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ArticlesPeer ReviewedFull Text
Protein design via deep learning
Author / Creator:Ding, Wenze ; Nakai, Kenta ; Gong, Haipeng
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2022-05, Vol.23 (3)
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ArticlesPeer ReviewedFull Text
PrognoScan: a new database for meta-analysis of the prognostic value of genes
Author / Creator:Mizuno, Hideaki ; Kitada, Kunio ; Nakai, Kenta ; Sarai, Akinori
Publisher:England: BioMed Central Ltd
Journal title:BMC medical genomics, 2009-04, Vol.2 (1), p.18-18, Article 18
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iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations
Author / Creator:Jin, Junru ; Yu, Yingying ; Wang, Ruheng ; Zeng, Xin ; Pang, Chao ; Jiang, Yi ; Li, Zhongshen ; Dai, Yutong ; Su, Ran ; Zou, Quan ; Nakai, Kenta ; Wei, Leyi
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2022-10, Vol.23 (1), p.219-219, Article 219
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ArticlesPeer ReviewedFull Text
Stable feature selection based on the ensemble L 1 -norm support vector machine for biomarker discovery
Author / Creator:Moon, Myungjin ; Nakai, Kenta
Publisher:England
Journal title:BMC genomics, 2016-12, Vol.17 (S13), p.1026-1026, Article 1026
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A hypothetical trivalent epigenetic code that affects the nature of human ESCs
Author / Creator:Ishikawa, Yasuhisa ; Nakai, Kenta
Publisher:San Francisco: Public Library of Science
Journal title:PloS one, 2020-09, Vol.15 (9), p.e0238742-e0238742
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Extreme value theory as a framework for understanding mutation frequency distribution in cancer genomes
Author / Creator:Tokutomi, Natsuki ; Nakai, Kenta ; Sugano, Sumio
Publisher:United States: Public Library of Science
Journal title:PloS one, 2021-08, Vol.16 (8), p.e0243595
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ArticlesPeer ReviewedFull Text
Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses
Author / Creator:Fujita, Naoya ; Mizuarai, Shinji ; Murakami, Katsuhiko ; Nakai, Kenta
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2018-06, Vol.8 (1), p.9743-10, Article 9743
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The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection
Author / Creator:Satoh, Takashi ; Takeuchi, Osamu ; Vandenbon, Alexis ; Yasuda, Koubun ; Tanaka, Yoshiaki ; Kumagai, Yutaro ; Miyake, Tohru ; Matsushita, Kazufumi ; Okazaki, Toshihiko ; Saitoh, Tatsuya ; Honma, Kiri ; Matsuyama, Toshifumi ; Yui, Katsuyuki ; Tsujimura, Tohru ; Standley, Daron M ; Nakanishi, Kenji ; Nakai, Kenta ; Akira, Shizuo
Publisher:New York: Nature Publishing Group US
Journal title:Nature immunology, 2010-10, Vol.11 (10), p.936-944
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A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations
Author / Creator:Jia, Hao ; Park, Sung-Joon ; Nakai, Kenta
Publisher:London: BioMed Central Ltd
Journal title:BMC bioinformatics, 2021-06, Vol.22 (S6), p.1-128, Article 128
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A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment
Author / Creator:Kinoshita-Daitoku, Ryo ; Kiga, Kotaro ; Miyakoshi, Masatoshi ; Otsubo, Ryota ; Ogura, Yoshitoshi ; Sanada, Takahito ; Bo, Zhu ; Phuoc, Tuan Vo ; Okano, Tokuju ; Iida, Tamako ; Yokomori, Rui ; Kuroda, Eisuke ; Hirukawa, Sayaka ; Tanaka, Mototsugu ; Sood, Arpana ; Subsomwong, Phawinee ; Ashida, Hiroshi ; Binh, Tran Thanh ; Nguyen, Lam Tung ; Van, Khien Vu ; Ho, Dang Quy Dung ; Nakai, Kenta ; Suzuki, Toshihiko ; Yamaoka, Yoshio ; Hayashi, Tetsuya ; Mimuro, Hitomi
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-04, Vol.12 (1), p.2085-12, Article 2085
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Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s
Author / Creator:Lee, Jong-Hun ; Park, Sung-Joon ; Nakai, Kenta
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2017-09, Vol.7 (1), p.11295-11, Article 11295
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Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks
Author / Creator:Zeng, Xin ; Liu, Shu ; Liu, Bowen ; Zhang, Weihang ; Xu, Wanzhe ; Toriumi, Fujio ; Nakai, Kenta
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2025-05, Vol.26 (1), p.134-19, Article 134
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STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration
Author / Creator:Yang, Yitao ; Cui, Yang ; Zeng, Xin ; Zhang, Yubo ; Loza, Martin ; Park, Sung-Joon ; Nakai, Kenta
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-01, Vol.16 (1), p.1067-15, Article 1067
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Comprehensive comparison of gene expression diversity among a variety of human stem cells
