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Publications

Original Articles

＊ … Corresponding author
† … These authors contributed equally to this work.

2026

  • PIC Tamura, K., Ohnishi, H., Hasebe, K., Fujimura, S., Katsuno, T., Zou, Z., Oki, S., Ohkawa, Y., Morita, S., Omori, K. (2026). Identification of stem cell marker-positive subpopulations in the vocal fold of the larynx through transcriptomic analyses. Nat Commun. Link.

    • In collaboration with Dr. Omori and Dr. Ohnishi (Kyoto Univ), we performed PIC RNA-seq on mouse vocal-fold mucosal epithelium and identified stem-cell markers involved in tissue repair. See the UV-irradiation scene here.

  • †Nduru, D., †Ohta, Y., Nita, A., Niimura, M., Ngurari, S., Moroishi, T. (2026). A YAP/TAZ-CDC6 Axis Initiates and Maintains Malignant Transformation. Cancer Sci. 117(2). 353–363. Link.
  • Joo, K., Matsuoka, R., Kitajima, K., Yashiro, K., Shiose, A., Tominaga, R., Shen, M.M., Oki, S., Meno, C. (2026). Cardiac conduction system malformations in heterotaxy result from dysregulated Pitx2 expression. JCI Insight. 11(6). Link.

2025

  • †Li, H., †Li, S., Kanamori, Y., Liu, S., Moroishi, T. (2025). Auranofin resensitizes ferroptosis-resistant lung cancer cells to ferroptosis inducers. Biochem Biophys Res Commun. 770. 151992. Link.
  • Hayashi, A., Ho, Y.J., Makohon-Moore, A.P., Zucker, A., Hong, J., Umeda, S., Karnoub, E.R., Huang, J., Baez, P., Kappagantula, R., Melchor, J.P., Park, W., O'Reilly, E.M., Socci, N.D., Oki, S., Iacobuzio-Donahue, C.A. (2025). The Noncoding Mutational Landscape of Pancreatic Cancer Reveals Recurrent Somatic Mutations in Enhancer Regions. Cancer Res Commun. 5(10). 1839–1851. Link.
  • PIC Semmy, D., Abe, K., Honda, M., Omori, H., Ogamino, S., Mercurio, T.C., Asakawa, K., Nishimura, E.K., Oki, S., Ohkawa, Y., Ishitani, T. (2025). ER Stress Ire1-Xbp1s Pathway Maintains Youthful Epidermal Basal Layer Through the Regulation of Cell Proliferation. Aging Cell. 24(12). e70258. Link.

    • In collaboration with Dr. Ishitani (Osaka Univ), we performed PIC RNA-seq on epidermal stem cells of the turquoise killifish, a species known for its extremely short lifespan, revealing age-associated expression changes as well as induction of rejuvenation-related genes after drug treatment. See the UV-irradiation scene here.

  • ChIP-Atlas Ikeda, S., Zou, Z., Bono, H., Moriya, Y., Kawashima, S., Katayama, T., Oki, S., Ohta, T. (2025). Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database. Gigascience. 14. Link.
  • PIC Qaqorh, T., Takahashi, Y., Sameshima, K., Otani, K., Yazawa, I., Nishida, Y., Tonai, K., Fujihara, Y., Honda, M., Oki, S., Ohkawa, Y., Thorburn, D.R., Frazier, A.E., Takeda, A., Ikeda, Y., Sakaguchi, H., Watanabe, T., Fukushima, N., Tsukamoto, Y., Makita, N., Yamaguchi, O., Murayama, K., Ohtake, A., Okazaki, Y., Kimura, T., Kato, H., Inoue, H., Matsuoka, K., Takashima, S., Shintani, Y. (2025). Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by spatial and single-cell transcriptomics. Sci Adv. 11(14). eadq1575. Link.

    • In collaboration with Dr. Shintani (National Cerebral and Cardiovascular Center), we performed PIC RNA-seq on stress response marker–positive and –negative cardiomyocytes in mouse myocardium, and revealed reduced expression of genes related to cardiac contraction and cellular respiration under stress response. See the UV-irradiation scene here.

