NAKAI Lab.

Laboratory of Functional Analysis in silico

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

All publications

»Latest 50

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).
(full text)

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).
(full text)

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).
(full text)

Kenta Nakai. Information science should take a lead in future biomedical research. (Perspective) Engineering, 5(6), 1155-1158 (2019).
(full text)

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).
(full text)

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).
(full text)

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).
(full text)

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).
(full text)

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).
(abstract)

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).
(full text)

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.
(full text)

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.
(full text)

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).
(full text)

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).
(full text)

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).
(full text)

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).
(full text)

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).
(full text)

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).
(abstract)

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).
(abstract)

Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, and Kenta Nakai, OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. Nucl. Acids Res., 44(D1), D1000-D1004 (2016).
(full text)

Yosvany López, Kenta Nakai, and Ashwini Patil, HitPredict version 4 - comprehensive reliablity scoring of physical protein-protein interactions from more than 100 species, DATABASE, 2015, bav117 (2015).
(full text).

Kuo-ching Liang, Ashwini Patil, and Kenta Nakai, Discovery of intermediary genes between pathways using sparse regression. PLoS One, 10(9), e0137222 (2015).
(full text).

Jong-Hun Lee, Sung-Joon Park, and Kenta Nakai, An integrative approach for efficient analysis of whole genome bisulfite sequencing data. BMC Genomics 16(Suppl 12), S14 (2015)
(full text).

Josep Basha Gutierrez, Martin Frith, and Kenta Nakai, A genetic algorithm for motif finding based on statistical significance. Bioinformatics and Biomedical Engineering (Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015, Proceedings, Part I), Springer, LNCS 9043, pp.438-449 (2015).

Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucl. Acids Res., 43, D87-D91 (2015).
(full text).

Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi and Kenta Nakai, DBTMEE: a database of transcriptome in mouse early embryos. Nucl. Acids Res., 43, D771-D776 (2015).
(full text).

Lucky R. Runtuwene, Kaori Noguchi, Akinori Tokunaga, Takashi Kobayashi, Kenta Nakai, and Yuki Eshita, Vector competence of Aedes aegypti to dengue virus. Urban Pest Management, 4(1), 1-14 (2014),

Ashwini Patil and Kenta Nakai, TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles, BMC Syst. Biol., 8(Suppl.4), S2 (2014).
(full text).

Yosvany López, Alexis Vandenbon, and Kenta Nakai, A Set of Structural Features Defines the Cis-Regulatory Modules of Antenna-Expressed Genes in Drosophila melanogaster, PLoS One 9(8), e104342 (2014).
(full text)

Sanaz Firouzi, Yosvany López, Yutaka Suzuki, Kenta Nakai, Sumio Sugano, Tadanori Yamochi and Toshiki Watanabe, Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites, Genone Medicine, 6, 46 (2014).
(full text)

Kenta Nakai, Overview of Bioinformatics Research in Japan, Asia Pacific Biotech, 18(9), 35-37 (2014).

Kyungtaek Lim, Ichizo Kobayashi, and Kenta Nakai, Alterations in rRNA-mRNA interaction during plastid evolution, Mol. Biol, Evol., 31(7), 1728-1740 (2014).
(PubMed)

Sung-Joon Park, Terumasa Umemoto, Mihoko Saito-Adachi, Yoshiko Shiratsuchi, Masayuki Yamato, and Kenta Nakai, Computational promoter modeling identifies the modes of transcriptional regulation in hematopoietic stem cells, PLoS One, 9(4), e93853 (2014).
(full text)

Alok Sharma, Abdollah Dehzangi, James Lyons, Seiya Imoto, Satoru Miyano, Kenta Nakai, and Ashwini Patil, Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function, PLoS One, 9(2), e89890 (2014).
(full text)

Asmaa Elzawahry, Ashwini Patil, Yutaro Kumagai, Yutaka Suzuki, and Kenta Nakai, Innate immunity interactome dynamics, Gene Regulation and Systems Biology, 8, 1-15 (2014)
(abstract & pdf)

Kuo-ching Liang, Yutaka Suzuki, Yutaro Kumagai, and Kenta Nakai, Analysis of changes in transcription start site distribution by a classification approach, Gene, 537(1), 29-40 (2014); published online 31 December 2013
(full text)

Sung-Joon Park, Makiko Komata, Fukashi Inoue, Kaori Yamada, Kenta Nakai, Miho Ohsugi and Katsuhiko Shirahige, Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis, Genes Dev., 27(24), 2736-2748 (2013).
(full text)

Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, and Kenta Nakai, Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response, PLoS Comput. Biol., 9(11), e1003323 (2013); Epub Nov.7, 2013
(full text)

Yosvany López, Ashwini Patil, and Kenta Nakai, Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana, BMC Systems Biol., 7(Suppl 3): S10 (2013).
(full text)

Yasunori Sasakura, Nicolas Sierro, Kenta Nakai, Kazuo Inaba, and Takehiro G. Kusakabe, Chapter 4: Genome structures, functional genomics, and proteomics in ascidians, in (Denny, P. & Kole, C. eds.) Genome mapping and genomics in laboratory animals, pp.87-132, Springer (2013).

Yuko Makita and Kenta Nakai, Chapter 8: Bacillus subtilis transcriptional network, in (M. Madan Babu ed.) Bacterial Gene Regulation and Transcriptional Networks, pp.155-165, Caister Academic Press (ISBN: 978-1-908230-14-0) (2013)

Rie Kusakabe, Saori Tani, Koki Nishitsuji, Miyuki Shindo, Kohji Okamura, Yuki Miyamoto, Kenta Nakai, Yutaka Suzuki, Takehiro G. Kusakabe, and Kunio Inoue, Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues, Gene Expression Patterns, 13(1-2), 43-50.(2013)
(PubMed)

Manabu Ozawa, Miki Sakatani, JiQiang Yao, Savita Shanker, Fahong Yu, Riu Yamashita, Shuichi Wakabayashi, Kenta Nakai, Kyle B Dobbs, Mateus J. Sudano, William G. Farmerie, and Peter J. Hensen, Global gene expression of the inner cell mass and trophectoderm of the bovine blastcyst, BMC Dev. Biol., 12, 33 (2012)
(full text)

Naganari Ohkura, Masahide Hamaguchi, Hiromasa Morikawa, Kyoko Sugimura, Atsushi Tanaka, Yoshinaga Ito, Motonao Osaki, Yoshiaki Tanaka, Riu Yamashita, Naoko Nakano, Jochen Huehn, Hans-Joerg Fehling, Tim Sparwasser, Kenta Nakai, and Shimon Sakaguchi, T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development, Immunity, 37(5), 785-799 (2012).
(PubMed)

Harry Amri Moesa, Shunichi Wakabayashi, Kenta Nakai, and Ashwini Patil, Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification. Mol. Biosystems, 8(12), 3262-3273 (2012); published online on 18 Oct 2012
(full text)

Sumiyo Morita, Ryou-u Takahashi, Riu Yamashita, Atsushi Toyoda, Takuro Horii, Mika Kimura, Asao Fujiyama, Kenta Nakai, Shoji Tajima, Ryo Matoba, Takahiro Ochiya and Izuho Hatada, Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells, Int. J. Mol. Sci., 13(7), 8259-8272 (2012).
(abstract)

Daniel Kraut, Eitan Israeli, Erin Schrade, Ashwini Patil, Kenta Nakai, Dhaval Nanavati, Tomonao Inobe, and Andreas Matouschek, Sequence- and species-dependence of proteasomal processivity, ACS Chemical Biology,7(8), 1444-1453 (2012); epub 2012 Jun. 22.
(abstract)

Kouichi Kimura, Asako Koike, and Kenta Nakai, A Bit-parallel dynamic programming algorithm suitable for DNA sequence alignment, J. Bioinformatics and Computational Biology, 10(4), 1250002 (2012); published online on Feb. 2, 2012.
(abstract)

Riu Yamashita, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS: database of transcriptional start sites progress report in 2012, Nucl. Acids Res., 40(Database Issue), D150-154 (2012); published online on Nov. 15, 2011.
(full text)

Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, and Daron M. Standley, Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator, Pacific Symposium on Biocomputing 17, 164-175 (2012)
(pdf)

Ashwini Patil, Kenta Nakai, and Kengo Kinoshita, Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks, BMC Genomics 12(Suppl. 3), S19 (2011).
(full text)

Kohji Okamura, Riu Yamashita, Noriko Takimoto, Koki Nishitsuji, Yutaka Suzuki, Takehiro G. Kusakabe, and Kenta Nakai, Profiling ascidian promoters as the primordial type of vertebrate promoter, BMC Genomics 12(Suppl. 3), S7 (2011).BEST PAPER AWARD in InCoB211
(full text)

Kouichi Kimura, Asako Koike and Kenta Nakai, Seed-set construction by equi-entropy partitioning for efficient and sensitive short-read mapping, Algorithms in Bioinformatics in (T.M.Przytycka and M.-F. Sagot ed.) Lecture Notes in Computer Science, 6833, 151-162 (2011). (ISBN: 978-3-642-23037-0).

