NAKAI Lab.

Laboratory of Functional Analysis in silico

Human Genome Center
The Institute of Medical Science
The University of Tokyo

Latest publications

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Yang Cui, Weihang Zhang, Xin Zeng, Yitao Yang, Sung-Joon Park and Kenta Nakai. Computational analysis of the functional impact of MHC-II-expressing triple-negative breast cancer. Frontiers in Immunology 15 1497251 (2024).
(doi: 10.3389/fimmu.2024.1497251)

Junichi Iwata and Kenta Nakai. Editorial: Emerging talents in computational genomics. Front. Genet. 15: 1512594 (2024).
(doi: 10.3389/fgene.2024.1512594)

Xin Zeng, Fuki Gyoja, Yang Cui, Martin Loza, Takehiro Kusakabe, and Kenta Nakai. Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina. NAR Genomics and Bioinformatics 6(4), lqae149 (2024).
(doi: 10.1093/nargab/lqae149)

Melissa García-Vega, Mara Anais Llamas-Covarrubias, Martin Loza, Mónica Reséndiz-Sandoval, Diana Hinojosa-Trujillo, Edgar A. Melgoza-González, Olivia Valenzuela, Verónica Mata-Haro, Miguel A. Hernández-Oñate, Alan Soto-Gaxiola, Karina Chávez-Rueda, Kenta Nakai, and Jesús Hernández. Single-cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID-19. J. Medical Virology 96(8), e29851 (2024).
(doi: 10.1002/jmv.29851)

Bowen Liu, Weihang Zhang, Xin Zeng, Martin Loza, Sung-Joon Park, and Kenta Nakai. TF-EPI: An Interpretable Enhancer-Promoter Interaction Detection Method Based on Transformer. Frontiers in Genetics 15, 1444459 (2024).
(doi: 10.3389/fgene.2024.1444459)

Yutong Dai, Jingmei Li, Keita Yamamoto, Susumu Goyama, Martin Loza, Sung-Joon Park, and Kenta Nakai. Integrative analysis of cancer multimodality data identifying COPS5 as a novel biomarker of diffuse large B-cell lymphoma. Front. Genet. 15, 1407765 (2024).
(doi: 10.3389/fgene.2024.1407765)

Rui Yokomori, Takehiro G. Kusakabe, and Kenta Nakai. Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing. NAR Genomics and Bioinformatics 6(2), lqae067 (2024).
(doi: 10.1093/nargab/lqae067)

Sung-Joon Park and Kenta Nakai. A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response. NAR Genomics and Bioinformatics 6(2), lqae050 (2024).
(doi: 10.1093/nargab/lqae050)

Weihang Zhang, Yang Cui, Bowen Liu, Martin Loza, Sung-Joon Park and Kenta Nakai. HyGAnno: Hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. Brief. Bioinform. 25(3), bbae152 (2024).
(doi: 10.1093/bib/bbae152)

Xingxing Chen, Yi Zheng, Jun Wang, Blake Yue, Xian Zhang, Kenta Nakai, Lijing L. Yan. Resting Heart Rate and Risk of Dementia: A Mendelian Randomization Study in the International Genomics of Alzheimer's Project and UK Biobank. PeerJ, 12:e17073 (2024).
(doi: 10.7717/peerj.17073)

Satoko Ishii, Taishi Kakizuka, Sung-Joon Park, Ayako Tagawa, Chiaki Sanbo, Hideyuki Tanabe, Yasuyuki Ohkawa, Mahito Nakanishi, Kenta Nakai, Yusuke Miyanari. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nature Genet. 56(3), 473-482 (2024) (published online Feb. 5, 2024).
(DOI: 10.1038/s41588-024-01658-1)

Yubo Zhang, Wenbo Yang,Yutaro Kumagai, Martin Loza,Weihang Zhang, Sung-Joon Park, and Kenta Nakai. Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization. Front. Immunol. 14, 1304778 (2023).
(full text)

Martin Loza, Alexis Vandenbon, and Kenta Nakai. Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression. Nucleic Acids Res. 52(3) 1107-1119 (2024). (published online on Dec. 12, 2023)
(full text)

Zhongshen Li, Junru Jin, Wenjia He, Wentao Long, Haoqing Yu, Xin Gao, Kenta Nakai, Quan Zou, and Leyi Wei. CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. Brief. Bioinform. 24(6), bbad352 (2023).
(abstract)