  • ChIP-Atlas Nobusada, T., Yip, C.W., Agrawal, S., Severin, J., Abugessaisa, I., Hasegawa, A., Hon, C.C., Ide, S., Koido, M., Kondo, A., Masuya, H., Oki, S., Tagami, M., Takada, T., Terao, C., Thalhath, N., Walker, S., Yasuzawa, K., Shin, J.W., de Hoon, M.J.L., Carninci, P., Kawaji, H., Kasukawa, T. (2025). Update of the FANTOM web resource: enhancement for studying noncoding genomes. Nucleic Acids Res. 53(D1). D419–D424. Link.
  • Matsuoka, R., Kitajima, K., Nii, T., Zou, Z., Tanaka, K., Joo, K., Ohkawa, Y., Ohga, S., Meno, C. (2025). Hyperglycaemia induces diet-dependent defects of the left-right axis by lowering intracellular pH. Biochim Biophys Acta Mol Basis Dis. 1871(1). 167550. Link.

2024

  • PIC Miyamoto, T., Kuboyama, K., Honda, M., Ohkawa, Y., Oki, S., Sawamoto, K. (2024). High spatial resolution gene expression profiling and characterization of neuroblasts migrating in the peri-injured cortex using photo-isolation chemistry. Front Neurosci. 18. 1504047. Link.

    • In collaboration Dr. Sawamoto (Nagoya City Univ), we performed PIC RNA-seq on neuroblasts migrating toward injured regions in the mouse brain and found updating of TGF-beta signaling. See the UV-irradiation scene here.

  • Cui, M., Yamano, K., Yamamoto, K., Yamamoto-Imoto, H., Minami, S., Yamamoto, T., Matsui, S., Kaminishi, T., Shima, T., Ogura, M., Tsuchiya, M., Nishino, K., Layden, B.T., Kato, H., Ogawa, H., Oki, S., Okada, Y., Isaka, Y., Kosako, H., Matsuda, N., Yoshimori, T., Nakamura, S. (2024). HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence. Proc Natl Acad Sci U S A. 121(2). e2306454120. Link.
  • PIC Katoh, H., Kimura, R., Sekizuka, T., Matsuoka, K., Hosogi, M., Kitai, Y., Akahori, Y., Kato, F., Kataoka, M., Kobayashi, H., Nagata, N., Suzuki, T., Ohkawa, Y., Oki, S., Takeda, M. (2024). Structural and molecular properties of mumps virus inclusion bodies. Sci Adv. 10(49). eadr0359. Link.

    • In collaboration work with Dr. Hiroshi Katoh (The Univ of Tokyo), we performed PIC RNA-seq on inclusion bodies formed during mumps virus infection and found enrichment of RNAs with G4 structures. See the UV-irradiation scene here.

  • PIC Nakamura, Y., Shimada, I.S., Maroofian, R., Falabella, M., Zaki, M.S., Fujimoto, M., Sato, E., Takase, H., Aoki, S., Miyauchi, A., Koshimizu, E., Miyatake, S., Arioka, Y., Honda, M., …, Oki, S., Tsunoda, T., Pitceathly, R.D.S., Taketomi, Y., Houlden, H., Murakami, M., Kato, Y., Saitoh, S. (2024). Biallelic null variants in PNPLA8 cause microcephaly by reducing the number of basal radial glia. Brain. 147(11). 3949–3967. Link.

    • In collaboration with Dr. Shinji Saitoh (Nagoya City Univ), we performed PIC RNA-seq on brain organoids from a microcephaly model carrying pathogenic variants. By comparing gene expression restricted to the ventricular zone, we found downregulation of genes involved in basal radial glia formation. See the UV-irradiation scene here.

  • ChIP-Atlas Zou, Z., Ohta, T., Oki, S.* (2024). ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. Nucleic Acids Res. 52(W1). W45–W53. Link.

2023

  • ChIP-Atlas Zou, Z., Yoshimura, Y., Yamanishi, Y., Oki, S.* (2023). Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data. Epigenetics Chromatin. 16(1). 34. Link.
  • ChIP-Atlas Miyazawa, K., Ito, K., Ito, M., Zou, Z., Kubota, M., Nomura, S., Matsunaga, H., Koyama, S., Ieki, H., Akiyama, M., Koike, Y., Kurosawa, R., Yoshida, H., Ozaki, K., Onouchi, Y., BioBank Japan Project, Takahashi, A., Matsuda, K., Murakami, Y., Aburatani, H., Kubo, M., Momozawa, Y., Terao, C., Oki, S., Akazawa, H., Kamatani, Y., Komuro, I. (2023). Cross-ancestry genome-wide analysis of atrial fibrillation unveils disease biology and enables cardioembolic risk prediction. Nat Genet. 55(2). 187–197. Link.

