Luis Augusto Eijy Nagai

Computational biologist, bioinformatician. biotechnologist, data scientist.

https://en-coding.github.io/ | My linkedin page | nagai@iqb.u-tokyo.ac.jp | @eijynagai

Current positions

Research Associate / Assistant Professor (助教)

Laboratory of Computational Genomics (Prof. Ryuichiro Nakato), Institute for Quantitative Biosciences, University of Tokyo, Japan.

Visiting Researcher (Sabbatical)

Research Group of Data Science of Systems Biology (Prof. Markus List), School of Life Sciences, Technical University of Munich, Germany.

Education

2015 - 2019 Doctor of Philosophy, Computational Biology and Medical Sciences

Grad. School of Frontier Sciences. The University of Tokyo. Chiba, Japan.
Supervisor: Prof. Kenta Nakai
MEXT Scholarship Award

2013 - 2015 Master of Science, Genetics and Molecular Biology

Biology Institute, University of Campinas, SP, Brazil.
Supervisor: Prof. Paula R. Kuser Falcao
Co-supervisor: Dr. Adhemar Zerlotini Neto
CNPq Scholarship Award

2009 - 2012 Bachelor of Science, Biotechnology

Federal University of Sao Carlos, SP, Brazil.

Research interest

Data-driven methods for functional analyses using large-scale biological datasets.
Focus on Next Generation Sequencing (NGS) datasets in single-cell transcriptomics and epigenetics (scRNA-seq and scATAC-seq), 3D chromatin structures (Hi-C), RNA-seq, and ChIP-Seq.
Network biology and network-based analysis

Competitive Research Fundings

2024 - 2026 Grant-in-Aid for Young Scientists (科研費若手) Developing Algorithms for Identifying Gene Modules in Single-Cell RNA-Seq Using Signed Graphs 24K18100

2024 - 2025 UTokyo Global Activity Support Program for Young Researchers (1 year sabbatical)

Publications

Journals

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

2024 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.
Modeling embryo-endometrial interface recapitulating human embryo implantation.
Sci. Adv. (2024), vol 10, issue 8. [SciAdv][PUBMED]

2023 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.
FXYD3 functionally demarcates an ancestral breast cancer stem cell subpopulation with features of drug-tolerant persisters.
J. of Clin. Invest. (2023), vol 133, issue 22. [JClinInvest][PUBMED]

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

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

2019 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 (2019), S1534-5807(19)30629-X. [Dev.Cell] [PUBMED]

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

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

Theses

2019 Luis Augusto Eijy Nagai. A Computational Analysis of the Impact of 3D Chromosome Organization on its Gene Expression Regulation. PhD Thesis, University of Tokyo.

2015 Luis Augusto Eijy Nagai. Identification of genes involved in meat tenderness in Angus and Nellore breeds using differential expression analysis. Master Dissertation, University of Campinas.

Articles, commentaries

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

Preprints

2023 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.
Distal regulatory sequences contribute to diversity in brain oxytocin receptor expression patterns and social behavior.
[bioRxiv], 2023.

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

Presentations

Talks

2024 Luis Augusto Eijy Nagai and Ryuichiro Nakato.
Improved community detection through signed graphs in single-cell co-expression networks.
ISMB2024, 593, July14, 2024. Montreal, Canada.

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

2023 Luis Augusto Eijy Nagai and Ryuichiro Nakato.
Navigating Cellular Complexity: Unraveling Gene Interactions in scRNA-seq with Signed Graphs and Network Analysis.
IIBMP2023, WS-1, Sep7, 2023. Chiba, Japan.

2022 Luis Augusto Eijy Nagai, Eiko Saijou, Ryuichiro Nakato.
Central genes in Cornelia de Lange Syndrome mouse cell lines using single-cell gene networks (Lightning Talk).
The 45th Annual Meeting of the Molecular Biology Society of Japan, 2SP-22-07, Dec1, 2022. Chiba, Japan.

2022 Hiroki Nagai, Luis Augusto Eijy Nagai, Ryuichiro Nakato, Masayuki Miura1, Yu-ichiro Nakajima.
Dedifferentiation of enteroendocrine cells promotes intestinal adaptation to nutrient environment.
The 45th Annual Meeting of the Molecular Biology Society of Japan, 1PW-08-5, Nov. 30, 2022. Chiba, Japan.

