Luis Augusto Eijy Nagai

Computational biologist, bioinformatician, translational bioinformatics.

Proactive and collaborative bioinformatics researcher with a strong foundation in NGS data analysis, single-cell transcriptomics, and network biology. Known for building robust, reproducible pipelines and creating value by turning complex datasets into actionable biological insights. Adept at interdisciplinary teamwork, with a proven ability to support both academic and clinical projects. Currently on sabbatical, exploring multilayer networks and innovative data-driven strategies to advance biomedical research.

Current positions

2022.4 - current Research Associate / Assistant Professor (助教)

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

2024.11 - current Visiting Researcher

• 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.

Professional activities

Previous experiences

2022 - 2024 In-house advisor at the University of Tokyo - Komaba International Lodge Annex.

• Required skills: Active listening, problem-solving, emotional intelligence, strategic thinking, encouraging cooperation, handling confidential or sensitive information responsibly, diplomacy.

2021 - 2022 Project Researcher (特任研究員)

• Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo.
• Single-cell RNA-seq, single-cell ATAC-seq (Multiome), project lead, collaborative work, trajectory analysis, rare population identification, biomarkers, Docker, Singularity, HPC server maintenance.

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.
• Single-cell RNA-seq, regulatory regions and motif analysis, CSS/HTML, SQL.

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.
• 3D Genome analysis, scientific writing, manuscript reviewing and preparation, Jupyter, Conda, Git.

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.
• Large-scale NGS analysis (Hi-C, RNA-seq, ATAC-seq, ChIP-seq, CAGE-seq), project management, collaborative work, teamwork.

2012 - 2015 Research Assistant

• Bioinformatics Multiuser Laboratory, EMBRAPA Agriculture Informatics, Campinas, Brazil.
• Galaxy platform and tool maintenance, NGS analyses for collaborators, UNIX systems, bioinformatics, YAML and JSON.

2011 - 2012 Undergraduate Research Fellow

• Laboratory of Biotechnology, Dept. of Phytopathology and Molecular Biology. The Sylvio Moreira Citrus Center (IAC), Cordeiropolis, Brazil.
• PCR, best-practices, pathogen DNA extraction (Xylella fastidiosa), media preparation, microbial culture maintenance, collaborative research, R.

2010 - 2011 Summer Undergraduate Research Fellow

• Laboratory of Molecular Genetics. Dept. of Plant Biotechnology. Federal University of São Carlos, Araras, Brazil.
• Genomic DNA extraction of sugarcane, restriction fragment length polymorphism (RFLP) analysis, molecular biology assays.

Teaching and tutoring

2024.11 - 2025.2

• Systems Biomedicine course. 2 SWS (6 ECTS).
• Technological University of Munich and Ludwig Maximilian University of Munich.
• Hands on project with weekly sessions and discussions.

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.

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)

Manuscript review

2022 - 2024 Ad hoc review for Frontier in Genetics.

2021 - 2024 Ad hoc review for MDPI journals: Cells, International Journal of Molecular Sciences, Genes, Applied Sciences, Healthcare.

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).

Research interests

• Translational bioinformatics and systems biology approaches for understanding chronic diseases.
• Data-driven analysis of large-scale omics datasets to uncover mechanisms of inflammation, metabolism, and mitochondrial dysfunction.
• Development of reproducible, scalable pipelines for integrative multi-omics and network biology.
• Focus on clinical data integration and early disease biomarker discovery in collaboration with experimental and clinical researchers.

Technical skills

Programming:

• Python, R, Bash.

Workflow & Reproducibility:

• Nextflow, Docker, Singularity, Git.

Data handling & Querying:

• SQL, HTML/CSS.

Cloud/HPC & Version Control:

• SLURM, Ubuntu server, GitHub/GitLab.

Professional Competencies

• Project management and cross-functional collaboration in interdisciplinary teams.
• Strong analytical thinking and data-driven problem solving.
• Proactive mindset with ability to independently drive technical solutions.
• Teamwork and effective scientific communication across disciplines.
• Active listening and adaptability in collaborative environments.
• Scientific writing and documentation for reproducible research.
• Continuous learning and integration of new bioinformatics tools and methods.

Areas of expertise

• Bioinformatics, single-cell and bulk transcriptomics, epigenomics, 3D chromatin architecture.
• Network biology, gene regulatory network inference, multi-omics data integration.
• Data visualization for biological interpretation.
• Translational research support: biomarker discovery, disease stratification, and inflammation-related pathways.

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

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 Protocols (2024), vol 5, issue 1. [STAR protocols][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.
• Science Advances (2024), vol 10, issue 8. [Science Advances][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.
• Nature Communications (2023), v.14, issue 1. [Nature Communications][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.
• Developmental Cell (2023), ISSN 1534-5807. [Developmental 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.
• Developmental Cell (2019), S1534-5807(19)30629-X. [Developtmental 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 Medical Genomics (2019), 11 (Suppl 7):127. [BMC Medical Genomics] [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]

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.

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.
• [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

2025 Luis Augusto Eijy Nagai, Markus List, Ryuichiro Nakato.

• CoSiNe: Enhancing interpretability of single-cell RNA-seq data through gene co-expression signed networks.
• ISMB/ECCB2025, p1636, July20-24, Liverpool, United Kingdom.

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 Luis Augusto Eijy Nagai and Ryuichiro Nakato.

• Navigating Cellular Complexity: Unraveling Gene Interactions in scRNA-seq with Signed Graphs and Network Analysis.
• IIBMP2023, P-136, Sep7-9, 2023. Chiba, Japan.

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 Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai.

• Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma.
• IIBMP2019, P-1 (poster), Sep.9-11, 2019, Tokyo, 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.

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.

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).

Other experiences

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.

2016.1 - 2016.11 Programming instructor

• Basic to intermediate programming concepts to junior students using Scratch and Python. Remote. 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.

Additional information

Languages

• Portuguese(Native), English(Full professional proficiency), Japanese(Intermediate), Spanish(Beginner), German(Beginner).