore.ieee.org/document/6916269/},
  timestamp    = {Mon, 09 Aug 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/fusion/SaitoIYMH14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SharmaPDLIM13,
  author       = {Alok Sharma and
                  Kuldip K. Paliwal and
                  Abdollah Dehzangi and
                  James G. Lyons and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {A strategy to select suitable physicochemical attributes of amino
                  acids for protein fold recognition},
  journal      = {{BMC} Bioinform.},
  volume       = {14},
  pages        = {233},
  year         = {2013},
  url          = {https://doi.org/10.1186/1471-2105-14-233},
  doi          = {10.1186/1471-2105-14-233},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/SharmaPDLIM13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KayanoIYM13,
  author       = {Mitsunori Kayano and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Satoru Miyano},
  title        = {Multi-omics Approach for Estimating Metabolic Networks Using Low-Order
                  Partial Correlations},
  journal      = {J. Comput. Biol.},
  volume       = {20},
  number       = {8},
  pages        = {571--582},
  year         = {2013},
  url          = {https://doi.org/10.1089/cmb.2013.0043},
  doi          = {10.1089/CMB.2013.0043},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcb/KayanoIYM13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlc/SharmaPIM13,
  author       = {Alok Sharma and
                  Kuldip K. Paliwal and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Principal component analysis using {QR} decomposition},
  journal      = {Int. J. Mach. Learn. Cybern.},
  volume       = {4},
  number       = {6},
  pages        = {679--683},
  year         = {2013},
  url          = {https://doi.org/10.1007/s13042-012-0131-7},
  doi          = {10.1007/S13042-012-0131-7},
  timestamp    = {Tue, 25 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/mlc/SharmaPIM13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fusion/SaitoIYMH13,
  author       = {Masaya M. Saito and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Satoru Miyano and
                  Tomoyuki Higuchi},
  title        = {Estimation of abrupt changes in sentinel observation data of influenza
                  epidemics in Japan},
  booktitle    = {Proceedings of the 16th International Conference on Information Fusion,
                  {FUSION} 2013, Istanbul, Turkey, July 9-12, 2013},
  pages        = {1385--1390},
  publisher    = {{IEEE}},
  year         = {2013},
  url          = {https://ieeexplore.ieee.org/document/6641160/},
  timestamp    = {Mon, 09 Aug 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/fusion/SaitoIYMH13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/NiidaTIM13,
  author       = {Atsushi Niida and
                  Georg Tremmel and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Jo{\~{a}}o C. Setubal and
                  Nalvo F. Almeida},
  title        = {Multilayer Cluster Heat Map Visualizing Biological Tensor Data},
  booktitle    = {Advances in Bioinformatics and Computational Biology - 8th Brazilian
                  Symposium on Bioinformatics, {BSB} 2013, Recife, Brazil, November
                  3-7, 2013, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {8213},
  pages        = {116--125},
  publisher    = {Springer},
  year         = {2013},
  url          = {https://doi.org/10.1007/978-3-319-02624-4\_11},
  doi          = {10.1007/978-3-319-02624-4\_11},
  timestamp    = {Tue, 14 May 2019 10:00:50 +0200},
  biburl       = {https://dblp.org/rec/conf/wob/NiidaTIM13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NiidaISM12,
  author       = {Atsushi Niida and
                  Seiya Imoto and
                  Teppei Shimamura and
                  Satoru Miyano},
  title        = {Statistical model-based testing to evaluate the recurrence of genomic
                  aberrations},
  journal      = {Bioinform.},
  volume       = {28},
  number       = {12},
  pages        = {115--120},
  year         = {2012},
  url          = {https://doi.org/10.1093/bioinformatics/bts203},
  doi          = {10.1093/BIOINFORMATICS/BTS203},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/NiidaISM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcgenomics/KojimaIYFYGM12,
  author       = {Kaname Kojima and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Andr{\'{e}} Fujita and
                  Mai Yamauchi and
                  Noriko Gotoh and
                  Satoru Miyano},
  title        = {Identifying regulational alterations in gene regulatory networks by
                  state space representation of vector autoregressive models and variational
                  annealing},
  journal      = {{BMC} Genom.},
  volume       = {13},
  number       = {{S-1}},
  pages        = {S6},
  year         = {2012},
  url          = {https://doi.org/10.1186/1471-2164-13-S1-S6},
  doi          = {10.1186/1471-2164-13-S1-S6},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcgenomics/KojimaIYFYGM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/OgamiYITAPM12,
  author       = {Kentaro Ogami and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Yoshinori Tamada and
                  Hiromitsu Araki and
                  Cristin G. Print and
                  Satoru Miyano},
  title        = {Computational gene network analysis reveals TNF-induced angiogenesis},
  journal      = {{BMC} Syst. Biol.},
  volume       = {6},
  number       = {{S-2}},
  pages        = {S12},
  year         = {2012},
  url          = {https://doi.org/10.1186/1752-0509-6-S2-S12},
  doi          = {10.1186/1752-0509-6-S2-S12},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/OgamiYITAPM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/SharmaIM12,
  author       = {Alok Sharma and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {A between-Class Overlapping Filter-Based Method for transcriptome
                  Data Analysis},
  journal      = {J. Bioinform. Comput. Biol.},
  volume       = {10},
  number       = {5},
  year         = {2012},
  url          = {https://doi.org/10.1142/S0219720012500102},
  doi          = {10.1142/S0219720012500102},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jbcb/SharmaIM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlc/SharmaIMS12,
  author       = {Alok Sharma and
                  Seiya Imoto and
                  Satoru Miyano and
                  Vandana Sharma},
  title        = {Null space based feature selection method for gene expression data},
  journal      = {Int. J. Mach. Learn. Cybern.},
  volume       = {3},
  number       = {4},
  pages        = {269--276},
  year         = {2012},
  url          = {https://doi.org/10.1007/s13042-011-0061-9},
  doi          = {10.1007/S13042-011-0061-9},
  timestamp    = {Tue, 25 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/mlc/SharmaIMS12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sighit/KatayamaYIMWI12,
  author       = {Kotoe Katayama and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Keiko Matsuura and
                  Kenji Watanabe},
  title        = {Connection between traditional medicine and disease},
  journal      = {{SIGHIT} Rec.},
  volume       = {2},
  number       = {1},
  pages        = {21},
  year         = {2012},
  url          = {https://doi.org/10.1145/2180796.2180813},
  doi          = {10.1145/2180796.2180813},
  timestamp    = {Thu, 20 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/sighit/KatayamaYIMWI12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SharmaIM12,
  author       = {Alok Sharma and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {A Top-r Feature Selection Algorithm for Microarray Gene Expression