Dan Li, Yoshikazu Johmura, Satoru Morimoto, Miyuki Doi, Keiko Nakanishi, Manabu Ozawa, Yuji Tsunekawa, Akane Inoue-Yamauchi, Hiroya Naruse, Takashi Matsukawa, Yukio Takeshita, Naoki Suzuki, Masashi Aoki, Ayumi Nishiyama, Xin Zeng, Chieko Konishi, Narumi Suzuki, Atsuya Nishiyama, Alexander Stephen Harris, Mariko Morita, Kiyoshi Yamaguchi, Yoichi Furukawa, Kenta Nakai, Shoji Tsuji, Satoshi Yamazaki, Yuji Yamanashi, Shoichi Shimada, Takashi Okada, Hideyuki Okano, Tatsushi Toda, Makoto Nakanishi, LONRF2 is a protein quality control ubiquitin ligase whose deficiency causes late-onset neurological deficits. Nature Aging 3(8), 1001-1019 (2023).
(PubMed)

Esra Büşra Işık, Michelle D. Brazas, Russell Schwartz, Bruno Gaeta, Patricia M. Palagi, Celia W. G. van Gelder, Prashanth Suravajhala, Harpreet Singh, Sarah L. Morgan, Hilyatuz Zahroh, Maurice Ling, Venkata P. Satagopam, Annette McGrath, Kenta Nakai, Tin Wee Tan, Ge Gao, Nicola Mulder, Christian Schönbach, Yun Zheng, Javier De Las Rivas & Asif M. Khan, Grand challenges in bioinformatics education and training (career feature). Nature Biotechnology 41, 1171-1174 (2023).
(bastract)

Shu Liu, Fujio Toriumi, Xin Zeng, Mao Nishiguchi, and Kenta Nakai. SignedS2V: Structural embedding method for signed networks. in (Hocine Cherifi, Rosario Nunzio Mantegna, Luis M. Rocha, Chantal Cherifi, & Salvatore Miccichè eds.) Complex Networks and Their Applications XI. (Proceedings of The Eleventh International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2022) Volume 1, pp.337-349 (2023). Springer ISBN: 978-3-031-21126-3
(DOI)

Ruheng Wang, Yi iang, Junru Jin, Chenglin Yin, Haoqing Yu, Fengsheng Wang, Jiuxin Feng, Ran Su, Kenta Nakai, Quan Zou, & Leyi Wei. DeepBIO: An automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation, and visualization analysis. Nucl. Acids Res. 51(7), 3017-3029 (2023). (Breakthrough Article)
(full text)

Yukiyo Yamatani and Kenta Nakai. Comprehensive comparison of gene expression diversity among a variety of human stem cells. NAR Genomics and Bioinformatics, 4(4), lqac087 (2022).
(full text)

Junru Jin, Yingying Yu, Ruheng Wang, Xin Zeng, Chao Pang, Yi Jiang, Zhongshen Li, Yutong Dai, Ran Su, Quan Zou, Kenta Nakai, andLeyi Wei. iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations. Genome Biology, 23, 219 (2022)..
(full text)

Hideo Satsu, Yusuke Gondo, Hana Shimanaka, Masato Imae, Shigeru Murakami, Kenji Watari, Shunichi Wakabayashi, Sung-Joon Park, Kenta Nakai, and Makoto Shimizu. Signaling pathway of taurine-induced up-regulation of TXNIP. Metabolites, 12(7), 636 (2022).
(full text)

Yuji Kubota, Yuko Fujioka, Ashwini Patil, Yusuke Takagi, Daisuke Matsubara, Masatomi Iijima, Isao Momose, Ryosuke Naka, Kenta Nakai, Nobuo Noda, and Mutsuhiro Takekawa. Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer. Nature Comm. 13, 4063 (2022).
(full text)

Ruheng Wang, Junru Jin, Quan Zou, Kenta Nakai, and Leyi Wei. Predicting protein-peptide binding residues via interpretable deep learning. Bioinformatics, 38(13), 3351-3360 (2022).
(PubMed)

Kenta Nakai and Leyi Wei. Recent advances in the prediction of subcellular localization of proteins and related topics. (review) Front. Bioinformatics, 2, 910531 (2022).
(doi: 10.3389/fbinf.2022.910531).