2022

  • ChIP-Atlas Zou, Z., Ohta, T., Miura, F., Oki, S.* (2022). ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Res. 50(W1). W175–W182. Link.
  • Hirata, H., Kamohara, A., Murayama, M., Nishioka, K., Honda, H., Urano, Y., Soejima, H., Oki, S., Kukita, T., Kawano, S., Mawatari, M., Kukita, A. (2022). A novel role of helix-loop-helix transcriptional factor Bhlhe40 in osteoclast activation. J Cell Physiol. 237(10). 3912–3926. Link.
  • ChIP-Atlas Eguchi, R., Hamano, M., Iwata, M., Nakamura, T., Oki, S., Yamanishi, Y. (2022). TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. Bioinformatics. 38(10). 2839–2846. Link.
  • ChIP-Atlas Yamamoto-Imoto, H., Minami, S., Shioda, T., Yamashita, Y., Sakai, S., Maeda, S., Yamamoto, T., Oki, S., Takashima, M., Yamamuro, T., Yanagawa, K., Edahiro, R., Iwatani, M., So, M., Tokumura, A., Abe, T., Imamura, R., Nonomura, N., Okada, Y., Ayer, D.E., Ogawa, H., Hara, E., Takabatake, Y., Isaka, Y., Nakamura, S., Yoshimori, T. (2022). Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis. Cell Rep. 38(9). 110444. Link.
  • PIC Honda, M., Kimura, R., Harada, A., Maehara, K., Tanaka, K., Ohkawa, Y.*, Oki, S.* (2022). Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections. STAR Protoc. 3(2). 101346. Link.
  • Kimura, R., Inoue, U.Y., Kikkawa, T., Tatehana, M., Morimoto, Y., Inada, H., Oki, S., Inoue, T., Osumi, N. (2022). Detection of REST expression in the testis using epitope-tag knock-in mice generated by genome editing. Dev Dyn. 251(3). 525–535. Link.

2021

  • PIC †Honda, M., †Oki, S.*, Kimura, R., Harada, A., Maehara, K., Tanaka, K., Meno, C., Ohkawa, Y.* (2021). High-depth spatial transcriptome analysis by photo-isolation chemistry. Nat Commun. 12(1). 4416. Link.
  • Pecori, F., Yokota, I., Hanamatsu, H., Miura, T., Ogura, C., Ota, H., Furukawa, J.I., Oki, S., Yamamoto, K., Yoshie, O., Nishihara, S. (2021). A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition. Sci Rep. 11(1). 1276. Link.
  • Yoshizaki, K., Kimura, R., Kobayashi, H., Oki, S., Kikkawa, T., Mai, L., Koike, K., Mochizuki, K., Inada, H., Matsui, Y., Kono, T., Osumi, N. (2021). Paternal age affects offspring via an epigenetic mechanism involving REST/NRSF. EMBO Rep. 22(2). e51524. Link.

2020

  • Hirayama, M., Wei, F.Y., Chujo, T., Oki, S., Yakita, M., Kobayashi, D., Araki, N., Takahashi, N., Yoshida, R., Nakayama, H., Tomizawa, K. (2020). FTO Demethylates Cyclin D1 mRNA and Controls Cell-Cycle Progression. Cell Rep. 31(1). 107464. Link.
  • Miyamoto, Y., Sasaki, M., Miyata, H., Monobe, Y., Nagai, M., Otani, M., Whiley, P.A.F., Morohoshi, A., Oki, S., Matsuda, J., Akagi, K.I., Adachi, J., Okabe, M., Ikawa, M., Yoneda, Y., Loveland, K.L., Oka, M. (2020). Genetic loss of importin α4 causes abnormal sperm morphology and impacts on male fertility in mouse. FASEB J. 34(12). 16224–16242. Link.
  • Suzuki, J., Inada, H., Han, C., Kim, M.J., Kimura, R., Takata, Y., Honkura, Y., Owada, Y., Kawase, T., Katori, Y., Someya, S., Osumi, N. (2020). "Passenger gene" problem in transgenic C57BL/6 mice used in hearing research. Neurosci Res. 158. 6–15. Link.
  • Nakagawa, T., Hattori, S., Nobuta, R., Kimura, R., Nakagawa, M., Matsumoto, M., Nagasawa, Y., Funayama, R., Miyakawa, T., Inada, T., Osumi, N., Nakayama, K.I., Nakayama, K. (2020). The Autism-Related Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression. iScience. 23(4). 101030. Link.
  • Tatehana, M., Kimura, R., Mochizuki, K., Inada, H., Osumi, N. (2020). Comprehensive histochemical profiles of histone modification in male germline cells during meiosis and spermiogenesis: Comparison of young and aged testes in mice. PLoS One. 15(4). e0230930. Link.
  • ChIP-Atlas Kaminuma, E., Baba, Y., Mochizuki, M., Matsumoto, H., Ozaki, H., Okayama, T., Kato, T., Oki, S., Fujisawa, T., Nakamura, Y., Arita, M., Ogasawara, O., Kashima, H., Takagi, T. (2020). DDBJ Data Analysis Challenge: a machine learning competition to predict Arabidopsis chromatin feature annotations from DNA sequences. Genes Genet Syst. 95(1). 43–50. Link.