                  Data},
  journal      = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
  volume       = {9},
  number       = {3},
  pages        = {754--764},
  year         = {2012},
  url          = {https://doi.org/10.1109/TCBB.2011.151},
  doi          = {10.1109/TCBB.2011.151},
  timestamp    = {Mon, 03 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcbb/SharmaIM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/KawanoSNIYNYPM12,
  author       = {Shuichi Kawano and
                  Teppei Shimamura and
                  Atsushi Niida and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Masao Nagasaki and
                  Ryo Yoshida and
                  Cristin G. Print and
                  Satoru Miyano},
  title        = {Identifying Gene Pathways Associated with Cancer Characteristics via
                  Sparse Statistical Methods},
  journal      = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
  volume       = {9},
  number       = {4},
  pages        = {966--972},
  year         = {2012},
  url          = {https://doi.org/10.1109/TCBB.2012.48},
  doi          = {10.1109/TCBB.2012.48},
  timestamp    = {Mon, 03 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcbb/KawanoSNIYNYPM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/KatayamaIWYMM12,
  author       = {Kotoe Katayama and
                  Seiya Imoto and
                  Kenji Watanabe and
                  Rui Yamaguchi and
                  Keiko Matsuura and
                  Satoru Miyano},
  title        = {Analysis of questionnaire for traditional medical and develop decision
                  support system},
  booktitle    = {2012 {IEEE} International Conference on Bioinformatics and Biomedicine
                  Workshops, {BIBMW} 2012, Philadelphia, USA, October 4-7, 2012},
  pages        = {762--763},
  publisher    = {{IEEE} Computer Society},
  year         = {2012},
  url          = {https://doi.org/10.1109/BIBMW.2012.6470235},
  doi          = {10.1109/BIBMW.2012.6470235},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/KatayamaIWYMM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fusion/SaitoIYMH12,
  author       = {Masaya M. Saito and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Satoru Miyano and
                  Tomoyuki Higuchi},
  title        = {Identifiability of local transmissibility parameters in agent-based
                  pandemic simulation},
  booktitle    = {15th International Conference on Information Fusion, {FUSION} 2012,
                  Singapore, July 9-12, 2012},
  pages        = {2466--2471},
  publisher    = {{IEEE}},
  year         = {2012},
  url          = {https://ieeexplore.ieee.org/document/6290603/},
  timestamp    = {Mon, 09 Aug 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/fusion/SaitoIYMH12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TamadaYIHYNM11,
  author       = {Yoshinori Tamada and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Osamu Hirose and
                  Ryo Yoshida and
                  Masao Nagasaki and
                  Satoru Miyano},
  title        = {SiGN-SSM: open source parallel software for estimating gene networks
                  with state space models},
  journal      = {Bioinform.},
  volume       = {27},
  number       = {8},
  pages        = {1172--1173},
  year         = {2011},
  url          = {https://doi.org/10.1093/bioinformatics/btr078},
  doi          = {10.1093/BIOINFORMATICS/BTR078},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/TamadaYIHYNM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijkesdp/KatayamaYIMWM11,
  author       = {Kotoe Katayama and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Keiko Matsuura and
                  Kenji Watanabe and
                  Satoru Miyano},
  title        = {Transform of visual analogue scale data and their clustering},
  journal      = {Int. J. Knowl. Eng. Soft Data Paradigms},
  volume       = {3},
  number       = {2},
  pages        = {143--151},
  year         = {2011},
  url          = {https://doi.org/10.1504/IJKESDP.2011.045726},
  doi          = {10.1504/IJKESDP.2011.045726},
  timestamp    = {Thu, 04 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ijkesdp/KatayamaYIMWM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jmlr/TamadaIM11,
  author       = {Yoshinori Tamada and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Parallel Algorithm for Learning Optimal Bayesian Network Structure},
  journal      = {J. Mach. Learn. Res.},
  volume       = {12},
  pages        = {2437--2459},
  year         = {2011},
  url          = {https://dl.acm.org/doi/10.5555/1953048.2021080},
  doi          = {10.5555/1953048.2021080},
  timestamp    = {Thu, 02 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jmlr/TamadaIM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nn/SogawaSSHWI11,
  author       = {Yasuhiro Sogawa and
                  Shohei Shimizu and
                  Teppei Shimamura and
                  Aapo Hyv{\"{a}}rinen and
                  Takashi Washio and
                  Seiya Imoto},
  title        = {Estimating exogenous variables in data with more variables than observations},
  journal      = {Neural Networks},
  volume       = {24},
  number       = {8},
  pages        = {875--880},
  year         = {2011},
  url          = {https://doi.org/10.1016/j.neunet.2011.05.017},
  doi          = {10.1016/J.NEUNET.2011.05.017},
  timestamp    = {Fri, 30 Nov 2018 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nn/SogawaSSHWI11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/TamadaIANPCM11,
  author       = {Yoshinori Tamada and
                  Seiya Imoto and
                  Hiromitsu Araki and
                  Masao Nagasaki and
                  Cristin G. Print and
                  Stephen D. Charnock{-}Jones and
                  Satoru Miyano},
  title        = {Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian
                  Network Models on Massively Parallel Computers},
  journal      = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
  volume       = {8},
  number       = {3},
  pages        = {683--697},
  year         = {2011},
  url          = {https://doi.org/10.1109/TCBB.2010.68},
  doi          = {10.1109/TCBB.2010.68},
  timestamp    = {Mon, 03 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcbb/TamadaIANPCM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/atal/SaitoIYMH11,
  author       = {Masaya M. Saito and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Satoru Miyano and
                  Tomoyuki Higuchi},
  editor       = {Francien Dechesne and
                  Hiromitsu Hattori and
                  Adriaan ter Mors and
                  Jose M. Such and
                  Danny Weyns and
                  Frank Dignum},
  title        = {Parallel Agent-Based Simulator for Influenza Pandemic},
  booktitle    = {Advanced Agent Technology - {AAMAS} 2011 Workshops, AMPLE, AOSE, ARMS,
                  DOCM3AS, ITMAS, Taipei, Taiwan, May 2-6, 2011. Revised Selected Papers},
  series       = {Lecture Notes in Computer Science},
  volume       = {7068},
  pages        = {361--370},
  publisher    = {Springer},
  year         = {2011},
  url          = {https://doi.org/10.1007/978-3-642-27216-5\_27},
  doi          = {10.1007/978-3-642-27216-5\_27},
  timestamp    = {Tue, 14 May 2019 10:00:54 +0200},
  biburl       = {https://dblp.org/rec/conf/atal/SaitoIYMH11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fusion/SaitoIYMH11,
  author       = {Masaya M. Saito and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Satoru Miyano and
                  Tomoyuki Higuchi},