2022 Hiroki Nagai, Luis Augusto Eijy Nagai, Ryuichiro Nakato, Masayuki Miura1, Yu-ichiro Nakajima.
Enteroendocrine cell dedifferentiates into intestinal stem cell upon nutrient fluctuation.
74th Annual Meeting of the Japanese Society for Cell Biology (JSCB), 1LH05, Jun. 28, 2022. Tokyo, Japan.

2022 Luis Augusto Eijy Nagai.
Towards understanding the orchestration of single-cell RNA-seq analysis.
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.

2021 Hiroki Nagai, Luis Augusto Eijy Nagai, Ryuichiro Nakato and Yuichiro Nakajima.
Nutrient-dependent dedifferentiation of Drosophila enteroendocrine cells dissected by single cell analyses.
The 44th Annual Meeting of the Molecular Biology Society of Japan, 2AW-11-3, Dec. 1-3, 2021, Yokohama, Japan.

2021 Eiko Saijou, Tohru Itoh, Atsushi Miyajima, Luis Augusto Eijy Nagai and Ryuichiro Nakato.
Integrative study of hepatic fibrosis resolution mechanisms using single-cell RNA sequencing.
The 44th Annual Meeting of the Molecular Biology Society of Japan, 2AW-11-4, Dec. 1-3, 2021, Yokohama, Japan.

2019 Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai.
Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma.
IBMP2019, O-3 (oral), Sep.9-11, 2019, Tokyo, Japan.

2018 Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai.
Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma.
The 17th International Conference On BioInformatics (InCoB2018), Sep. 26-28, 2018, New Delhi, India. [Best oral presentation award].

2018 Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai.
Three-Dimensional Chromatin Structures Coordinate with Gene Expression Levels and Reveals Inter-chromosomal Interactions in B-Cell Lymphoma.
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.

Poster

2024 Luis Augusto Eijy Nagai, Ryuichiro Nakato.
The Role of Negative Links in Single-Cell Gene Networks with Louvain Signed.
APBJC2024, p387, Oct23, Okinawa, Japan.

2023 Luis Augusto Eijy Nagai, Ryuichiro Nakato.
Unveiling Cellular Heterogeneity with Signed Graphs: A Novel Approach for Single-Cell RNA-seq Data Analysis.
MBSJ2023, 3P-158, Dec8, 2023. Kobe, Japan.

2023 Luis Augusto Eijy Nagai, Ryuichiro Nakato.
ShortCake: A Dockerized Platform for Scalable Single-Cell Analysis.
MBSJ2023, 3P-159, Dec8, 2023. Kobe, Japan.

2023 Qi Zhang, Luis AE Nagai, Itohara Shigeyoshi, Larry Young.
Does “Volized” mouse become more social? -Transcriptional lability of brain oxytocin receptor (Oxtr) generates diversity in brain OXTR disribution and social behaviors.
MBSJ2023, 2P-707, Dec7, 2023. Kobe, Japan.

2023 Luis Augusto Eijy Nagai and Ryuichiro Nakato.
Leveraging signed graphs and network analysis for comprehensive exploration of single-cell technologies.
CEEHRC2023, ID123, Nov13-16, 2023. Banff, Canada.

2023 Shun Shibata, Luis A.E. Nagai, Akira Oike, Eri H Kobayashi, Norio Kobayashi, Ryuichiro Nakato, Mikita Suyama, Hiroaki Okae, Takahiro Arima.
Modeling Embryo-Endometrium Interface Recapitulating Human Embryo Implantation.
CEEHRC2023, ID110, Nov13-16, 2023. Banff, Canada.

2023 Alícia Lie de Melo, Túlio Campos, Alexandre Colato, Elaine Dias, Hylio Lagana Fernandes, Luis Augusto Eijy Nagai, João Vitor Leite Novoletti, Laura Setten, Raissa Melo de Sousa, Luciano Moura Beserra de Sousa, Thayana Vieira Tavares, Davi Salles Xavier, Renato Augusto Corrêa dos Santos.
An inclusive strategy for increasing awareness on computational reproducibility in Life Sciences in Brazil.
The 19th International Congress of the Brazilian Association of Bioinformatics and Computational Biology (X-meeting2023), Jun. 13-16, 2023, Curitiba, Brazil.