Daisuke Ohshima, Junwen Qin, Hiroyasu Konnno, Akihisa Hirosawa, Takuma Shiraishi, Hiromi Yanai, Yusuke Shimo, Nobuko Akiyama, Riu Yamashita, Kenta Nakai, and Jun-ichiro Inoue, RANK signaling induces interferon-stimulated genes in the fetal thymic stroma, Biochem. Biophys. Res. Comm., 408(4), 530-536 (2011).
(PubMed)

Takuma Irie, Sung-Joon Park, Riu Yamashita, Masahide Seki, Tetsushi Yada, Sumio Sugano, Kenta Nakai, and Yutaka Suzuki, Predicting promoter activities of primary human DNA sequences, Nucl. Acids Res., 39(11), e75 (2011); published online on April 12, 2011.
(full text)

Riu Yamashita, Nuankanya P Sathira, Akinori Kanai, Kousuke Tanimoto, Takako Arauchi, Yoshiaki Tanaka, Shin-ichi Hashimoto, Sumio Sugano, Kenta Nakai, and Yutaka Suzuki, Genome-wide characterization of transcription start sites in humans by integrative transcriptome analysis, Genome Res., 21(5), 775-789 (2011); published online on March 3, 2011.
(abstract)

Parul Khare, Sanra I. Mortimer, Cynthia L. Cleto, Kohji Okamura, Yutaka Suzuki, Takehiro Kusakabe, Kenta Nakai, Thomas H. Meedel, and Kenneth E. M. Hastings, Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene, Nucleic Acids Res., 39(7), 2638-2648 (2011); published online on November 24, 2010.
(full text)

Sung-Joon Park and Kenta Nakai, A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns, BMC Bioinformatics, 12(Suppl 1), S50 (Feb 15, 2011).
(full text)

Ashwini Patil, Kenta Nakai, and Haruki Nakamura, HitPredict: a database of quality assessed protein-protein interactions in nine species, Nucl. Acids Res., 39, D744-D799 (2011); published online on October 14, 2010.
(full text)

Shoba Ranganathan, Christian Schönbach, Kenta Nakai, Tin Wee Tan, Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010), BMC Genomics, 11(Suppl 4), S1 (2 December 2010).
(full text)

Kenichiro Imai and Kenta Nakai, Prediction of subcellular location of proteins: where to proceed?, Proteomics, 10(22), 3970-3983 (2010); first published online Nov. 2, 2010.
(abstract)

Takashi Satoh, Osamu Takeuchi, Alexis Vandenbon, Koubun Yasuda, Yoshiaki Tanaka, Yutaro Kumagai, Tohru Miyake, Kazufumi Matsushita, Toshihiko Okazaki, Tatsuya Saitoh, Kiri Honma, Toshifumi Matsuyama, Katsuyuki Yui, Tohru Tsujimura, Daron M. Standley, Kenji Nakanishi, Kenta Nakai and Shizuo Akira, The JMJD3-IRF4 axis regulates M2 macrophage polarization and host responses against helminth infection, Nature Immunol., 11(10), 936-944 (2010); published online: 22 Aug. 2010
(PubMed)

Kohji Okamura, Kazuaki A. Matsumoto, and Kenta Nakai, Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution, BMC Bioinformatics, 11(Suppl 7), S2 (15 October 2010).
(full text)

Christian Schönbach, Kenta Nakai, Tin Wee Tan, and Shoba Ranganathan, InCoB2010 -- 9th Internatonal Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010, BMC Bioinformatics, 11(Suppl 7), S1 (15 October 2010).
(full text)

Harumi Kawaki, Satoshi Kubota, Eriko Aoyama, Naoya Fujita, Hiroshi Hanagata, Akira Miyauchi, Kenta Nakai, and Masaharu Takigawa, Design and utility of CCN2 anchor peptide aptamers, Biochemie, 92(8), 1010-1015 (2010).
(PubMed)

Yoshiaki Tanaka, Riu Yamashita, Yutaka Suzuki, and Kenta Nakai, Effects of Alu elements on global nucleosome positioning in the human genome, BMC Genomics, 11, 309 (2010).
(full text)