  title        = {Estimation of macroscopic parameter in agent-based pandemic simulation},
  booktitle    = {Proceedings of the 14th International Conference on Information Fusion,
                  {FUSION} 2011, Chicago, Illinois, USA, July 5-8, 2011},
  pages        = {1--6},
  publisher    = {{IEEE}},
  year         = {2011},
  url          = {https://ieeexplore.ieee.org/document/5977691/},
  timestamp    = {Mon, 09 Aug 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/fusion/SaitoIYMH11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/HasegawaYNIM11,
  author       = {Takanori Hasegawa and
                  Rui Yamaguchi and
                  Masao Nagasaki and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Ion I. Mandoiu and
                  Satoru Miyano and
                  Teresa M. Przytycka and
                  Sanguthevar Rajasekaran},
  title        = {Poster: Comprehensive pharmacogenomic pathway screening by data assimilation},
  booktitle    = {{IEEE} 1st International Conference on Computational Advances in Bio
                  and Medical Sciences, {ICCABS} 2011, Orlando, FL, USA, February 3-5,
                  2011},
  pages        = {246},
  publisher    = {{IEEE} Computer Society},
  year         = {2011},
  url          = {https://doi.org/10.1109/ICCABS.2011.5729899},
  doi          = {10.1109/ICCABS.2011.5729899},
  timestamp    = {Thu, 23 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/iccabs/HasegawaYNIM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/HasegawaYNIM11,
  author       = {Takanori Hasegawa and
                  Rui Yamaguchi and
                  Masao Nagasaki and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Jianer Chen and
                  Jianxin Wang and
                  Alexander Zelikovsky},
  title        = {Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation},
  booktitle    = {Bioinformatics Research and Applications - 7th International Symposium,
                  {ISBRA} 2011, Changsha, China, May 27-29, 2011. Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {6674},
  pages        = {160--171},
  publisher    = {Springer},
  year         = {2011},
  url          = {https://doi.org/10.1007/978-3-642-21260-4\_18},
  doi          = {10.1007/978-3-642-21260-4\_18},
  timestamp    = {Fri, 21 Aug 2020 17:12:20 +0200},
  biburl       = {https://dblp.org/rec/conf/isbra/HasegawaYNIM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/KatayamaYIMWM11,
  author       = {Kotoe Katayama and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Keiko Matsuura and
                  Kenji Watanabe and
                  Satoru Miyano},
  editor       = {Cihan H. Dagli},
  title        = {Clustering for Visual Analogue Scale Data in Symbolic Data Analysis},
  booktitle    = {Proceedings of the Complex Adaptive Systems 2011 Conference, Chicago,
                  Illinois, USA, October 31-November 2, 2011},
  series       = {Procedia Computer Science},
  volume       = {6},
  pages        = {370--374},
  publisher    = {Elsevier},
  year         = {2011},
  url          = {https://doi.org/10.1016/j.procs.2011.08.068},
  doi          = {10.1016/J.PROCS.2011.08.068},
  timestamp    = {Thu, 08 Jul 2021 16:04:01 +0200},
  biburl       = {https://dblp.org/rec/journals/procedia/KatayamaYIMWM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/daglib/p/ImotoTAM11,
  author       = {Seiya Imoto and
                  Yoshinori Tamada and
                  Hiromitsu Araki and
                  Satoru Miyano},
  editor       = {Henry Horng{-}Shing Lu and
                  Bernhard Sch{\"{o}}lkopf and
                  Hongyu Zhao},
  title        = {Computational Drug Target Pathway Discovery: {A} Bayesian Network
                  Approach},
  booktitle    = {Handbook of Statistical Bioinformatics},
  series       = {Springer Handbooks of Computational Statistics},
  pages        = {501--532},
  publisher    = {Springer},
  year         = {2011},
  url          = {https://doi.org/10.1007/978-3-642-16345-6\_24},
  doi          = {10.1007/978-3-642-16345-6\_24},
  timestamp    = {Wed, 14 Nov 2018 10:12:21 +0100},
  biburl       = {https://dblp.org/rec/books/daglib/p/ImotoTAM11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShimamuraIYNM10,
  author       = {Teppei Shimamura and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Masao Nagasaki and
                  Satoru Miyano},
  title        = {Inferring dynamic gene networks under varying conditions for transcriptomic
                  network comparison},
  journal      = {Bioinform.},
  volume       = {26},
  number       = {8},
  pages        = {1064--1072},
  year         = {2010},
  url          = {https://doi.org/10.1093/bioinformatics/btq080},
  doi          = {10.1093/BIOINFORMATICS/BTQ080},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ShimamuraIYNM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NiidaIYNFSM10,
  author       = {Atsushi Niida and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Masao Nagasaki and
                  Andr{\'{e}} Fujita and
                  Teppei Shimamura and
                  Satoru Miyano},
  title        = {Model-free unsupervised gene set screening based on information enrichment
                  in expression profiles},
  journal      = {Bioinform.},
  volume       = {26},
  number       = {24},
  pages        = {3090--3097},
  year         = {2010},
  url          = {https://doi.org/10.1093/bioinformatics/btq592},
  doi          = {10.1093/BIOINFORMATICS/BTQ592},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/NiidaIYNFSM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jmlr/KojimaPIM10,
  author       = {Kaname Kojima and
                  Eric Perrier and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Optimal Search on Clustered Structural Constraint for Learning Bayesian
                  Network Structure},
  journal      = {J. Mach. Learn. Res.},
  volume       = {11},
  pages        = {285--310},
  year         = {2010},
  url          = {https://dl.acm.org/doi/10.5555/1756006.1756015},
  doi          = {10.5555/1756006.1756015},
  timestamp    = {Thu, 02 Jun 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jmlr/KojimaPIM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/HigashigakiKYIIM10,
  author       = {Tomoya Higashigaki and
                  Kaname Kojima and
                  Rui Yamaguchi and
                  Masato Inoue and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Identifying Hidden Confounders in Gene Networks by Bayesian Networks},
  booktitle    = {10th {IEEE} International Conference on Bioinformatics and Bioengineering,
                  {BIBE} 2010, Philadelphia, Pennsylvania, USA, May 31-June 3 2010},
  pages        = {168--173},
  publisher    = {{IEEE} Computer Society},
  year         = {2010},
  url          = {https://doi.org/10.1109/BIBE.2010.35},
  doi          = {10.1109/BIBE.2010.35},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibe/HigashigakiKYIIM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/KawanoSNIYNYPM10,
  author       = {Shuichi Kawano and
                  Teppei Shimamura and
                  Atsushi Niida and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Masao Nagasaki and
                  Ryo Yoshida and
                  Cristin G. Print and
                  Satoru Miyano},
  editor       = {Taesung Park and
                  Stephen Kwok{-}Wing Tsui and
                  Luonan Chen and
                  Michael K. Ng and
                  Limsoon Wong and
                  Xiaohua Hu},
  title        = {Discovering functional gene pathways associated with cancer heterogeneity
                  via sparse supervised learning},