Chichi Dai, Yi Jiang, Chenglin Yin, Ran Su, Xiangxiang Zeng, Quan Zou, Kenta Nakai, and Leyi Wei. scIMC: a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods. Nucl. Acids Res., 50(9), 4877-4899 (2022).
(full text)

Wenze Ding, Kenta Nakai and Haipeng Gong. Protein design via deep learning (review). Brief. Bioinformatics 23(3) bbac102 (2022)..
(PubMed)

Kenta Nakai and Alexis Vandenbon. (Chapter 2) Higher-order chromatin structure and gene regulation. in (Chandra Boosani and Ritobrata Goswami eds.) Epigenetics in Organ Specific Disorders. pp.11-32, 2023. Academic Press. ISBN: 978-0-12-823931-5

Natsuki Tokutomi, Kenta Nakai and Sumio Sugano. Extreme value theory as a framework for understanding mutation frequency distribution in cancer genomes. PLoS One 16(8), e0243595 (2021).
(full text)

Xin Zeng, Sung-Joon Park, and Kenta Nakai. Characterizing promoter and enhancer sequences by a deep learning method. Front. Genet. 12, 681259 (2021).
(full text)

Ryo Kinoshita-Daitoku, Kotaro Kiga, Masatoshi Miyakoshi, Ryota Otsubo, Yoshitoshi Ogura, Takahito Sanada, Zhu Bo, Tuan Phuoc, Tokuju Okano, Tamako Iida, Rui Yokomori, Eisuke Kuroda, Sayaka Hirukawa, Mototsugu Tanaka, Arpana Sood, Phawinee Subsomwong, Hiroshi Ashida, Tran Binh, Lam Nguyen, Khien Van, Dang Ho, Kenta Nakai, Toshihiko Suzuki, Yoshio Yamaoka, Tetsuya Hayashi, and Hitomi Mimuro. A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment. Nature Comm. 12, 2085 (2021).
(full text)

Sung-Joon Park and Kenta Nakai. OpenContami: A web-based application for detecting microbial contaminants in next-generation sequencing data. Bioinformatics 37(18) 3021-3022 (2021).
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Hao Jia, Sung-Joon Park and Kenta Nakai. A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations. BMC Bioinformatics 22, 128 (2021).
(full text)

Kenichiro Imai & Kenta Nakai, (review) Tools for the recognition of sorting signals and the prediction of subcellular localization of proteins from their amino acid sequences. Front. Genet. 11, 607812 (2020).
(full text)

Jong-Hun Lee, Yutaka Saito, Sung-Joon Park and Kenta Nakai, Existence and possible roles of independent non-CpG methylation in the mammalian brain. DNA Res., 27(4), dsaa020 (2020).
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Yasuhisa Ishikawa and Kenta Nakai, A hypothetical trivalent epigenetic code that affects the nature of human ESCs. PLoS One, 15(9), e0238742 (2020).
(full text)

Satoru Onizuka, Yasuharu Yamazaki, Sung-Joon Park, Takayuki Sugimoto, Yumiko Sone, Sebastian Sjöqvist; Michihiko Usui, Akira Takeda, Kenta Nakai, Keisuke Nakashima, and Takanori Iwata. RNA-sequencing reveals positional memory of multipotent mesenchymal stromal cells from oral and maxillofacial tissue transcriptomes BMC Genomics 21, 417 (2020).
(full text)

Reina Takeda, Shuhei Asada, Sung-Joon Park, Akihiko Yokoyama, Hans Becker, Akinori Kanai, Valeria Visconte, Courtney Hershberger, Yasutaka Hayashi, Taishi Yonezawa, Moe Tamura, Tsuyoshi Fukushima, Yosuke Tanaka, Tomofusa Fukuyama, Akiko Matsumoto, Satoshi Yamasaki, Kenta Nakai, Satoshi Yamazaki, Toshiya Inaba, Tatsuhiro Shibata, Daichi Inoue, Hiroaki Honda, Susumu Goyama, Jaroslaw Maciejewski, and Toshio Kitamura. HHEX promotes myeloid transformation in cooperation with mutant ASXL1. Blood, 136(14), 1670-1684 (2020).
(PubMed) .