Atsushi Kubo, Nobuhiro Suzuki, Xuyang Yuan, Kenta Nakai, Nori Satoh, Kaoru S. Imai, and Yutaka Satou, Genomic cis-regulatory networks in the Ciona intestinalis embryo, Development, 137(10), 1613-1623 (2010).
(PubMed)

Yoshiaki Tanaka, Itsuki Yoshimura, and Kenta Nakai, Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin, Chromosoma, 119(4), 391-404 (2010); Epub on March 12, 2010
(full text)

Nuankanya Sathira, Riu Yamashita, Kousuke Tanimoto, Akinori Kanai, Takako Arauchi,Soutaro Kanematsu, Kenta Nakai, Yutaka Suzuki, and Sumio Sugano, Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer, DNA Res., 17(3), 169-183 (2010); published online on April 17, 2010.
(full text)

Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai, DBTSS provides a tissue specific dynamic view of Transcription Start Sites, Nucl. Acids Res., 38, D98-D104 (2010); published online on November 13, 2009.
(full text)

Alexis Vandenbon and Kenta Nakai, Modeling tissue-specific structural patterns in human and mouse promoters, Nucl. Acids Res., 38(1), 17-25 (2010); published online on October 22, 2009.
(full text)

Yoshiaki Tanaka and Kenta Nakai, An assessment of prediction algorithms for nucleosome positioning, Genome Informatics, 23, 169-178 (2009); ISSN: 0919-9454.
(eProceedings)

Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takeshi Oshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, and Ichiro Nakagawa, Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content, BMC Genomics, 10, 358 (2009); published online on August 5, 2009.
(full text)

Hideaki Mizuno, Kunio Kitada, Kenta Nakai, and Akinori Sarai, PrognoScan: a new database for meta-analysis of the prognositic value of genes, BMC Med. Genomics, 2, 18 (2009); published online on April 24, 2009.
(full text)

Katsuya Tsuchihara, Yutaka Suzuki, Hiroyuki Wakaguri, Takuma Irie, Kousuke Tanimoto, Shin-ichi Hashimoto, Kouji Matsushima, Junko Mizushima-Sugano, Riu Yamashita, Kenta Nakai, David Bentley, Hiroyasu Esumi, and Sumio Sugano, Massive transcriptional start site analysis of human genes in hypoxia cells, Nucl. Acids Res., 37, 2249-2263 (2009); published online on February 22, 2009.
(full text)

Keishin Nishida, Martin Frith, and Kenta Nakai, Pseudocounts for transcription factor binding sites, Nucl. Acids Res., 37(3), 939-944 (2009); published online on December 23, 2008
(full text)

Nicolas Sierro, Shuang Li, Yutaka Suzuki, Riu Yamashita, and Kenta Nakai, Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis, Gene, 430, 44-49 (2009); available online on October 21, 2008
(PubMed)

Alexis Vandenbon and Kenta Nakai, Using simple rules on presence and positioning of motifs for promoter structure modeling and tissue specific expression prediction, Genome Informatics (J. Arthur and S.-K. Ng ed.), vol. 21, pp. 188-199 (2008), Imperial College Press, London.
(pdf)

Yosuke Hatanaka, Masao Nagasaki, Rui Yamaguchi, Takeshi Obayashi, Kazuyuki Numata, Andre Fujita, Teppei Shimomura, Yoshinoi Tamada, Seiya Imoto, Kengo Kinoshita, Kenta Nakai, and Satoru Miyano, A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human, Genome Informatics, 20, 212-221 (2008)
(pdf)

Genome Information Integration Project and H-invitational 2 Consortium, The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts, Nucl. Acids Res., 36(Database issue), D793-D799 (2008); advanced access published online on December 18, 2007.
(full text) Izuho Hatada, Sumiyo Morita, Mika Kimura, Takuro Horii, Riu Yamashita, and Kenta Nakai, Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells, J. Human Genet., 53(2), 185-191 (2008).
(full text) Koshiro Miura, Hidehiro Toh, Hideki Hirakawa, Manabu Sugii, Masayuki Murata, Kenta Nakai, Kosuke Tashiro, Satoru Kuhara, Yoshinao Azuma, and Mutsunori Shirai, Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infection, DNA Res., 15(2), 83-91 (2008); advance access published online on January 24, 2008.
(full text) Alexis Vandenbon, Yuki Miyamoto, Noriko Takimoto, Takehiro Kusakabe, and Kenta Nakai, Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction, DNA Res., 15(1), 3-11 (2008); advance access originally published online on February 7, 2008.
(full text) Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori, and Kenta Nakai, Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions, BMC Genomics, 9(1), 112 (2008).
(full text) Kohji Okamura and Kenta Nakai, Retrotransposition as a source of new promoters, Mol. Biol. Evol., 25(6), 1231-1238 (2008); published online on March 25, 2008.
(full text) Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, and Kenta Nakai, Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs, BMC Genomics, 9, 152 (2008).
(full text) Riu Yamashita, Yutaka Suzuki, Nono Takeuchi, Hiroyuki Wakaguri, Takuya Ueda, Sumio Sugano, and Kenta Nakai, Comprehensive detection of human terminal oligo-pyrimidine (TOP) gene and analysis of their characteristics, Nucl. Acids Res., 36(11), 3707-3715 (2008); published online on May 14, 2008.
(full text)