  booktitle    = {2010 {IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2010, Hong Kong, China, December 18-21, 2010, Proceedings},
  pages        = {253--258},
  publisher    = {{IEEE} Computer Society},
  year         = {2010},
  url          = {https://doi.org/10.1109/BIBM.2010.5706572},
  doi          = {10.1109/BIBM.2010.5706572},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/KawanoSNIYNYPM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ShimamuraINNYM10,
  author       = {Teppei Shimamura and
                  Seiya Imoto and
                  Atsushi Niida and
                  Masao Nagasaki and
                  Rui Yamaguchi and
                  Satoru Miyano},
  title        = {Network profiling analysis for generating modulator-dependent gene
                  networks},
  booktitle    = {2010 {IEEE} International Conference on Bioinformatics and Biomedicine
                  Workshops, {BIBMW} 2010, Hong Kong, December 18, 2010},
  pages        = {836},
  publisher    = {{IEEE}},
  year         = {2010},
  url          = {https://doi.org/10.1109/BIBMW.2010.5703933},
  doi          = {10.1109/BIBMW.2010.5703933},
  timestamp    = {Wed, 24 Nov 2021 15:06:06 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/ShimamuraINNYM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icann/SogawaSHWSI10,
  author       = {Yasuhiro Sogawa and
                  Shohei Shimizu and
                  Aapo Hyv{\"{a}}rinen and
                  Takashi Washio and
                  Teppei Shimamura and
                  Seiya Imoto},
  editor       = {Konstantinos I. Diamantaras and
                  Wlodek Duch and
                  Lazaros S. Iliadis},
  title        = {Discovery of Exogenous Variables in Data with More Variables Than
                  Observations},
  booktitle    = {Artificial Neural Networks - {ICANN} 2010 - 20th International Conference,
                  Thessaloniki, Greece, September 15-18, 2010, Proceedings, Part {I}},
  series       = {Lecture Notes in Computer Science},
  volume       = {6352},
  pages        = {67--76},
  publisher    = {Springer},
  year         = {2010},
  url          = {https://doi.org/10.1007/978-3-642-15819-3\_10},
  doi          = {10.1007/978-3-642-15819-3\_10},
  timestamp    = {Tue, 14 May 2019 10:00:49 +0200},
  biburl       = {https://dblp.org/rec/conf/icann/SogawaSHWSI10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/jsai/ImotoKPTM10,
  author       = {Seiya Imoto and
                  Kaname Kojima and
                  Eric Perrier and
                  Yoshinori Tamada and
                  Satoru Miyano},
  editor       = {Takashi Onada and
                  Daisuke Bekki and
                  Eric McCready},
  title        = {Searching Optimal Bayesian Network Structure on Constraint Search
                  Space: Super-Structure Approach},
  booktitle    = {New Frontiers in Artificial Intelligence - JSAI-isAI 2010 Workshops,
                  LENLS, JURISIN, AMBN, ISS, Tokyo, Japan, November 18-19, 2010, Revised
                  Selected Papers},
  series       = {Lecture Notes in Computer Science},
  volume       = {6797},
  pages        = {210--218},
  publisher    = {Springer},
  year         = {2010},
  url          = {https://doi.org/10.1007/978-3-642-25655-4\_19},
  doi          = {10.1007/978-3-642-25655-4\_19},
  timestamp    = {Tue, 14 May 2019 10:00:36 +0200},
  biburl       = {https://dblp.org/rec/conf/jsai/ImotoKPTM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NiidaSIAZA09,
  author       = {Atsushi Niida and
                  Andrew D. Smith and
                  Seiya Imoto and
                  Hiroyuki Aburatani and
                  Michael Q. Zhang and
                  Tetsu Akiyama},
  title        = {Gene set-based module discovery in the breast cancer transcriptome},
  journal      = {{BMC} Bioinform.},
  volume       = {10},
  year         = {2009},
  url          = {https://doi.org/10.1186/1471-2105-10-71},
  doi          = {10.1186/1471-2105-10-71},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/NiidaSIAZA09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ShimamuraIYFNM09,
  author       = {Teppei Shimamura and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Andr{\'{e}} Fujita and
                  Masao Nagasaki and
                  Satoru Miyano},
  title        = {Recursive regularization for inferring gene networks from time-course
                  gene expression profiles},
  journal      = {{BMC} Syst. Biol.},
  volume       = {3},
  pages        = {41},
  year         = {2009},
  url          = {https://doi.org/10.1186/1752-0509-3-41},
  doi          = {10.1186/1752-0509-3-41},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcsb/ShimamuraIYFNM09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcst/YamaguchiIM09,
  author       = {Rui Yamaguchi and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Network-Based Predictions and Simulations by Biological State Space
                  Models: Search for Drug Mode of Action},
  journal      = {J. Comput. Sci. Technol.},
  volume       = {25},
  number       = {1},
  pages        = {131--153},
  year         = {2009},
  url          = {https://doi.org/10.1007/s11390-010-9311-7},
  doi          = {10.1007/S11390-010-9311-7},
  timestamp    = {Sun, 28 May 2017 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcst/YamaguchiIM09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bicob/MiyanoYTNI09,
  author       = {Satoru Miyano and
                  Rui Yamaguchi and
                  Yoshinori Tamada and
                  Masao Nagasaki and
                  Seiya Imoto},
  editor       = {Sanguthevar Rajasekaran},
  title        = {Gene Networks Viewed through Two Models},
  booktitle    = {Bioinformatics and Computational Biology, First International Conference,
                  BICoB 2009, New Orleans, LA, USA, April 8-10, 2009. Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {5462},
  pages        = {54--66},
  publisher    = {Springer},
  year         = {2009},
  url          = {https://doi.org/10.1007/978-3-642-00727-9\_8},
  doi          = {10.1007/978-3-642-00727-9\_8},
  timestamp    = {Sun, 25 Oct 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/bicob/MiyanoYTNI09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/TamadaAINDNTYDSHPCTKM09,
  author       = {Yoshinori Tamada and
                  Hiromitsu Araki and
                  Seiya Imoto and
                  Masao Nagasaki and
                  Atsushi Doi and
                  Yukiko Nakanishi and
                  Yuki Tomiyasu and
                  Kaori Yasuda and
                  Ben Dunmore and
                  Deborah Sanders and
                  Sally Humphreys and
                  Cristin G. Print and
                  Stephen D. Charnock{-}Jones and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Tiffany Murray and
                  Teri E. Klein},
  title        = {Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response
                  Transcriptome Networks},
  booktitle    = {Biocomputing 2009: Proceedings of the Pacific Symposium, Kohala Coast,
                  Hawaii, USA, 5-9 January 2009},
  pages        = {251--263},
  year         = {2009},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb09/tamada.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/TamadaAINDNTYDSHPCTKM09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HiroseYIYHCPM08,
  author       = {Osamu Hirose and
                  Ryo Yoshida and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Tomoyuki Higuchi and
                  Stephen D. Charnock{-}Jones and
                  Cristin G. Print and
                  Satoru Miyano},
  title        = {Statistical inference of transcriptional module-based gene networks