Munmee Dutta, Hidewaki Nakagawa, Hiroaki Kato, Kazuhiro Maejima, Shota Sasagawa, Kaoru Nakano, Aya Sasaki-Oku, Akihiro Fujimoto, Raúl Nicolás Mateos, Ashwini Patil, Hiroko Tanaka, Satoru Miyano, Takushi Yasuda, Kenta Nakai, and Masashi Fujita. Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma. PeerJ 8, e9294 (2020).
(full text)

Ryo Kinoshita-Daitoku, Kotaro Kiga, Takahito Sanada, Yoshitoshi Ogura, Zhu Bo, Tamako Iida, Rui Yokomori, Eisuke Kuroda, Mototsugu Tanaka, Sood Arpana, Toshihiko Suzuki, Kenta Nakai, Tetsuya Hayashi and Hitomi Mimuro. Mutational diversity in mutY deficient Helicobacter pylori and its effect on adaptation to the gastric environment. Biochem. Biophys. Res. Comm., 525(3), 806-811 (2020).
(PubMed)

Sung-Joon Park, Satoru Onizuka, Masahide Seki, Yutaka Suzuki, Takanori Iwata, and Kenta Nakai. A systematic sequencing-based approach for microbial contaminant detection and functional inference. BMC Biol. 17, 72 (2019).
(full text)

Soichiro Yamanaka, Hidenori Nishihara, Hidehiro Toh , Luis Augusto Eijy Nagai, Kosuke Hashimoto, Sung-Joon Park, Aoi Shibuya, Ana Maria Suzuki, Yujiro Tanaka, Kenta Nakai, Piero Carninci, Hiroyuki Sasaki, and Haruhiko Siomi. Broad heterochromatic domains open in gonocyte development prior to de novo DNA methylation. Dev. Cell 51(1), 21-34 (2019).
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Kenta Nakai. Information science should take a lead in future biomedical research. (Perspective) Engineering, 5(6), 1155-1158 (2019).
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Raúl Mateos, Hidewaki Nakagawa, Seiko Hirono, Shinichi Takano, Mitsuharu Fukasawa, Akio Yanagisawa, Satoru Yasukawa, Kazuhiro Maejima, Aya Oku-Sasaki, Kaoru Nakano, Munmee Dutta, Hiroko Tanaka, Satoru Miyano, Nobuyuki Enomoto, Hiroki Yamaue, Kenta Nakai, and Masashi Fujita. Genomic analysis of pancreatic juice DNA assesses malignant risk of intraductal papillary mucinous neoplasm of pancreas. Cancer Medicine 8, 4565-4573 (2019).
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Kenta Nakai, Kenichiro Imai. Prediction of protein localization. In Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach (eds.) Encyclopedia of Bioinformatics and Computational Biology, Academic Press, 2019, vol.2, Pages 53-59, ISBN 9780128114322.
(abstract)

Kenta Nakai. Prediction of protein-binding sites in DNA sequences. In Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach (eds.) Encyclopedia of Bioinformatics and Computational Biology, Academic Press, 2019, vol.3, Pages 447-451, ISBN 9780128114322.
(abstract)

Luis A. E. Nagai, Sung-Joon Park, and Kenta Nakai. Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma. BMC Medical Genomics,11(Suppl 7), 127 (2019).
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Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki, and Kenta Nakai. Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation. Genome Biol., 19, 138 (2018).
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Naoya Fujita, Shinji Mizuarai, Katsuhiko Murakami, and Kenta Nakai. Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses. Sci. Rep. 8, 9743 (2018).
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Phit Ling Tan, Yosvany López, Kenta Nakai, and Ashwini Patil, TimeXNet Web: Identifying cellular response networks from diverse omics time-course data. Bioinformatics 34(21), 3764-3765 (2018)..
(PubMed)

Yasuo Ouchi, Ashwini Patil, Yusuke Tamura, Hiroshi Nishimasu, Aina Negishi, Sudip Kumar Paul, Naoki Takemura, Takeshi Satoh, Yasumasa Kimura, Makoto Kurachi, Osamu Nureki, Kenta Nakai, Hiroshi Kiyono, Satoshi Uematsu. Generation of tumor antigen-specific murine CD8+ T cells with enhanced anti-tumor activity via highly efficient CRISPR/Cas9 genome editing. Int. Immunol., 30(4) 141-154 (2018).
(full text) Editor's choice

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