Sierro, N., Makita, Y., de Hoon, M., and Nakai, K., DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information, Nucl. Acids Res., 36(Database issue), D93-D96 (2008); advanced access published online on October 25, 2007.
(full text)

Wakaguri, H., Yamashita, R., Suzuki, Y., Sugano, S., and Nakai, K., DBTSS: DataBase of Transcription Start Sites, progress report 2008, Nucl. Acids Res., 36(Database issue), D97-D101 (2008); advanced access published online on October 16, 2007.
(full text)

Okumura, T., Makiguchi, H., Makita, Y., Yamashita, R., and Nakai, K., Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions, Nucl. Acids Res., 35, W227-W231 (2007); advanced access published online on May 30, 2007.
(full text)

Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J., and Nakai, K., WoLF PSORT: protein localization predictor, Nucl. Acids Res., 35, W585-W587, (2007); advanced access published online on May 21, 2007.
(full text)

Tsuritani, K., Irie, T., Yamashita, R., Wakaguri, H., Kanai, A., Mizushima-Sugano, J., Sugano, S., Nakai, K., and Suzuki, Y., Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes, Genome Res., 17(7), 1005-1014 (2007); published online before print June 13, 2007.
(abstract).

Sakakibara, Y., Irie, T., Suzuki, Y., Yamashita, R., Wakaguri, H., Kanai, A., Chiba, J., Takagi, T., Mizushima-Sugano, J., Hashimoto, S., Nakai, K., and Sugano, S., Intrinsic promoter activities of primary DNA sequences in the human genome, DNA Res., 14(2), 71-77 (2007); advance access published online on May 23, 2007.
(full text)

Nakai, K. and Horton, P., Chapter 29: Computational prediction of subcellular localization (in M. van der Giezen ed., Protein Targeting Protocols (2nd ed.), Methods in Molecular Biology, vol. 390), pp.429-466, Humana Press, Totowa, 2007, (ISBN 13 978-1-58829-702-0)
(abstract)

Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., and Ohta, H., ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis, Nucl. Acids Res., 35, Database issue D863-D869 (2007); advance access published online on Nov. 27, 2006.
(full text)

Cheong, J., Yamada, Y., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., Nakai, K., Ito, T., Saito, I., Sugano, S., and Suzuki, Y., Diverse DNA methylation status at alternative promoters of human genes in various normal tissues, DNA Res., 13(14), 155-167 (2006).
(full text)

Yamashita, R., Suzuki, Y., Wakaguri, H., Tsuritani, K., Nakai, K., and Sugano, S., DBTSS: Database of Human Transcription Start Sites, Progress Report 2006, Nucl. Acids Res., 34, D86-D89 (2006).
(full text)

Sierro, N., Kusakabe, T., Park, K.-J., Yamashita, R., Kinoshita, K., and Nakai, K., DBTGR: a database of tunicate promoters and their regulatory elements, Nucl. Acids Res., 34, D552-D555 (2006)
(full text)

Kimura, K., Watanabe, A., Suzuki, Y., Ota, T., Nishikawa, T., Yamashita, R., Yamamoto, J., Sekine, M., Tsuritani, K., Ishii, S., Sugiyama, T., Saito, K., Isono, Y., Irie, R., Kushida, N., Yoneyama, T., Otsuka, R., Kanda, K., Yokoi, T., Kondo, H., Wagatsuma, M., Murakawa, K., Ishida, S., Ishibashi, T., Takahashi-Fujii, A., Tanase, T., Nagai, K., Kikuchi, H., Nakai, K., Isogai, T., and Sugano, S., Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes, Genome Res., 16, 55-65 (2006).
(abstract)

Horton, P., Park, K.-J., Obayashi, T., and Nakai, K., Protein subcellular localization prediction with WoLF PSORT, (Jiang, T. et al. eds) Proc. 4th Asia-Pacific BIOINFORMATICS Conference (APBC2006), 39-48, Imperial College Press (2006).