                  from time course gene expression profiles by using state space models},
  journal      = {Bioinform.},
  volume       = {24},
  number       = {7},
  pages        = {932--942},
  year         = {2008},
  url          = {https://doi.org/10.1093/bioinformatics/btm639},
  doi          = {10.1093/BIOINFORMATICS/BTM639},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HiroseYIYHCPM08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YoshidaNYIMH08,
  author       = {Ryo Yoshida and
                  Masao Nagasaki and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Satoru Miyano and
                  Tomoyuki Higuchi},
  title        = {Bayesian learning of biological pathways on genomic data assimilation},
  journal      = {Bioinform.},
  volume       = {24},
  number       = {22},
  pages        = {2592--2601},
  year         = {2008},
  url          = {https://doi.org/10.1093/bioinformatics/btn483},
  doi          = {10.1093/BIOINFORMATICS/BTN483},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/YoshidaNYIMH08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NiidaSITAZA08,
  author       = {Atsushi Niida and
                  Andrew D. Smith and
                  Seiya Imoto and
                  Shuichi Tsutsumi and
                  Hiroyuki Aburatani and
                  Michael Q. Zhang and
                  Tetsu Akiyama},
  title        = {Integrative bioinformatics analysis of transcriptional regulatory
                  programs in breast cancer cells},
  journal      = {{BMC} Bioinform.},
  volume       = {9},
  year         = {2008},
  url          = {https://doi.org/10.1186/1471-2105-9-404},
  doi          = {10.1186/1471-2105-9-404},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/NiidaSITAZA08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NumataYNSIM08,
  author       = {Kazuyuki Numata and
                  Ryo Yoshida and
                  Masao Nagasaki and
                  Ayumu Saito and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {ExonMiner: Web service for analysis of GeneChip Exon array data},
  journal      = {{BMC} Bioinform.},
  volume       = {9},
  year         = {2008},
  url          = {https://doi.org/10.1186/1471-2105-9-494},
  doi          = {10.1186/1471-2105-9-494},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/NumataYNSIM08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/asiams/HiroseYYIHM08,
  author       = {Osamu Hirose and
                  Ryo Yoshida and
                  Rui Yamaguchi and
                  Seiya Imoto and
                  Tomoyuki Higuchi and
                  Satoru Miyano},
  title        = {Analyzing Time Course Gene Expression Data with Biological and Technical
                  Replicates to Estimate Gene Networks by State Space Models},
  booktitle    = {Second Asia International Conference on Modelling and Simulation,
                  {AMS} 2008, Kuala Lumpur, Malaysia, May 13-15, 2008},
  pages        = {940--946},
  publisher    = {{IEEE} Computer Society},
  year         = {2008},
  url          = {https://doi.org/10.1109/AMS.2008.150},
  doi          = {10.1109/AMS.2008.150},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/asiams/HiroseYYIHM08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/NumataIM08,
  author       = {Kazuyuki Numata and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Xue{-}wen Chen and
                  Xiaohua Hu and
                  Sun Kim},
  title        = {Partial Order-Based Bayesian Network Learning Algorithm for Estimating
                  Gene Networks},
  booktitle    = {2008 {IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2008, Philadephia, Pennsylvania, USA, November 3-5, 2008},
  pages        = {357--360},
  publisher    = {{IEEE} Computer Society},
  year         = {2008},
  url          = {https://doi.org/10.1109/BIBM.2008.85},
  doi          = {10.1109/BIBM.2008.85},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/NumataIM08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/spm/YamaguchiYIHM07,
  author       = {Rui Yamaguchi and
                  Ryo Yoshida and
                  Seiya Imoto and
                  Tomoyuki Higuchi and
                  Satoru Miyano},
  title        = {Finding module-based gene networks with state-space models - Mining
                  high-dimensional and short time-course gene expression data},
  journal      = {{IEEE} Signal Process. Mag.},
  volume       = {24},
  number       = {1},
  pages        = {37--46},
  year         = {2007},
  url          = {https://doi.org/10.1109/MSP.2007.273053},
  doi          = {10.1109/MSP.2007.273053},
  timestamp    = {Thu, 03 Dec 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/spm/YamaguchiYIHM07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/YoshidaNINDUM07,
  author       = {Ryo Yoshida and
                  Kazuyuki Numata and
                  Seiya Imoto and
                  Masao Nagasaki and
                  Atsushi Doi and
                  Kazuko Ueno and
                  Satoru Miyano},
  title        = {Computational Genome-Wide Discovery of Aberrant Splice Variations
                  with Exon Expression Profiles},
  booktitle    = {Proceedings of the 7th {IEEE} International Conference on Bioinformatics
                  and Bioengineering, {BIBE} 2007, October 14-17, 2007, Harvard Medical
                  School, Boston, MA, {USA}},
  pages        = {715--722},
  publisher    = {{IEEE} Computer Society},
  year         = {2007},
  url          = {https://doi.org/10.1109/BIBE.2007.4375639},
  doi          = {10.1109/BIBE.2007.4375639},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibe/YoshidaNINDUM07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/NumataIM07,
  author       = {Kazuyuki Numata and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {A Structure Learning Algorithm for Inference of Gene Networks from
                  Microarray Gene Expression Data Using Bayesian Networks},
  booktitle    = {Proceedings of the 7th {IEEE} International Conference on Bioinformatics
                  and Bioengineering, {BIBE} 2007, October 14-17, 2007, Harvard Medical
                  School, Boston, MA, {USA}},
  pages        = {1280--1284},
  publisher    = {{IEEE} Computer Society},
  year         = {2007},
  url          = {https://doi.org/10.1109/BIBE.2007.4375731},
  doi          = {10.1109/BIBE.2007.4375731},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibe/NumataIM07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/GuptaYIYM07,
  author       = {Pramod K. Gupta and
                  Ryo Yoshida and
                  Seiya Imoto and
                  Rui Yamaguchi and
                  Satoru Miyano},
  editor       = {Ion I. Mandoiu and
                  Alexander Zelikovsky},
  title        = {Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression
                  Data},
  booktitle    = {Bioinformatics Research and Applications, Third International Symposium,
                  {ISBRA} 2007, Atlanta, GA, USA, May 7-10, 2007, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {4463},
  pages        = {146--157},
  publisher    = {Springer},
  year         = {2007},
  url          = {https://doi.org/10.1007/978-3-540-72031-7\_14},
  doi          = {10.1007/978-3-540-72031-7\_14},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/isbra/GuptaYIYM07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mlg/TermierTNIWH07,
  author       = {Alexandre Termier and
                  Yoshinori Tamada and
                  Kazuyuki Numata and
                  Seiya Imoto and
                  Takashi Washio and
                  Tomoyuki Higuchi},