2022 Luis Augusto Eijy Nagai, Eiko Saijou, Ryuichiro Nakato.
Central genes in Cornelia de Lange Syndrome mouse cell lines using single-cell gene networks The 45th Annual Meeting of the Molecular Biology Society of Japan, 2P-130, Nov30-Dec2, 2022, Chiba, Japan.

2022 Luis Augusto Eijy Nagai, Eiko Saijou, Ryuichiro Nakato.
A computational method to extract central genes in Cornelia de Lange Syndrome-like cell line obtained from single-cell co-dependency networks.
IIBMP2022, P-81, Sep13-15, Osaka, Japan.

2021 Luis Augusto Eijy Nagai, Hiroki Nagai, Yuichiro Nakajima and Ryuichiro Nakato.
Single-cell RNA trajectory to infer dedifferentiation in Drosophila midgut.
The 44th Annual Meeting of the Molecular Biology Society of Japan, 3P-0707, Dec. 1-3, 2021, Yokohama, Japan.

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

2019 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.
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.
第21回日本RNA学会年会, P-45, Jul.17-19, 2019, Tokyo, Japan.

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

Recognitions: scholarships and awards

2024 - 2025 UTokyo Global Activity Support Program for Young Researcher (Travel + stipend).

2015 - 2018 Japanese Government (MEXT) Scholarship (PhD tuition fees + enhanced stipend).

2015 - 2015 Japanese Government (MEXT) Scholarship (Research student tuition fees + stipend).

2011 - 2012 National Council for Scientific and Technological Scholarship (stipend).

Professional activities

Professional activities: teaching and tutoring

2023-03-(06-22) Bioinformatics Analysis and Visualisation of Medical Genomics Data (Course ID: 5633).
Karolinska Institutet and University of Tokyo Joint Course 2023 (first).
Seminars and hands-on practice sessions on bioinformatics analysis.

Professional activities: seminar presentations

2022-12-14 Databases of single-cell gene expression Seminar for 生命科学の最前線 (Grad. School of Frontier Sciences - UTokyo)

Professional activities: manuscript review

2022 - current Ad hoc review for Frontier in Genetics.

2021 - current Ad hoc review for MDPI journals: Cells, International Journal of Molecular Sciences, Genes, Applied Sciences, Healthcare.

Professional activities: memberships

2023 - current Member at the Japanese Society for Epigenetics (JSEpi).

2018 - current Member at the International Society for Computational Biology (ISCB).

2018 - current Member at the Japanese Society for Bioinformatics (JSBi).

2018 - current Member at the Molecular Biology Society of Japan (MBSJ).

Professional activities: resident advisor (RA)

2022 - current In-house advisor at the University of Tokyo - Komaba International Lodge Annex.

Prior positions

2021 - 2022 Project Researcher (特任研究員)

Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo.

2020 - 2020 Project Research Associate (特任助教)

Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan.

2019 - 2020 Project Researcher (特任研究員)

Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan.

2015 - 2019 Predoctoral Fellow

Laboratory of Functional Analysis in silico, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

2017 - 2019 English tutor

Kanda Foreign Language Institute, at Kanda University of International Studies. Tokyo, Japan.

2016 - 2019 English tutor

LbE Japan, Global Education Project. Tokyo, Japan.

2015 - 2015 Research Student

Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan.

2012 - 2015 Research Assistant

Bioinformatics Multiuser Laboratory, EMBRAPA Agriculture Informatics, Campinas, Brazil.

2011 - 2012 Undergraduate Research Fellow

Laboratory of Biotechnology, Dept. of Phytopathology and Molecular Biology. The Sylvio Moreira Citrus Center (IAC), Cordeiropolis, Brazil.

2010 - 2011 Summer Undergraduate Research Fellow

Laboratory of Molecular Genetics. Dept. of Plant Biotechnology. Federal University of São Carlos, Araras, Brazil.

Additional information

Technical skills

R, Python, Bash, UNIX, Git, HTML, CSS, SQL.

Areas of expertise

Bioinformatics, transcriptomics, epigenetics, chromatin structure, data visualization.

Languages

Portuguese(Native), English(Fluent), Japanese(Intermediate), Spanish(Beginner), German(Beginner).