De Hoon, M.J.L., Makita, Y., Nakai, K., and Miyano, S., Prediction of transcriptional terminators in Bacillus subtilis and related species, PLoS Comput. Biol., 1(3), e25 (2005).
(full text)

Nakao, M., Barrero, R.A., Mukai, Y., Motono, C., Suwa, M., and Nakai, K., Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals, Nucl. Acids Res., 33(8), 2355-2363, (2005); published online 28 April 2005
(full text)

Yamashita, R., Suzuki, Y., Sugano, S., and Nakai, K., Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue-specificity, Gene, 350(2), 129-136 (2005); Mar 17, 2005 (Epub)
(abstract)

Poluliakh, N., Konno, M., Horton, P., and Nakai, K., Parameter landscape analysis for common motif discovery programs, in Eskin, E. & Workman, C. (eds.), Regulatory Genomics, RECOMB 2004 International Workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004, Revised Selected Papers. Lecture Notes in Computer Science 3318, pp. 79-87, Springer (2005).
(abstract)

Makita, Y., De Hoon, M.J.L., Ogasawara, N., Miyano, S., and Nakai, K., Bayesian joint prediction of associated transcription factors in Bacillus subtilis, Pacific Symposium on Biocomputing 2005 (Altman et al ed.), 507-518, World Scientific (2005).
(full paper)

Kato, K., Yamashita, R., Matoba, R., Monden, M., Noguchi, S., Takagi, T., and Nakai, K., Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues, Nucl. Acids Res., 33, D533-D536 (2005).
(full text)

Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., and Miyano, S., An O(N^2) algorithm for discovering optimal boolean pattern pairs, IEEE/ACM Transactions on Computational Biology and Bioinformatics (special section on the Workshop on Algorithms in Bioinformatics), 1(4), 159-170 (2004).

Inenaga, S., Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., and Miyano, S., Finding optimal pairs of cooperative and competing patterns with bounded distance, Lecture Notes in Comp. Sci. (DS 2004),, 3245 32-46 (2004).
(abstract)

Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., and Miyano, S., Finding optimal pairs of patterns, Lecture Notes in Comp. Sci. (WABI 2004), 3240, 450-462 (2004).
(abstract)

Suzuki, Y., Yamashita, R., Shirota, M., Sakakibara, Y., Chiba, J., Mizushima-Sugano, J., Nakai, K., and Sugano, S., Sequence comparison of human and mouse genes reveals a homolgous block structure in the promoter regions, Genome Res., 14, 1711-1718 (2004).
(abstract)

Suzuki, Y., Yamashita, R., Shirota, M., Sakakibara, Y., Chiba, J., Mizushima-Sugano, J., Kel, A. E., Arakawa, T., Caminci, P., Kawai, J., Hayashizaki, Y., Takagi, T., Nakai, K., and Sugano, S., Large-scale collection and characterization of promoters of human and mouse genes, In silico Biol., 4, 0036 (2004).
(full text)

De Hoon, M.J.L., Makita, Y., Imoto, S., Kobayashi, K., Ogasawara, N., Nakai, K., and Miyano, S., Predicting gene regulation by sigma factors in Bacilllus subtilis from genome-wide data, Bioinformatics, 20(Supp. 1), I101-I108 (2004).
(PubMed)

Horton, P., Mukai, Y., and Nakai, K., Chapter 14: Protein subcellular localization prediction, in L. Wong (ed.), Practical Bioinformatician, World Scientific Publishing Co., pp.193-216, 2004.