  editor       = {Paolo Frasconi and
                  Kristian Kersting and
                  Koji Tsuda},
  title        = {DIGDAG, a First Algorithm to Mine Closed Frequent Embedded Sub-DAGs},
  booktitle    = {Mining and Learning with Graphs, {MLG} 2007, Firence, Italy, August
                  1-3, 2007, Proceedings},
  year         = {2007},
  url          = {http://mlg07.dsi.unifi.it/pdf/01\_Termier.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/mlg/TermierTNIWH07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YoshidaHIM06,
  author       = {Ryo Yoshida and
                  Tomoyuki Higuchi and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {ArrayCluster: an analytic tool for clustering, data visualization
                  and module finder on gene expression profiles},
  journal      = {Bioinform.},
  volume       = {22},
  number       = {12},
  pages        = {1538--1539},
  year         = {2006},
  url          = {https://doi.org/10.1093/bioinformatics/btl129},
  doi          = {10.1093/BIOINFORMATICS/BTL129},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/YoshidaHIM06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijait/NakamichiIM06,
  author       = {Reiichiro Nakamichi and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Statistical Model Selection Method to Analyze Combinatorial Effects
                  of Snps and Environmental Factors for Binary Disease},
  journal      = {Int. J. Artif. Intell. Tools},
  volume       = {15},
  number       = {5},
  pages        = {711--724},
  year         = {2006},
  url          = {https://doi.org/10.1142/S0218213006002898},
  doi          = {10.1142/S0218213006002898},
  timestamp    = {Tue, 12 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ijait/NakamichiIM06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/ImotoTAYPCSSTKM06,
  author       = {Seiya Imoto and
                  Yoshinori Tamada and
                  Hiromitsu Araki and
                  Kaori Yasuda and
                  Cristin G. Print and
                  Stephen D. Charnock{-}Jones and
                  Deborah Sanders and
                  Christopher J. Savoie and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  editor       = {Russ B. Altman and
                  Tiffany Murray and
                  Teri E. Klein and
                  A. Keith Dunker and
                  Lawrence Hunter},
  title        = {Computational Strategy for Discovering Druggable Gene Networks from
                  Genome-Wide {RNA} Expression Profiles},
  booktitle    = {Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii,
                  USA, 3-7 January 2006},
  pages        = {559--571},
  publisher    = {World Scientific},
  year         = {2006},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb06/imoto.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/ImotoTAYPCSSTKM06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/TamadaBIKKM05,
  author       = {Yoshinori Tamada and
                  Hideo Bannai and
                  Seiya Imoto and
                  Toshiaki Katayama and
                  Minoru Kanehisa and
                  Satoru Miyano},
  title        = {Utilizing Evolutionary Information and Gene Expression Data for Estimating
                  Gene Networks with Bayesian Network Models},
  journal      = {J. Bioinform. Comput. Biol.},
  volume       = {3},
  number       = {6},
  pages        = {1295--1314},
  year         = {2005},
  url          = {https://doi.org/10.1142/S0219720005001569},
  doi          = {10.1142/S0219720005001569},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jbcb/TamadaBIKKM05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/YoshidaIH05,
  author       = {Ryo Yoshida and
                  Seiya Imoto and
                  Tomoyuki Higuchi},
  title        = {Estimating Time-Dependent Gene Networks from Time Series Microarray
                  Data by Dynamic Linear Models with Markov Switching},
  booktitle    = {Fourth International {IEEE} Computer Society Computational Systems
                  Bioinformatics Conference, {CSB} 2005, Stanford, CA, USA, August 8-11,
                  2005},
  pages        = {289--298},
  publisher    = {{IEEE} Computer Society},
  year         = {2005},
  url          = {https://doi.org/10.1109/CSB.2005.32},
  doi          = {10.1109/CSB.2005.32},
  timestamp    = {Thu, 23 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/csb/YoshidaIH05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/NariaiTIM05,
  author       = {Naoki Nariai and
                  Yoshinori Tamada and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Estimating gene regulatory networks and protein-protein interactions
                  of \emph{Saccharomyces cerevisiae} from multiple genome-wide data},
  booktitle    = {ECCB/JBI'05 Proceedings, Fourth European Conference on Computational
                  Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas
                  de BioInform{\'{a}}tica), Palacio de Congresos, Madrid, Spain,
                  September 28 - October 1, 2005},
  pages        = {212},
  year         = {2005},
  url          = {https://doi.org/10.1093/bioinformatics/bti1133},
  doi          = {10.1093/BIOINFORMATICS/BTI1133},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/eccb/NariaiTIM05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccsa/HiroseNTBIM05,
  author       = {Osamu Hirose and
                  Naoki Nariai and
                  Yoshinori Tamada and
                  Hideo Bannai and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Osvaldo Gervasi and
                  Marina L. Gavrilova and
                  Vipin Kumar and
                  Antonio Lagan{\`{a}} and
                  Heow Pueh Lee and
                  Youngsong Mun and
                  David Taniar and
                  Chih Jeng Kenneth Tan},
  title        = {Estimating Gene Networks from Expression Data and Binding Location
                  Data via Boolean Networks},
  booktitle    = {Computational Science and Its Applications - {ICCSA} 2005, International
                  Conference, Singapore, May 9-12, 2005, Proceedings, Part {III}},
  series       = {Lecture Notes in Computer Science},
  volume       = {3482},
  pages        = {349--356},
  publisher    = {Springer},
  year         = {2005},
  url          = {https://doi.org/10.1007/11424857\_38},
  doi          = {10.1007/11424857\_38},
  timestamp    = {Thu, 28 Apr 2022 16:17:38 +0200},
  biburl       = {https://dblp.org/rec/conf/iccsa/HiroseNTBIM05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccsa/YoshidaIH05,
  author       = {Ryo Yoshida and
                  Seiya Imoto and
                  Tomoyuki Higuchi},
  editor       = {Osvaldo Gervasi and
                  Marina L. Gavrilova and
                  Vipin Kumar and
                  Antonio Lagan{\`{a}} and
                  Heow Pueh Lee and
                  Youngsong Mun and
                  David Taniar and
                  Chih Jeng Kenneth Tan},
  title        = {A Penalized Likelihood Estimation on Transcriptional Module-Based
                  Clustering},
  booktitle    = {Computational Science and Its Applications - {ICCSA} 2005, International
                  Conference, Singapore, May 9-12, 2005, Proceedings, Part {III}},
  series       = {Lecture Notes in Computer Science},
  volume       = {3482},
  pages        = {389--401},
  publisher    = {Springer},
  year         = {2005},
  url          = {https://doi.org/10.1007/11424857\_42},
  doi          = {10.1007/11424857\_42},
  timestamp    = {Wed, 24 May 2017 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/iccsa/YoshidaIH05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/ImotoHGTKM04,