Before 2019

  • Wu, Z., Rao, Y., Zhang, S., Kim, E.J., Oki, S., Harada, H., Cheung, M., Jung, H.S. (2019). Cis-control of Six1 expression in neural crest cells during craniofacial development. Dev Dyn. 248(12). 1264–1272. Link.
  • ChIP-Atlas Lizio, M., Abugessaisa, I., Noguchi, S., Kondo, A., Hasegawa, A., Hon, C.C., de Hoon, M., Severin, J., Oki, S., Hayashizaki, Y., Carninci, P., Kasukawa, T., Kawaji, H. (2019). Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. Nucleic Acids Res. 47(D1). D752–D758. Link.
  • ChIP-Atlas Oki, S.*, Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., Meno, C. (2018). ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. EMBO Rep. 19(12). Link.
  • Mochizuki, K., Hayashi, Y., Sekinaka, T., Otsuka, K., Ito-Matsuoka, Y., Kobayashi, H., Oki, S., Takehara, A., Kono, T., Osumi, N., Matsui, Y. (2018). Repression of Somatic Genes by Selective Recruitment of HDAC3 by BLIMP1 Is Essential for Mouse Primordial Germ Cell Fate Determination. Cell Rep. 24(10). 2682–2693.e6. Link.
  • Anan, K., Hino, S., Shimizu, N., Sakamoto, A., Nagaoka, K., Takase, R., Kohrogi, K., Araki, H., Hino, Y., Usuki, S., Oki, S., Tanaka, H., Nakamura, K., Endo, F., Nakao, M. (2018). LSD1 mediates metabolic reprogramming by glucocorticoids during myogenic differentiation. Nucleic Acids Res. 46(11). 5441–5454. Link.
  • Yoshizaki, K., Koike, K., Kimura, R., Osumi, N. (2017). Early postnatal vocalizations predict sociability and spatial memory in C57BL/6J mice: Individual differences in behavioral traits emerge early in development. PLoS One. 12(11). e0186798. Link.
  • Semba, Y., Harada, A., Maehara, K., Oki, S., Meno, C., Ueda, J., Yamagata, K., Suzuki, A., Onimaru, M., Nogami, J., Okada, S., Akashi, K., Ohkawa, Y. (2017). Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells. Nucleic Acids Res. 45(15). 8758–8772. Link.
  • Ohshima, K., Nojima, S., Tahara, S., Kurashige, M., Hori, Y., Hagiwara, K., Okuzaki, D., Oki, S., Wada, N., Ikeda, J.I., Kanai, Y., Morii, E. (2017). Argininosuccinate Synthase 1-Deficiency Enhances the Cell Sensitivity to Arginine through Decreased DEPTOR Expression in Endometrial Cancer. Sci Rep. 7. 45504. Link.
  • Matsuda, K., Mikami, T., Oki, S., Iida, H., Andrabi, M., Boss, J.M., Yamaguchi, K., Shigenobu, S., Kondoh, H. (2017). ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network. Development. 144(11). 1948–1958. Link.
  • Honda, M., Nakashima, K., Katada, S. (2017). PRMT1 regulates astrocytic differentiation of embryonic neural stem/precursor cells. J Neurochem. 142(6). 901–907. Link.
  • Yoshizaki, K., Furuse, T., Kimura, R., Tucci, V., Kaneda, H., Wakana, S., Osumi, N. (2016). Paternal Aging Affects Behavior in Pax6 Mutant Mice: A Gene/Environment Interaction in Understanding Neurodevelopmental Disorders. PLoS One. 11(11). e0166665. Link.
  • Hayashi, M., Maehara, K., Harada, A., Semba, Y., Kudo, K., Takahashi, H., Oki, S., Meno, C., Ichiyanagi, K., Akashi, K., Ohkawa, Y. (2016). Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2. J Cell Biochem. 117(3). 780–92. Link.
  • Kimura, R., Yoshizaki, K., Osumi, N. (2015). Dynamic expression patterns of Pax6 during spermatogenesis in the mouse. J Anat. 227(1). 1–9. Link.
