PUBLICATIONS

PUBLICATIONS

The future objectives of the International Mouse Phenotyping Consortium (IMPC): functional evaluation of human disease-relevant cis-regulatory elements in the mouse genome
Naoki Kubo, Akiko Oguchi, Hiroshi Masuya, Takanori Amano, Akihiko Sakashita, Hideya Kawaji, Takeya Kasukawa, Shinya Oki, Shinya Ayabe, Toyoyuki Takada, Atsuo Ogura, Kimiko Inoue, Yasuhiro Murakawa, Masaru Tamura, Atsushi Yoshiki, Toshihiko Shiroishi
Mammalian Genome 37 (2026)

Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells
Naoki Kubo, Ryuji Uehara, Shuhei Uemura, Hiroaki Ohishi, Kenjiro Shirane, Hiroyuki Sasaki
Nature Communications 15 (2024)

H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation
Naoki Kubo, Poshen B. Chen, Rong Hu, Zhen Ye, Hiroyuki Sasaki, Bing Ren
Molecular Cell (2024)

The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes
Ryuji Uehara, Wan Kin Au Yeung, Keisuke Toriyama, Hiroaki Ohishi, Naoki Kubo, Hidehiro Toh, Isao Suetake, Kenjiro Shirane, Hiroyuki Sasaki
PLOS Genetics 19(8), e1010855 (2023)

Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation
Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, Ren B
Cell Reports 41(6) (2022)

MUNIn—multiple-sample-unifying long-range chromatin Interaction detector: a statistical framework for identifying long-range chromatin interactions from multiple samples
Weifang Liu, Armen Abnousi, Qian Zhang, Naoki Kubo, Joshua S. Martin Beem, Yun Li, Ming Hu, Yuchen Yang
Human Genetics and Genomics Advances 2(3), 100036 (2021)

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum
Yang E. Li, Sebastian Preissl, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Yunjiang Qiu, Olivier Poirion, Bin Li, Joshua Chiou, Hanqing Liu, Antonio Pinto-Duarte, Naoki Kubo, Xiaoyu Yang, Rongxin Fang, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Samantha Kuan, David Gorkin, Kyle J. Gaulton, Yin Shen, Michael Nunn, Eran A. Mukamel, M. Margarita Behrens, Joseph R. Ecker, Bing Ren
Nature 598(7879), 129–136 (2021)

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
Naoki Kubo, Haruhiko Ishii, Xiong Xiong, Simona Bianco, Franz Meitinger, Rong Hu, James D Hocker, Mattia Conte, David Gorkin, Miao Yu, Bin Li, Jesse R Dixon, Ming Hu, Mario Nicodemi, Huimin Zhao, Bing Ren
Nature Structural & Molecular Biology 28(2), 152–161 (2021)

Paired genetic analysis by next-generation sequencing of lung cancer and associated idiopathic pulmonary fibrosis
Kohei Otsubo, Eiji Iwama, Kayo Ijichi, Naoki Kubo, Yasuto Yoneshima, Hiroyuki Inoue, Kentaro Tanaka, Atsushi Osoegawa, Tetsuzo Tagawa, Yoichi Nakanishi, Isamu Okamoto
Cancer Science 111(7), 2482–2487 (2020)

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention
Elena M Pugacheva, Naoki Kubo, Dmitri Loukinov, Md Tajmul, Sungyun Kang, Alexander L Kovalchuk, Alexander V Strunnikov, Gabriel E Zentner, Bing Ren, Victor V Lobanenkov
Proceedings of the National Academy of Sciences of the United States of America 117(4), 2020–2031 (2020)

Joint profiling of DNA methylation and chromatin architecture in single cells
Guoqiang Li, Yaping Liu, Yanxiao Zhang, Naoki Kubo, Miao Yu, Rongxin Fang, Manolis Kellis, Bing Ren
Nature Methods 16(10), 991–993 (2019)

Identification of Genomic Alterations Acquired During Treatment With EGFR-TKIs in Non-small Cell Lung Cancer
Naoki Kubo, Taishi Harada, Yoshimasa Shiraishi, Kaname Nosaki, Noriaki Nakagaki, Masafumi Takeshita, Hiroshi Ouchi, Eiji Iwama, Kentaro Tanaka, Isamu Okamoto, Hiroyuki Sasaki, Yoichi Nakanishi
Anticancer Research 39(2), 671–677 (2019)

Intrinsic and Extrinsic Regulation of PD-L2 Expression in Oncogene-Driven Non-Small Cell Lung Cancer
Daisuke Shibahara, Kentaro Tanaka, Eiji Iwama, Naoki Kubo, Keiichi Ota, Koichi Azuma, Taishi Harada, Jiro Fujita, Yoichi Nakanishi, Isamu Okamoto
Journal of Thoracic Oncology 13(7), 926–937 (2018)

Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline
So Maezawa, Kazuteru Hasegawa, Masashi Yukawa, Naoki Kubo, Akihiko Sakashita, Kris G Alavattam, Ho-Su Sin, Andrey V Kartashov, Hiroyuki Sasaki, Artem Barski, Satoshi H Namekawa
Proceedings of the National Academy of Sciences of the United States of America 115(19), 4957–4962 (2018)

Most T790M mutations are present on the same EGFR allele as activating mutations in patients with non-small cell lung cancer
Noriko Hidaka, Eiji Iwama, Naoki Kubo, Taishi Harada, Kohta Miyawaki, Kentaro Tanaka, Isamu Okamoto, Eishi Baba, Koichi Akashi, Hiroyuki Sasaki, Yoichi Nakanishi
Lung Cancer 108, 75–82 (2017)

Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing
Hidehiro Toh, Kenjiro Shirane, Fumihito Miura, Naoki Kubo, Kenji Ichiyanagi, Katsuhiko Hayashi, Mitinori Saitou, Mikita Suyama, Takashi Ito, Hiroyuki Sasaki
BMC Genomics 18(1), 31 (2017)

DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis
Naoki Kubo, Hidehiro Toh, Kenjiro Shirane, Takayuki Shirakawa, Hisato Kobayashi, Tetsuya Sato, Hidetoshi Sone, Yasuyuki Sato, Shin-ichi Tomizawa, Yoshinori Tsurusaki, Hiroki Shibata, Hirotomo Saitsu, Yutaka Suzuki, Naomichi Matsumoto, Mikita Suyama, Tomohiro Kono, Kazuyuki Ohbo, Hiroyuki Sasaki
BMC Genomics 16(1), 624 (2015)

Interstitial pneumonia during bevacizumab-based chemotherapy for colorectal cancer
Shingo Tamura, Hitoshi Kusaba, Naoki Kubo, Kayo Ijichi, Kenji Tsuchihashi, Masato Komoda, Keita Uchino, Hiroshi Ariyama, Koichi Akashi, Eishi Baba
Medical Oncology 31(3), 856 (2014)

Carboplatin plus paclitaxel in the successful treatment of advanced inflammatory myofibroblastic tumor
Naoki Kubo, Taishi Harada, Satoshi Anai, Kohei Otsubo, Yasuto Yoneshima, Kayo Ijichi, Takaomi Koga, Koichi Takayama, Yoichi Nakanishi
Internal Medicine 51(17), 2399–2401 (2012)

A juvenile case of pulmonary lymphangitic carcinomatosis caused by sigmoid colon cancer with a component of micropapillary carcinoma
Kohei Otsubo, Naoki Kubo, Nobutaka Nakashima, Miiru Izumi, Mari Nakamori, Hiroshi Koto
Internal Medicine 50(20), 2361–2365 (2011)