  author       = {Seiya Imoto and
                  Tomoyuki Higuchi and
                  Takao Goto and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  title        = {Combining Microarrays and Biological Knowledge for Estimating Gene
                  Networks via Bayesian Networks},
  journal      = {J. Bioinform. Comput. Biol.},
  volume       = {2},
  number       = {1},
  pages        = {77--98},
  year         = {2004},
  url          = {https://doi.org/10.1142/S021972000400048X},
  doi          = {10.1142/S021972000400048X},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jbcb/ImotoHGTKM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/NakamichiIM04,
  author       = {Reiichiro Nakamichi and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Case-Control Study of Binary Disease Trait Considering Interactions
                  between SNPs and Environmental Effects using Logistic Regression},
  booktitle    = {4th {IEEE} International Symposium on BioInformatics and BioEngineering
                  {(BIBE} 2004), 19-21 March 2004, Taichung, Taiwan},
  pages        = {73--78},
  publisher    = {{IEEE} Computer Society},
  year         = {2004},
  url          = {https://doi.org/10.1109/BIBE.2004.1317327},
  doi          = {10.1109/BIBE.2004.1317327},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibe/NakamichiIM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/ImotoHKJM04,
  author       = {Seiya Imoto and
                  Tomoyuki Higuchi and
                  SunYong Kim and
                  Euna Jeong and
                  Satoru Miyano},
  editor       = {Vincent Danos and
                  Vincent Sch{\"{a}}chter},
  title        = {Residual Bootstrapping and Median Filtering for Robust Estimation
                  of Gene Networks from Microarray Data},
  booktitle    = {Computational Methods in Systems Biology, International Conference,
                  {CMSB} 2004, Paris, France, May 26-28, 2004, Revised Selected Papers},
  series       = {Lecture Notes in Computer Science},
  volume       = {3082},
  pages        = {149--160},
  publisher    = {Springer},
  year         = {2004},
  url          = {https://doi.org/10.1007/978-3-540-25974-9\_12},
  doi          = {10.1007/978-3-540-25974-9\_12},
  timestamp    = {Tue, 14 May 2019 10:00:49 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/ImotoHKJM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/YoshidaHI04,
  author       = {Ryo Yoshida and
                  Tomoyuki Higuchi and
                  Seiya Imoto},
  title        = {A Mixed Factors Model for Dimension Reduction and Extraction of a
                  Group Structure in Gene Expression Data},
  booktitle    = {3rd International {IEEE} Computer Society Computational Systems Bioinformatics
                  Conference, {CSB} 2004, Stanford, CA, USA, August 16-19, 2004},
  pages        = {161--172},
  publisher    = {{IEEE} Computer Society},
  year         = {2004},
  url          = {https://doi.org/10.1109/CSB.2004.1332429},
  doi          = {10.1109/CSB.2004.1332429},
  timestamp    = {Thu, 23 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/csb/YoshidaHI04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/HoonMIKONM04,
  author       = {Michiel J. L. de Hoon and
                  Yuko Makita and
                  Seiya Imoto and
                  Kazuo Kobayashi and
                  Naotake Ogasawara and
                  Kenta Nakai and
                  Satoru Miyano},
  title        = {Predicting gene regulation by sigma factors in Bacillus subtilis from
                  genome-wide data},
  booktitle    = {Proceedings Twelfth International Conference on Intelligent Systems
                  for Molecular Biology/Third European Conference on Computational Biology
                  2004, Glasgow, UK, July 31-August 4, 2004},
  pages        = {101--108},
  year         = {2004},
  url          = {https://doi.org/10.1093/bioinformatics/bth927},
  doi          = {10.1093/BIOINFORMATICS/BTH927},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/ismb/HoonMIKONM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kelsi/AndoIM04,
  author       = {Tomohiro Ando and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Jes{\'{u}}s A. L{\'{o}}pez and
                  Emilio Benfenati and
                  Werner Dubitzky},
  title        = {Functional Data Analysis of the Dynamics of Gene Regulatory Networks},
  booktitle    = {Knowledge Exploration in Life Science Informatics, International Symposium,KELSI
                  2004, Milan, Italy, November 25-26, 2004, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {3303},
  pages        = {69--83},
  publisher    = {Springer},
  year         = {2004},
  url          = {https://doi.org/10.1007/978-3-540-30478-4\_7},
  doi          = {10.1007/978-3-540-30478-4\_7},
  timestamp    = {Tue, 14 May 2019 10:00:43 +0200},
  biburl       = {https://dblp.org/rec/conf/kelsi/AndoIM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/HoonIKOM04,
  author       = {Michiel J. L. de Hoon and
                  Seiya Imoto and
                  Kazuo Kobayashi and
                  Naotake Ogasawara and
                  Satoru Miyano},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Tiffany A. Jung and
                  Teri E. Klein},
  title        = {Predicting the Operon Structure of Bacillus subtilis Using Operon
                  Length, Intergene Distance, and Gene Expression Information},
  booktitle    = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
                  6-10 January 2004},
  pages        = {276--287},
  publisher    = {World Scientific},
  year         = {2004},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb04/dehoon.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/HoonIKOM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/NariaiKIM04,
  author       = {Naoki Nariai and
                  SunYong Kim and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Tiffany A. Jung and
                  Teri E. Klein},
  title        = {Using Protein-Protein Interactions for Refining Gene Networks Estimated
                  from Microarray Data by Bayesian Networks},
  booktitle    = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
                  6-10 January 2004},
  pages        = {336--347},
  publisher    = {World Scientific},
  year         = {2004},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb04/nariai.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/NariaiKIM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/OttIM04,
  author       = {Sascha Ott and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Tiffany A. Jung and
                  Teri E. Klein},
  title        = {Finding Optimal Models for Small Gene Networks},
  booktitle    = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
                  6-10 January 2004},
  pages        = {557--567},
  publisher    = {World Scientific},
  year         = {2004},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb04/ott.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/OttIM04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KimIM03,
  author       = {SunYong Kim and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Inferring gene networks from time series microarray data using dynamic
                  Bayesian networks},
  journal      = {Briefings Bioinform.},
  volume       = {4},
  number       = {3},
  pages        = {228},
  year         = {2003},
  url          = {https://doi.org/10.1093/bib/4.3.228},
  doi          = {10.1093/BIB/4.3.228},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/KimIM03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/ImotoKGATKM03,
  author       = {Seiya Imoto and
