Journal, peer-reviewed

Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform
Luis Augusto Eijy Nagai, Seohyun Lee, Ryuichiro Nakato STAR Protocols (2024), vol 5, issue 1. STAR Protocols PUBMED

Modeling embryo-endometrial interface recapitulating human embryo implantation
Shun Shibata, Shun Endo, Luis A E Nagai, Eri H Kobayashi, Akira Oike, Norio Kobayashi, Akane Kitamura, Takeshi Hori, Yuji Nashimoto, Ryuichiro Nakato, Hirotaka Hamada, Hirokazu Kaji, Chie Kikutake, Mikita Suyama, Masatoshi Saito, Nobuo Yaegashi, Hiroaki Okae, Takahiro Arima
Science Advances (2024), vol 10, issue 8. Science Advances PUBMED

FXYD3 functionally demarcates an ancestral breast cancer stem cell subpopulation with features of drug-tolerant persisters
Li M, Nishimura T, Takeuchi Y, Hongu T, Wang Y, Shiokawa D, Wang K, Hirose H, Sasahara A, Yano M, Ishikawa S, Inokuchi M, Ota T, Tanabe M, Tada K, Akiyama T, Cheng X, Liu C, Yamashita T, Sugano S, Uchida Y, Chiba T, Asahara H, Nakagawa M, Sato S, Miyagi Y, Shimamura T, Nagai LAE, Kanai A, Katoh M, Nomura S, Nakato R, Suzuki Y, Tojo A, Voon D, Ogawa S, Okamoto K, Foukakis T, Gotoh N
J. of Clin. Invest.(2023), vol 133, issue 22. JClinInvest PUBMED

Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
Ryuichiro Nakato, Toyonori Sakata, Jiankang Wang, Luis Augusto Eijy Nagai, Yuya Nagaoka, Gina Miku Oba, Masashige Bando and Katsuhiko Shirahige
Nature Communications (2023), v.14, issue 1. Nature Communications PUBMED

Nutrient-driven dedifferentiation of enteroendocrine cells promotes adaptive intestinal growth in Drosophila
Hiroki Nagai, Luis Augusto Eijy Nagai, Sohei Tasaki, Ryuichiro Nakato, Daiki Umetsu, Erina Kuranaga, Masayuki Miura, Yuichiro Nakajima
Developmental Cell (2023), ISSN 1534-5807. Developmental Cel PUBMED

Broad heterochromatic domains open in gonocyte development prior to de novo DNA methylation
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
Developmental Cell (2019), S1534-5807(19)30629-X. Developmental Cell PUBMED

Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma
Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai
BMC Medical Genomics (2019), 11 (Suppl 7):127. BMC Medical Genomics PUBMED

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species
Leyi Wei, Shasha Luan, Luis Augusto Eijy Nagai, Ran Su, Quan Zou
Bioinformatics (2019), v. 35, p. 1326-1333. Bioinformatics PUBMED

Articles, commentaries

Towards an increased awareness on the importance of Computational Reproducibility in Biological Sciences in Latin America
Renato Augusto Corrêa dos Santos, Alicia Lie de Melo, Maryam Chaib, Luis Augusto Eijy Nagai, Luisa Matiz, Tulio Campos, Raissa Melo de Sousa
ecrLife, Aug. 31, 2023. [ecrLife]

Preprints, submitted articles

Distal regulatory sequences contribute to diversity in brain oxytocin receptor expression patterns and social behavior
Qi Zhang, Luis Augusto Eijy Nagai, Mina Tsukamoto, Lenin C. Kandasamy, Kiyoshi Inoue, Maria F. Pires, Minsoo Shin, Yutaro Nagasawa, Tsetsegee Sambuu, Sonoko Ogawa, Kenta Nakai, Shigeyoshi Itohara, Larry J Young
Preprint (2023), [bioRxiv]

Nutrient-driven dedifferentiation of enteroendocrine cells promotes adaptive intestinal growth
Hiroki Nagai, Luis Augusto Eijy Nagai, Sohei Tasaki, Ryuichiro Nakato, Daiki Umetsu, Erina Kuranaga, Masayuki Miura, Yuichiro Nakajima
Preprint (2023), [bioRxiv]

Context-dependent 3D genome regulation by cohesin and related factors
Ryuichiro Nakato, Toyonori Sakata, Jiankang Wang, Luis Augusto Eijy Nagai, Gina Miku Oba, Masashige Bando, Katsuhiko Shirahige Preprint (2022), [bioRxiv]

Talks

Improved community detection through signed graphs in single-cell co-expression networks
Luis Augusto Eijy Nagai and Ryuichiro Nakato
ISMB2024, 593, Jul14, 2024. Montreal, Canada

Does “Volized” mouse become more social? -Transcriptional lability of brain oxytocin receptor (Oxtr) generates diversity in brain OXTR distribution and social behaviors
Qi Zhang, Luis AE Nagai, Itohara Shigeyoshi, Larry Young
MBSJ2023, 2AS-09-02, Dec7, 2023. Kobe, Japan

Navigating Cellular Complexity: Unraveling Gene Interactions in scRNA-seq with Signed Graphs and Network Analysis
Luis Augusto Eijy Nagai and Ryuichiro Nakato
IIBMP2023, WS-1, Sep. 7-9, 2023, Chiba, Japan

Towards understanding the orchestration of single-cell RNA-seq analysis
Luis Augusto Eijy Nagai
細胞ダイバース第4回若手ワークショップ(The 4th Cell Diversity Workshop), O-11, Jan. 26-28, 2022, (Online), Japan

Genome-wide chromatin structural analysis reveals inter-chromosomal translocations in B-cell lymphoma
Luis Augusto Eijy Nagai, Sung-Joon Park, Kenta Nakai
The 42nd Annual Meeting of the Molecular Biology Society of Japan, 1P-0002, Dec. 3-6, 2019, Fukuoka, Japan

Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma
Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai
IIBMP2019, oral (0-3) and poster (P-1), Sep.9-11, 2019, Tokyo, Japan

マウス胎仔期生殖細胞におけるクロマチンリプログラミング
山中総一郎, 西原秀典, 藤英博, Luis Augusto Eijy Nagai, 橋本浩介, 朴聖俊, 渋谷あおい, Ana Maria Suzuki, 田中悠二郎, 中井謙太, Piero Carninci, 佐々木裕之, 塩見春彦
第21回日本RNA学会年会, P-45, Jul.17-19, 2019, Tokyo, Japan

Genome-wide chromatin structural analysis reveals inter-chromosomal translocations in B-cell lymphoma cell line
Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai
The Biology of Genomes, P177, May 7-11, 2019, Cold Spring Harbor Laboratory, NY, USA

Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma
Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai
The 17th International Conference On BioInformatics (InCoB-2018), Sep. 26-28, 2018, New Delhi, India [Best oral presentation award]

Three-Dimensional Chromatin Structures Coordinate with Gene Expression Levels and Reveals Inter-chromosomal Interactions in B-Cell Lymphoma
Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai
生命医薬情報学連合大会 (IIBMP2018), P-31 (oral presentation), 2018年9月19日～21日, 鶴岡、日本