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

Myungjin Moon and Kenta Nakai, Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers. J. Bioinf. Comput. Biol., 16(2), 1850006 (2018).
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Masashi Fujita, Nagahide Matsubara, Ikuo Matsuda, Kazuhiro Maejima, Ayako Ohsawa, Tomoki Yamano,, Akihiro Fujimoto, Mayuko Furuta, Kaoru Nakano, Aya Oku-Sasaki, Hiroko Tanaka, Yuichi Shiraishi, Raúl Mateos, Kenta Nakai, Satoru Miyano, Naohiro Tomita, Seiichi Hirota, Hiroki Ikeuchi, Hidewaki Nakagawa, Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in the Wnt signaling. Oncotarget 9, 969-981 (2018).
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Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Kazuhiro Nitta, Magali Naville, Jacques Piette, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah Lowe, Mickael Mendez, Wendy Reeves, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C. Titus Brown, Christian Cambillau, Lionel Christiaen, Frédéric Delsuc, Emmanuel Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie Swalla, Michael Veeman, Jean-Nicolas Volff, and Patrick Lemaire, ANISEED 2017 : Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucl. Acids Res., 46(D1), D718-D725 (2018); published on 15 Nov. 2017.
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Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, and Yutaka Suzuki, DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucl. Acids Res., 46(D1), D229-D238 (2018); published online on Nov. 8, 2017.
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Motohiko Kadoki, Ashwini Patil, Cornelius C. Thaiss, Donald J. Brooks, Surya Pandey, Deeksha Deep, David Alvarez, Ulrich H. von Andrian, Amy J. Wagers, Kenta Nakai, Tarjei S. Mikkelsen, Magali Soumillon, and Nicolas Chevrier, Organism-level analysis of vaccination reveals networks of protection across tissues. Cell 171(2), 398-413.e21 (2017),, published September 21, 2017.
(abstract)

Jong-Hun Lee, Sung-Joon Park, Kenta Nakai, Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s, Sci. Rep. 7, 11295 (2017).
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Yosvany López, Alexis Vandenbon, Akinao Nose, and Kenta Nakai, Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster, PeerJ, 5, e3389 (2017).
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Yasunori Sasakura, Yosuke Ogura, Nicholas Treen, Rui Yokomori, Sung-Joon Park, Kenta Nakai, Hidetoshi Saiga, Tetsushi Sakuma, Takashi Yamamoto, Shigeki Fujiwara, and Keita Yoshida, Transcriptional regulation of a horizontally transferred gene from bacterium to chordate. Proc. Royal Soc. B. 283(1845), pii: 20161712 (2016).
(PubMed)

Josep Basha Gutierrez and Kenta Nakai, A study on the application of topic models to motif finding algorithms. BMC Bioinformatics 17(Suppl. 19), 1364 (2016).
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Myungjin Moon and Kenta Nakai, Stable feature selection based on the ensemble L₁-norm support vector machine for biomarker discovery. BMC Genomics 17(Suppl. 13), 3320 (2016).
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Satoru Onizuka, Takanori Iwata, Sung-Joon Park, Kenta Nakai, Masayuki Yamato, Teruo Okano, and Yuichi Izumi, ZBTB16, a downstream target gene of Osterix, regulates osteoblastogenesis of human multipotent mesenchymal stromal cells. J. Cell. Biochem., 117(10), 2423-2434 (2016).
(PubMed)

Kazuhiro Fukumura, Shunichi Wakabayashi, Naoyuki Kataoka, Hiroshi Sakamoto, Yutaka Suzuki, Kenta Nakai, Akila Mayeda, and Kunio Inoue, The exon junction complex controls the efficient and faithful splicing of a subset of transcripts involved in miotic cell-cycle progression. Int. J. Mol. Sci., 17(8), 1153 (2016).
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Sung-Joon Park and Kenta Nakai, Chapter 7: Computational inference of gene regulation from whole-transcriptome analysis of early embryos. in (Ivan V. Ivanov, Xiaoning Qian, and Ranadip Pal eds.) Emerging Research in the Analysis and Modeling of Gene Regulatory Networks, pp.241-279, IGI Global, ISBN: 9781522503538 (2016).

Yuzuru Sasamoto, Ryuhei Hayashi, Sung-Joon Park, Mihoko Saito-Adachi, Yutaka Suzuki, Satoshi Kawasaki, Andrew Quantock, Kenta Nakai, Motokazu Tsujikawa, and Kohji Nishida, PAX6 isoforms, along with reprogramming factors, differentially regulate the induction of cornea-specific genes. Sci. Rep., 6, 20807 (2016).
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Sung-Joon Park, Mihoko Saito-Adachi, Yusuke Komiyama, and Kenta Nakai, Advances, practice, and clinical perspectives in high-throughput sequencing, Oral Diseases, 22(5), 353-364 (2016).
(PubMed)

Rui Yokomori, Kotaro Shimai, Koki Nishitsuji, Yutaka Suzuki, Takehiro G. Kusakabe, and Kenta Nakai, Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. Genome Res., 26, 140-150 (2016).
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