                  SunYong Kim and
                  Takao Goto and
                  Sachiyo Aburatani and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  title        = {Bayesian Network and Nonparametric Heteroscedastic Regression for
                  Nonlinear Modeling of Genetic Network},
  journal      = {J. Bioinform. Comput. Biol.},
  volume       = {1},
  number       = {2},
  pages        = {231--252},
  year         = {2003},
  url          = {https://doi.org/10.1142/S0219720003000071},
  doi          = {10.1142/S0219720003000071},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jbcb/ImotoKGATKM03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/ImotoSAKTKM03,
  author       = {Seiya Imoto and
                  Christopher J. Savoie and
                  Sachiyo Aburatani and
                  SunYong Kim and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  title        = {Use of Gene Networks for Identifying and Validating Drug Targets},
  journal      = {J. Bioinform. Comput. Biol.},
  volume       = {1},
  number       = {3},
  pages        = {459--474},
  year         = {2003},
  url          = {https://doi.org/10.1142/S0219720003000290},
  doi          = {10.1142/S0219720003000290},
  timestamp    = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jbcb/ImotoSAKTKM03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/KimIM03,
  author       = {SunYong Kim and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Corrado Priami},
  title        = {Dynamic Bayesian Network and Nonparametric Regression for Nonlinear
                  Modeling of Gene Networks from Time Series Gene Expression Data},
  booktitle    = {Computational Methods in Systems Biology, First International Workshop,
                  {CMSB} 2003, Roverto, Italy, February 24-26, 2003, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {2602},
  pages        = {104--113},
  publisher    = {Springer},
  year         = {2003},
  url          = {https://doi.org/10.1007/3-540-36481-1\_9},
  doi          = {10.1007/3-540-36481-1\_9},
  timestamp    = {Tue, 14 May 2019 10:00:49 +0200},
  biburl       = {https://dblp.org/rec/conf/cmsb/KimIM03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/ImotoHGTKM03,
  author       = {Seiya Imoto and
                  Tomoyuki Higuchi and
                  Takao Goto and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  title        = {Combining Microarrays and Biological Knowledge for Estimating Gene
                  Networks via Bayesian Networks},
  booktitle    = {2nd {IEEE} Computer Society Bioinformatics Conference, {CSB} 2003,
                  Stanford, CA, USA, August 11-14, 2003},
  pages        = {104--113},
  publisher    = {{IEEE} Computer Society},
  year         = {2003},
  url          = {https://doi.org/10.1109/CSB.2003.1227309},
  doi          = {10.1109/CSB.2003.1227309},
  timestamp    = {Thu, 23 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/csb/ImotoHGTKM03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/TamadaKBITKM03,
  author       = {Yoshinori Tamada and
                  SunYong Kim and
                  Hideo Bannai and
                  Seiya Imoto and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  title        = {Estimating gene networks from gene expression data by combining Bayesian
                  network model with promoter element detection},
  booktitle    = {Proceedings of the European Conference on Computational Biology {(ECCB}
                  2003), September 27-30, 2003, Paris, France},
  pages        = {227--236},
  year         = {2003},
  timestamp    = {Thu, 02 Feb 2017 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/eccb/TamadaKBITKM03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/HoonIKOM03,
  author       = {Michiel J. L. de Hoon and
                  Seiya Imoto and
                  Kazuo Kobayashi and
                  Naotake Ogasawara and
                  Satoru Miyano},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Teri E. Klein},
  title        = {Inferring Gene Regulatory Networks from Time-Ordered Gene Expression
                  Data of Bacillus Subtilis Using Differential Equations},
  booktitle    = {Proceedings of the 8th Pacific Symposium on Biocomputing, {PSB} 2003,
                  Lihue, Hawaii, USA, January 3-7, 2003},
  pages        = {17--28},
  year         = {2003},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb03/dehoon.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/HoonIKOM03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoonIM02,
  author       = {Michiel J. L. de Hoon and
                  Seiya Imoto and
                  Satoru Miyano},
  title        = {Statistical analysis of a small set of time-ordered gene expression
                  data using linear splines},
  journal      = {Bioinform.},
  volume       = {18},
  number       = {11},
  pages        = {1477--1485},
  year         = {2002},
  url          = {https://doi.org/10.1093/bioinformatics/18.11.1477},
  doi          = {10.1093/BIOINFORMATICS/18.11.1477},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HoonIM02.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/ImotoKGATKM02,
  author       = {Seiya Imoto and
                  SunYong Kim and
                  Takao Goto and
                  Sachiyo Aburatani and
                  Kousuke Tashiro and
                  Satoru Kuhara and
                  Satoru Miyano},
  title        = {Bayesian Network and Nonparametric Heteroscedastic Regression for
                  Nonlinear Modeling of Genetic Network},
  booktitle    = {1st {IEEE} Computer Society Bioinformatics Conference, {CSB} 2002,
                  Stanford, CA, USA, August 14-16, 2002},
  pages        = {219--227},
  publisher    = {{IEEE} Computer Society},
  year         = {2002},
  url          = {https://doi.org/10.1109/CSB.2002.1039344},
  doi          = {10.1109/CSB.2002.1039344},
  timestamp    = {Thu, 23 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/csb/ImotoKGATKM02.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dis/HoonIM02,
  author       = {Michiel J. L. de Hoon and
                  Seiya Imoto and
                  Satoru Miyano},
  editor       = {Steffen Lange and
                  Ken Satoh and
                  Carl H. Smith},
  title        = {Inferring Gene Regulatory Networks from Time-Ordered Gene Expression
                  Data Using Differential Equations},
  booktitle    = {Discovery Science, 5th International Conference, {DS} 2002, L{\"{u}}beck,
                  Germany, November 24-26, 2002, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {2534},
  pages        = {267--274},
  publisher    = {Springer},
  year         = {2002},
  url          = {https://doi.org/10.1007/3-540-36182-0\_24},
  doi          = {10.1007/3-540-36182-0\_24},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/dis/HoonIM02.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/ImotoGM02,
  author       = {Seiya Imoto and
                  Takao Goto and
                  Satoru Miyano},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Teri E. Klein},
  title        = {Estimation of Genetic Networks and Functional Structures Between Genes
                  by Using Bayesian Networks and Nonparametric Regression},
  booktitle    = {Proceedings of the 7th Pacific Symposium on Biocomputing, {PSB} 2002,
                  Lihue, Hawaii, USA, January 3-7, 2002},
  pages        = {175--186},
  year         = {2002},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb02/imoto.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/ImotoGM02.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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