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Md M, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, and Sugano S., Integrative annotation of 21,037 human genes validated by full-length cDNA clones, PLoS Biol., 2(6), E162 (2004).
(full text)

Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, and Sugano S, Complete sequencing and characterization of 21,243 full-length human cDNAs, Nat. Genet., 36(1), 40-45 (2004).
(PubMed)

Suzuki, Y., Yamashita, R., Sugano, S., and Nakai, K., DBTSS (DataBase of Transcriptional Start Sites): Progress Report 2004, Nucl. Acids Res., 32, D78-D81 (2004).
(full text)

Makita, Y., Nakao, M., Ogasawara, N., and Nakai, K., DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics, Nucl. Acids Res., 32, D75-D77 (2004)
(full text)

Yamashita, R., Suzuki, Y., Nakai, K., and Sugano, S., Small open reading frames in 5' untranslated regions of mRNAs, C. R. Biol., 326(10-11), 987-991 (2003).
(abstract)

Gardy, J. L., Spencer, C., Wang, K., Ester, M., Tusnady, G. E., Simon, I., Hua, S., deFays, K., Lambert, C., Nakai, K., and Brinkman, F. S. L., PSORT-B: Improving protein subcelular localization prediction for Gram-negative bacteria, Nucl. Acids Res., 31(13), 3613-3617 (2003).
(abstract)

Poluliakh, N., Takagi, T., and Nakai, K., MELINA: motif extraction from promoter regions of potentially co-regulated genes, Bioinformatics, 19(3), 423-424 (2003).
(PubMed)

Ott, S., Tamada, Y., Bannai, H., Nakai, K., and Miyano, S., Intrasplicing: analysis of long intron sequences, Pacific Symposium on Biocomputing, 8, 339-350 (2003).
(pdf).

Koike, A., Nakai, K., and Takagi, T., The origin and evolution of eukaryotic protein kinases, Genome Lett., 1(2), 83-104 (2002).
(abstract).

Terashima, H., Fukuchi, S., Nakai, K., Arisawa, M., Hamada, K., Yabuki, N., and Kitada, K., Sequence-based approach for identification of cell wall proteins in Saccharomyces cerevisiae, Current Genetics, 40(5), 311-316 (2002).
(abstract, pdf).

Nakai, K. Chapter 14: Signal peptides, in Ulo Langel (ed.), Cell-Penetrating Peptides: Processes and Applications, 295-324, CRC Press (2002).

Nakai, K. and Vert, J.-P., Genome informatics for data-driven biology: A report on the twelfth international conference on genome informatics, Tokyo, Japan, December 17-19, 2001, Genome Biology, 3(4), reports4010.1-4010.3 (2002).
(PubMed)

Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Extensive feature detection of N-terminal protein sorting signals, Bioinformatics, 18(2), 298-305 (2002).
(abstract)

Suzuki, Y., Yamashita, R., Nakai, K., and Sugano, S., DBTSS: database of human transcriptional start sites and full-length cDNAs, Nucl. Acids Res., 30(1), 328-331 (2002).
(abstract / pdf)

Terai, G., Takagi, T., and Nakai, K., Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species, Genome Biology, 2(11), research0048.1-0048.12 (2001).
(full text / pdf)

Nakai, K., Prediction of in vivo fates of proteins in the era of genomics and proteomics, J. Struct. Biol., 134(2/3), 103-116 (2001).
(PubMed)

Miura, F., Yada, T., Nakai, K., Sakaki, Y., and Ito, T., Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast, FEBS Lett., 505, 103-108 (2001).
(PubMed)

Yada, T., Totoki, Y., Takagi, T., and Nakai, K., A novel bacterial gene-finding system with top-class accuracy in locating start codons, DNA Res., 8(3), 97-106 (2001).
(PDF)

Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Views: fundamental building blocks in the process of knowledge discovery, Proc. 14th Int. FLAIRS Conf., 233-238, AAAI Press (2001).
(PDF)

Hishigaki, H., Nakai, K., Ono, T., Tanigami, A., and Takagi, T., Assessment of prediction accuracy of protein function from protein-protein interaction data, Yeast, 18(6), 523-531 (2001).
(PubMed)

Mizuno, H., Tanaka, Y., Nakai, K., and Sarai, A., ORI-GENE: gene classification based on the evolutionary tree, Bioinformatics, 17(2), 167-173 (2001).
(PubMed)

Ishii, T., Yoshida, K., Terai, G., Fujita, Y., and Nakai, K., DBTBS: A database of Bacillus subtilis promoters and transcription factors, Nucleic Acids Res., 29, 278-280 (2001).
(PubMed)

Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O. and Zhang, M.Q., An alternative exon database (AEDB) and its statistical analysis, DNA Cell Biol., 19(12), 739-756 (2000).
(PubMed)

Nakai, K, Protein sorting signals and prediction of subcellular localization, Adv. Protein Chem., 54, 277-344 (2000).
(PubMed)

Yada, T., Nakao, M., Totoki, Y., and Nakai, K., Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models, Bioinformatics, 15(12) 987-993 (1999).
(PubMed)

Nakai, K. and Horton, P., PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization, Trends Biochem. Sci, 24(1) 34-35 (1999).
(PubMed)

Miyajima, S., Mori, A., Hagiwara, K., Kobayashi, J., Yoshimura, T., Nakai, K., Suzuki, Y., and Tomita, M., Microheterogeneity in the polyhedrin gene of Bombyx mori, a cytoplasmic polyhedrosis virus, J. Seric. Sci. Jpn, 67(4) 287-294 (1998).

