Research Assistant Professor : Naoki Kubo
Original Research Papers
- Kubo, N., Chen, P.B., Hu, R., Ye, Z., Sasaki, H. & Ren, B.
- H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation.
- Mol. Cell 84, 1-11 (2024).
- Uehara, R., Au Yeung, W.K., Toriyama, K., Ohishi, H., Kubo, N., Toh, H., Suetake, I., Shirane, K. & Sasaki, H.
- The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes.
- PLoS Genet. 19:e1010855 (2023)
Pubmed
- 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.
- Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation.
- Cell Rep. 8, 111630 (2022)
- PubMed
- Li, E.Y., Preissl, S., Hou, X. Zhang, Z., Zhang, K., Qiu, Y., Poirion, O.B., Li, B., Chiou, J., Liu, H., Pinto-Duarte, A., Kubo, N., Yang, X., Fang, R., Wang, X., Han, J.Y., Lucero, J., Yan, Y., Miller, M., Kuan, S., Gorkin, D., Gaulton, K.J., Shen, Y., Nunn, M., Mukamel, E.A., Behrens, M.M., Ecker, J.R. & Ren, B.
- An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum.
- Nature 598, 129-136 (2021)
- PubMed
- Liu, W., Yang, Y., Abnousi, A., Zhang, Q., Kubo, N., Beem, J.S.M., Li, Y. & Hu, M.
- MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples.
- HGG Adv. 2, 100036 (2021)
- PubMed
- Kubo, K., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J.D., Conte, M., Gorkin, D., Yu M., Li, B., Dixon, J.R., Hu, M., Nicodemi, M., Zhao, H. & Ren, B.
- Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.
- Nat. Struct. Mol. Biol. 28, 152-161 (2021)
- PubMed
- Pugacheva, E.M., Kubo, K., Loukinov, D., Tajmul, M., Kang, S., Kovalchuk, A.L., Strunnikov, A.V., Zentner, G.E., Ren, B. & Lobanenkov, V.V.
- CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention.
- Proc. Natl. Acad. Sci. USA 117, 2020-2031 (2020)
- PubMed
- Li, G., Liu, Y., Zhang, Y., Kubo, N., Yu, M., Fang, R., Kellis, M. & Ren, B.
- Joint profiling of DNA methylation and chromatin architecture in single cells.
- Nat. Methods 16, 991-993 (2019)
- PubMed
- Kubo, N., Harada, T., Shiraishi, Y., Nosaki, K., Nakagaki, N., Takeshita, M., Ouchi, H., Iwama, E., Tanaka, K., Okamoto, I., Sasaki, H. & Nakanishi, Y.
- Identification of genomic alterations acquired during treatment with EGFR-TKIs in non-small cell lung cancer.
- Anticancer Res. 39, 671-677 (2019)
- PubMed
- Maezawa, S., Hasegawa, K., Yukawa, M., Kubo, N., Sakashita, A., Alabattam, K.G., Sin, H.S., Kartashov, A.V., Sasaki, H., Barski, A. & Namekawa, S.H.
- Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline.
- Proc. Natl. Acad. Sci. USA 115, 4957-4962 (2018)
- PubMed
- Shibahara, S., Tanaka, K., Iwama, E., Kubo, N., Ota, K., Azuma, K., Harada, T., Fujita, J., Nakanishi, Y. & Okamoto, I.
- Intrinsic and Extrinsic Regulation of PD-L2 Expression in Oncogene-Driven Non-Small Cell Lung Cancer.
- J. Thorac. Oncol. 13, 926-937 (2018)
- PubMed
- Hidaka, N., Iwama, E., Kubo, N., Harada, T., Miyawaki, K., Tanaka, K., Okamoto, I., Baba, E., Akashi, K., Sasaki, H. & Nakanishi, Y.
- Most T790M mutations are present on the same EGFR allele as activating mutations in patients with non-small cell lung cancer.
- Lung Cancer 108, 75-82 (2017)
- PubMed
- Toh, H., Shirane, K., Miura, F., Kubo, N., Ichiyanagi, K., Hayashi, K., Saitou, M., Suyama, M., Ito, T. & Sasaki, H.
- Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.
- BMC Genomics 18, 31 (2017)
- PubMed
- Kubo, N., Toh, H., Shirane, K., Shirakawa, T., Kobayashi, H., Sato, T., Sone, H., Sato, Y., Tomizawa, S., Tsurusaki, Y., Shibata, H., Saitsu, H., Suzuki, Y., Matumoto, N., Suyama, M., Kono, T., Ohbo, K. & Sasaki, H.
- DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis.
- BMC Genomics 16, 624 (2015)
- PubMed
- Tamura, S., Kusaba, H., Kubo, N., Ijichi, K., Tsuchihashi, K., Komoda, M., Uchino, K., Ariyama, H., Akashi, K. & Baba E.
- Interstitial pneumonia during bevacizumab-based chemotherapy for colorectal cancer.
- Med. Oncol. 31, 856 (2014)
- PubMed
- Kubo, N., Harada, T., Anai, S., Otsubo, K., Yoneshima, Y., Ijichi, K., Koga, T., Takayama, K. & Nakanishi, Y.
- Carboplatin plus paclitaxel in the successful treatment of advanced inflammatory myofibroblastic tumor.
- Intern. Med. 51, 2399-2401 (2012)
- PubMed
- Otsubo, K., Kubo, N., Nakashima, N., Izumi, M., Nakamori, M., Koto, H.
- A juvenile case of pulmonary lymphangitic carcinomatosis caused by sigmoid colon cancer with a component of micropapillary carcinoma.
- Intern. Med. 50, 2361-2365 (2011)
- PubMed
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