  • Hachisuga, M., Oki, S., Kitajima, K., Ikuta, S., Sumi, T., Kato, K., Wake, N., Meno, C. (2015). Hyperglycemia impairs left-right axis formation and thereby disturbs heart morphogenesis in mouse embryos. Proc Natl Acad Sci U S A. 112(38). E5300–7. Link.
  • Shiratori, H., Yashiro, K., Iwai, N., Oki, S., Minegishi, K., Ikawa, Y., Kanata, K., Hamada, H. (2014). Self-regulated left-right asymmetric expression of Pitx2c in the developing mouse limb. Dev Biol. 395(2). 331–41. Link.
  • Suzuki, J., Oshima, T., Yoshida, N., Kimura, R., Takata, Y., Owada, Y., Kobayashi, T., Katori, Y., Osumi, N. (2014). Preservation of cochlear function in Fabp3 (H-Fabp) knockout mice. Neurosci Res. 81-82. 64–8. Link.
  • Oki, S., Maehara, K., Ohkawa, Y., Meno, C. (2014). SraTailor: graphical user interface software for processing and visualizing ChIP-seq data. Genes Cells. 19(12). 919–26. Link.
  • Kitajima, K., Oki, S., Ohkawa, Y., Sumi, T., Meno, C. (2013). Wnt signaling regulates left-right axis formation in the node of mouse embryos. Dev Biol. 380(2). 222–32. Link.
  • Guo, N., Yoshizaki, K., Kimura, R., Suto, F., Yanagawa, Y., Osumi, N. (2013). A sensitive period for GABAergic interneurons in the dentate gyrus in modulating sensorimotor gating. J Neurosci. 33(15). 6691–704. Link.
  • Sumi, T., Oki, S., Kitajima, K., Meno, C. (2013). Epiblast ground state is controlled by canonical Wnt/β-catenin signaling in the postimplantation mouse embryo and epiblast stem cells. PLoS One. 8(5). e63378. Link.
  • Miki, R., Yoshida, T., Murata, K., Oki, S., Kume, K., Kume, S. (2012). Fate maps of ventral and dorsal pancreatic progenitor cells in early somite stage mouse embryos. Mech Dev. 128(11-12). 597–609. Link.
  • Noda, T., Oki, S., Kitajima, K., Harada, T., Komune, S., Meno, C. (2012). Restriction of Wnt signaling in the dorsal otocyst determines semicircular canal formation in the mouse embryo. Dev Biol. 362(1). 83–93. Link.
  • Oki, S., Kitajima, K., Meno, C. (2010). Dissecting the role of Fgf signaling during gastrulation and left-right axis formation in mouse embryos using chemical inhibitors. Dev Dyn. 239(6). 1768–78. Link.
  • Oki, S., Kitajima, K., Marques, S., Belo, J.A., Yokoyama, T., Hamada, H., Meno, C. (2009). Reversal of left-right asymmetry induced by aberrant Nodal signaling in the node of mouse embryos. Development. 136(23). 3917–25. Link.
  • Oki, S., Hashimoto, R., Okui, Y., Shen, M.M., Mekada, E., Otani, H., Saijoh, Y., Hamada, H. (2007). Sulfated glycosaminoglycans are necessary for Nodal signal transmission from the node to the left lateral plate in the mouse embryo. Development. 134(21). 3893–904. Link.
  • Saijoh, Y., Oki, S., Tanaka, C., Nakamura, T., Adachi, H., Yan, Y.T., Shen, M.M., Hamada, H. (2005). Two nodal-responsive enhancers control left-right asymmetric expression of Nodal. Dev Dyn. 232(4). 1031–6. Link.
  • Saijoh, Y., Oki, S., Ohishi, S., Hamada, H. (2003). Left-right patterning of the mouse lateral plate requires nodal produced in the node. Dev Biol. 256(1). 160–72. Link.
  • Todoriki, M., Oki, S., Matsuyama, S., Ko-Mitamura, E.P., Urabe, I., Yomo, T. (2002). An observation of the initial stage towards a symbiotic relationship. Biosystems. 65(2-3). 105–12. Link.

