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Japan

Activities

Works (19)

Validation of machine learning-assisted screening of PKC ligands: PKC binding affinity and activation

Bioscience, Biotechnology, and Biochemistry
2025-01-25 | Journal article
Contributors: Jumpei Maki; Asami Oshimura; Yudai Shiotani; Maki Yamanaka; Sogen Okuda; Ryo C Yanagita; Shigeru Kitani; Yasuhiro Igarashi; Yutaka Saito; Yasubumi Sakakibara et al.
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Leveraging Tree-Transformer VAE with fragment tokenization for high-performance large chemical generative model

2024-11-08 | Preprint
Contributors: Tensei Inukai; Aoi Yamato; Manato Akiyama; Yasubumi Sakakibara
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Transcriptomic dynamics of petal development in the one-day flower species, Japanese morning glory (Ipomoea nil)

2024-08-30 | Preprint
Contributors: Soya Nakagawa; Atsushi Hoshino; Kazuyo Ito; Hiroyo Nishide; Katsuhiro Shiratake; Atsushi J. Nagano; Yasubumi Sakakibara
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A Tree-Transformer based VAE with fragment tokenization for large chemical models

2024-06-24 | Preprint
Contributors: Tensei Inukai; Aoi Yamato; Manato Akiyama; Yasubumi Sakakibara
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A Tree-Transformer based VAE with fragment tokenization for large chemical models

2024-05-20 | Preprint
Contributors: Tensei Inukai; Aoi Yamato; Manato Akiyama; Yasubumi Sakakibara
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Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine

mSystems
2024-05-16 | Journal article
Contributors: Mika Uehara; Takashi Inoue; Sumitaka Hase; Erika Sasaki; Atsushi Toyoda; Yasubumi Sakakibara; Mani Arumugam
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Deep learning of multimodal networks with topological regularization for drug repositioning

2024-01-10 | Preprint
Contributors: Yuto Ohnuki; Manato Akiyama; Yasubumi Sakakibara
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Quantum Algorithm for Position Weight Matrix Matching

IEEE Transactions on Quantum Engineering
2023 | Journal article
Contributors: Koichi Miyamoto; Naoki Yamamoto; Yasubumi Sakakibara
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Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine

2023-08-11 | Preprint
Contributors: Mika Uehara; Takashi Inoue; Sumitaka Hase; Erika Sasaki; Atsushi Toyoda; Yasubumi Sakakibara
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Automatic Detection and Measurement of Renal Cysts in Ultrasound Images: A Deep Learning Approach

Healthcare
2023-02-07 | Journal article
Contributors: Yurie Kanauchi; Masahiro Hashimoto; Naoki Toda; Saori Okamoto; Hasnine Haque; Masahiro Jinzaki; Yasubumi Sakakibara
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Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots

Genes
2022-11-18 | Journal article
Contributors: Manato Akiyama; Yasubumi Sakakibara; Kengo Sato
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Preferred source (of 2)‎

A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains

Genes
2022-07-26 | Journal article
Contributors: Afiahayati; Stefanus Bernard; Gunadi; Hendra Wibawa; Mohamad Saifudin Hakim; Marcellus; Arli Aditya Parikesit; Chandra Kusuma Dewa; Yasubumi Sakakibara
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Preferred source (of 2)‎

Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning

NAR Genomics and Bioinformatics
2022-01-13 | Journal article
Contributors: Manato Akiyama; Yasubumi Sakakibara
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Deep learning integration of molecular and interactome data for protein–compound interaction prediction

Journal of Cheminformatics
2021-12 | Journal article
Contributors: Narumi Watanabe; Yuuto Ohnuki; Yasubumi Sakakibara
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Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine

2021-10-13 | Preprint
Contributors: Mika Uehara; Takashi Inoue; Minori Kominato; Sumitaka Hase; Erika Sasaki; Atsushi Toyoda; Yasubumi Sakakibara
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Informative RNA-base embedding for functional RNA structural alignment and clustering by deep representation learning

2021-08-24 | Preprint
Contributors: Manato Akiyama; Yasubumi Sakakibara
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Genomic style: yet another deep-learning approach to characterize bacterial genome sequences

2021-08-10 | Preprint
Contributors: Yuka Yoshimura; Akifumi Hamada; Yohann Augey; Manato Akiyama; Yasubumi Sakakibara
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Deep learning integration of molecular and interactome data for protein-compound interaction prediction

2021-02-01 | Preprint
Contributors: Narumi Watanabe; Yuuto Ohnuki; Yasubumi Sakakibara
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DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions

PLOS ONE
2017-11-21 | Journal article
Contributors: Yoshimasa Aoto; Christian Schönbach; Tsuyoshi Hachiya; Kazuhiro Okumura; Sumitaka Hase; Kengo Sato; Yuichi Wakabayashi; Yasubumi Sakakibara
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Peer review (2 reviews for 1 publication/grant)

Review activity for BMC bioinformatics (2)