Author / Creator:Yamatani, Yukiyo ; Nakai, Kenta
Publisher:Oxford: Oxford University Press
Journal title:NAR genomics and bioinformatics, 2022-12, Vol.4 (4)
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Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer
Author / Creator:Kubota, Yuji ; Fujioka, Yuko ; Patil, Ashwini ; Takagi, Yusuke ; Matsubara, Daisuke ; Iijima, Masatomi ; Momose, Isao ; Naka, Ryosuke ; Nakai, Kenta ; Noda, Nobuo N. ; Takekawa, Mutsuhiro
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-07, Vol.13 (1), p.4063-4063, Article 4063
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HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data
Author / Creator:Zhang, Weihang ; Cui, Yang ; Liu, Bowen ; Loza, Martin ; Park, Sung-Joon ; Nakai, Kenta
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2024-03, Vol.25 (3)
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A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response
Author / Creator:Park, Sung-Joon ; Nakai, Kenta
Publisher:England: Oxford University Press
Journal title:NAR genomics and bioinformatics, 2024-06, Vol.6 (2), p.lqae050-lqae050
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Grand challenges in bioinformatics education and training
Author / Creator:Işık, Esra Büşra ; Brazas, Michelle D. ; Schwartz, Russell ; Gaeta, Bruno ; Palagi, Patricia M. ; van Gelder, Celia W. G. ; Suravajhala, Prashanth ; Singh, Harpreet ; Morgan, Sarah L. ; Zahroh, Hilyatuz ; Ling, Maurice ; Satagopam, Venkata P. ; McGrath, Annette ; Nakai, Kenta ; Tan, Tin Wee ; Gao, Ge ; Mulder, Nicola ; Schönbach, Christian ; Zheng, Yun ; De Las Rivas, Javier ; Khan, Asif M.
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2023-08, Vol.41 (8), p.1171-1174
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Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation
Author / Creator:Vandenbon, Alexis ; Kumagai, Yutaro ; Lin, Mengjie ; Suzuki, Yutaka ; Nakai, Kenta
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2018-09, Vol.19 (1), p.138-138, Article 138
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A study on the application of topic models to motif finding algorithms
Author / Creator:Basha Gutierrez, Josep ; Nakai, Kenta
Publisher:England: BioMed Central
Journal title:BMC bioinformatics, 2016-12, Vol.17 (S19), p.502-502, Article 502
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Protein design via deep learning

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PrognoScan: a new database for meta-analysis of the prognostic value of genes

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iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations

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Stable feature selection based on the ensemble L 1 -norm support vector machine for biomarker discovery

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A hypothetical trivalent epigenetic code that affects the nature of human ESCs

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Extreme value theory as a framework for understanding mutation frequency distribution in cancer genomes

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Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses

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The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection

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A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations

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A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment

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Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s

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Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks

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STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration

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Comprehensive comparison of gene expression diversity among a variety of human stem cells

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Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer

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HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data

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A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response

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Grand challenges in bioinformatics education and training

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Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

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A study on the application of topic models to motif finding algorithms

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