Reviews & Books

  • 鄒 兆南 (2025). 生物情報–DNA・RNAデータ–エピゲノム. 理論生物学事典.
  • 鄒 兆南, 沖 真弥 (2025). ChIP-Atlas: 多層的エピゲノム情報の解析基盤. 実験医学増刊. 43(20). 3244.
  • 鄒 兆南, 沖 真弥 (2024). ChIP-Atlas 3.0: 世界最大のエピゲノムデータ解析インフラ. 実験医学. 42(16). 2554.
  • 鄒 兆南, 沖 真弥 (2023). ChIP-Atlas 〜転写制御ランドスケープの歩き方〜. JSBi bioinform rev. 4(1). 1–9. Link.
  • 鄒 兆南, 沖 真弥 (2022). ChIP-Atlas 2.0 ─ 転写制御機構＆エピゲノムランドスケープを可視化する. 実験医学増刊. 40(17). 2848–2851. Link.
  • 本田瑞季, 沖 真弥 (2022). 空間トランスクリプトミクス. 生物工学会誌. 100(6). 295–297. Link.
  • 本田瑞季, 沖 真弥 (2021). Photo-Isolation Chemistry：光照射による高解像度かつ高感度なトランスクリプトーム技術. 実験医学. 39(14). Link.
  • 沖 真弥, 大川恭行 (2021). 概論―空間トランスクリプトーム技術の最前線. 実験医学. 39(14). Link.
  • Oki, S., Ohta, T. (2021). ChIP-Atlas. Practical Guide to Life Science Databases.
  • 沖 真弥, 本田瑞季 (2020). 局所的かつ高深度の空間トランスクリプトーム技術：Photo-Isolation Chemistry. 実験医学別冊: クロマチン解析実践プロトコール. 247–250.
  • 木村龍一, 吉崎嘉一, 大隅典子 (2020). エピゲノムの経世代影響. 遺伝子医学. 10(1). 68–73.
  • 舘花美沙子, 木村龍一, 大隅典子 (2020). 老化による精子の変化と発達障害発症リスク. 実験医学. 38(6). 932–936.
  • 沖 真弥, 大田達郎 (2019). ChIP-Atlas：公共ChIP-seqデータを統合的に活用するためのウェブサービス. The Lung. 27. 243–249.
  • 沖 真弥, 大田達郎 (2019). ChIP-Atlas：既報のChIP-seqデータをフル活用するためのウェブサービス. 実験医学. 37(16). 2760–2763. Link.
  • 木村龍一, 稲田仁, 大隅典子 (2019). 自閉スペクトラム症発症リスクとエピジェネティクス. 医学のあゆみ. 268(3). 180–183.
  • Honda, M., Nakashima, K., Katada, S. (2018). Epigenetic Regulation of Human Neural Stem Cell Differentiation. Results Probl Cell Differ. 66. 125–136.
  • Kimura, R., Yoshizaki, K., Osumi, N. (2018). Risk of Neurodevelopmental Disease by Paternal Aging: A Possible Influence of Epigenetic Alteration in Sperm. Adv Exp Med Biol. 1012. 75–81.
  • 大隅典子, 木村龍一 (2017). 父加齢・エピゲノム・精神疾患. Medical Science Digest. 43(12). 612–615.
  • 大隅典子, 木村龍一 (2016). 精子形成過程におけるエピゲノム修飾と次世代への影響. BIO Clinica. 31(5). 470–474.
  • 沖 真弥 (2014). SraTailor: 誰でも使えるChIP-seqデータの可視化ツール. 実験医学. 32(19). 3101–3106.
  • 本田瑞季, 堅田明子, 中島欽一 (2014). エピジェネティクスの基礎（エピジェネティクスを制御する分子機構）. アレルギー・免疫. 21(12). 13–19.
  • Sakayori, N., Kimura, R., Osumi, N (2013). Impact of Lipid Nutrition on Neural Stem/Progenitor Cells. Stem Cells Int. 2013.
  • 沖 真弥, 目野主税 (2010). マウス初期発生における硫酸化グリコサミノグリカンの役割. 福岡医学雑誌. 101(8). 157–164.
  • 沖 真弥, 目野主税, 濱田博司 (2008). 左右決定におけるNodalシグナル. 細胞工学. 27(6).