Yada, T., Totoki, Y., Ishikawa, M., Asai, K., and Nakai, K., Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences, Bioinformatics, 14(4) 317-325 (1998).
(PubMed)

Hagiwara, K., Tomita, M., Nakai, K., Kobayashi, J., Miyajima, S., and Yoshimura, T., Determination of the nucleotide sequence of Bombyx mori cytoplasmic polyhedrosis virus segment 9 and its expression in BmN4 cells, J. Virol., 72(7) 5762-5768 (1998).
(PubMed)

Yoshikawa, H., Fujiyama, A., Nakai, K., Inazawa, J., and Matsubara, K., Detection and isolation of a novel human gene located on Xp11.2-p11.4 that escapes X-inactivation using a two-dimensional DNA mapping method, Genomics, 49(2), 237-246 (1998).
(PubMed)

Yoshioka, S., Kato, K., Nakai, K., Okayama, H., and Nojima, H., Identification of Open Reading Frames in Schizosaccharomyces pombe cDNAs, DNA Res., 4, 363-369 (1997).
(PubMed)

Fujiwara, Y., Asogawa, M., and Nakai, K., Prediction of mitochondrial targeting signals using hidden Markov models, Genome Informatics 1997, 53-60, (1997).
(PubMed)

Yada, T., Totoki, Y., Ishii, T., and Nakai, K., Functional prediction of B. subtilis genes from their regulatory sequences Intellig. Syst. Mol. Biol. 5, 354-357 (1997).
(PubMed)

Horton, P. and Nakai, K., Better prediction of protein cellular localization sites with the k nearest neighbor classifier, Intellig. Syst. Mol. Biol. 5, 147-152 (1997).
(PubMed)

Nakai, K., Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerevisiae and Bacillus subtilis, Genome Informatics Workshop GIW-96,72-81 (1996).
(Click here to get more information)

Horton, P. and Nakai, K., A probabilistic classification system for predicting the cellular localization sites of proteins, Intellig. Syst. Mol. Biol. 4, 109-115 (1996).
(PubMed)

Nakai, K., Tokimori, T., Ogiwara, A., Uchiyama, I., and Niiyama, T., Gnome -- an Internet-based sequence analysis tool, Comp. Appl. Biosci. 10, 547-550 (1994).
(PubMed)

Nakai, K. and Sakamoto, H., Construction of a novel database containing aberrant splicing mutations of mammalian genes, Gene 141, 171-177 (1994).
(PubMed)

Goffeau, A., Slonimski, P., Nakai, K., and Risler, J.L., How many yeast genes code for membrane-spanning proteins?, Yeast 9, 691-702 (1993).
(PubMed)

Goffeau, A., Nakai, K., Slonimski, P., and Risler, J.-L., The membrane proteins encoded by yeast chromosome III genes, FEBS Lett. 325, 112-117 (1993).
(PubMed)

Nakai, K. and Kanehisa, M., A knowledge base for predicting protein localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
(PubMed)

Nakai, K., Predicting various targeting signals in amino acid sequences, Bull. Inst. Chem. Res., Kyoto Univ. 69, 269-291 (1991).
(Click here to get more information)

Nakai, K. and Kanehisa, M., Expert system for predicting protein localization sites in Gram-negative bacteria, PROTEINS: Structure, Function, and Genetics 11, 95-110 (1991).
(PubMed)

Tomita, M., Nakai, K., Yamada, A., Taguchi, R., and Ikezawa, H., Secondary structure of sphingomyelinase from Bacillus cereus, J. Biochem. (Tokyo) 108, 811-815 (1990).
(PubMed)

Nakai, K. and Kanehisa, M., Prediction of in-vivo modification sites of proteins from their primary structures, J. Biochem. (Tokyo) 104, 693-699 (1988).
(PubMed)

Nakai, K., Kidera, A., and Kanehisa, M., Cluster analysis of amino acid indices for prediction of protein structure and function, Protein Engineering 2, 93-100 (1988).
(PubMed)

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