CV

Education

• M.S. in Computer Science: Inteligent Systems, Universidade Federal de Sao Paulo (UNIFESP), 2017-2019
  • Evaluation of global network alignment in obesity metagenomics data
• B.S. in Computer Science, Universidade Federal de Sao Paulo (UNIFESP), 2016-2018
  • Modeling and analysis of metabolic networks using graph theory
• B.S. in Science and Technology, Universidade Federal de Sao Paulo (UNIFESP), 2013-2016

Work experience

• 12/2016-04/2017: Intern Delta Life
  • FullStack web developer

Scholarships

• Social Work of Universidade Federal de São Paulo. (06/2016 - 12/2016)
  • Development of data analytics framework to drive the university cultural programs.
• Junior Reasearcher of Universidade Federal de São Paulo by Biocomputional Capes Project. (2014 - 2015)

Skills

• Computer Science Development Languages
  • C/C++
  • Java
  • Python2/3
  • Perl
  • R/Shiny
  • SQL
  • PHP
  • HTML/CSS
• Java Design Patterns and Agile (Scrum)
• Statistical Analysis
• Machine Learning Problems
• Complex Networks
• Data Mining

Languages

• Japanese (Certificate N2, Japanese Language Proficiency Test in 2013)
• English (TOEFL ATP A2 level)

Publications

Platelet-instructed SPP1+ macrophages drive myofibroblast activation in fibrosis in a CXCL4-dependent manner

Hoeft, K., Schaefer, G. J., Kim, H., Schumacher, D., Bleckwehl, T., Long, Q., ... & Kramann, R. (2023). Platelet-instructed SPP1+ macrophages drive myofibroblast activation in fibrosis in a CXCL4-dependent manner. Cell Reports, 42(2).

scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Li, Z., Nagai, J. S., Kuppe, C., Kramann, R., & Costa, I. G. (2023). scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference. Bioinformatics Advances, 3(1), vbad003.

Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

Joodaki, M., Shaigan, M., Parra, V., Buelow, R. D., Kuppe, C., Hölscher, D. L., ... & Costa, I. G. (2022). Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT). bioRxiv, 2022-12.

Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease

Xu, Y., Kuppe, C., Perales-Patón, J., Hayat, S., Kranz, J., Abdallah, A. T., ... & Kramann, R. (2022). Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease. Nature genetics, 54(11), 1690-1701.

Spatial multi-omic map of human myocardial infarction

Kuppe, C., Ramirez Flores, R. O., Li, Z., Hayat, S., Levinson, R. T., Liao, X., ... & Kramann, R. (2022). Spatial multi-omic map of human myocardial infarction. Nature, 1-12.

Mapping the cardiac vascular niche in heart failure

Peisker, F., Halder, M., Nagai, J., Ziegler, S., Kaesler, N., Hoeft, K., ... & Kramann, R. (2022). Mapping the cardiac vascular niche in heart failure. Nature Communications, 13(1), 1-20.

Single-cell analysis of cultured bone marrow stromal cells reveals high similarity to fibroblasts in situ

Stalmann, U. S., Banjanin, B., Snoeren, I. A., Nagai, J. S., Leimkühler, N. B., Li, R., ... & Schneider, R. K. (2022). Single-cell analysis of cultured bone marrow stromal cells reveals high similarity to fibroblasts in situ. Experimental Hematology, 110, 28-33.

Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling

Jansen, J., van den Berge, B. T., van den Broek, M., Maas, R. J., Daviran, D., Willemsen, B.,..., Nagai. J. S.,... & Smeets, B. (2022). Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling. Development, 149(9), dev200198.

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Jansen, J., Reimer, K. C., Nagai, J. S., Varghese, F. S., Overheul, G. J., de Beer, M., ... & Powell, A. (2022). SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell stem cell, 29(2), 217-231.

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

Dimitrov, D., Türei, D., Garrido-Rodriguez, M., Burmedi, P. L., Nagai, J. S., Boys, C., ... & Saez-Rodriguez, J. (2022). Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nature Communications, 13(1), 1-13.

Microbial co-occurrence network and its key microorganisms in soil with permanent application of composted tannery sludge

Ishimoto, Caroline Kie, Alexandre Hild Aono, James Shiniti Nagai, Hério Sousa, Ana Roberta Lima Miranda, Vania Maria Maciel Melo, Lucas William Mendes et al. "Microbial co-occurrence network and its key microorganisms in soil with permanent application of composted tannery sludge." Science of The Total Environment (2021): 147945.

CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks

Nagai, James Shiniti, Nils Leimkuehler, Michael Schaub, Rebekka Schneider, and Ivan Gesteira Costa Filho. "CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks." Bioinformatics (2021).

The Wild Sugarcane and Sorghum Kinomes: Insights into Expansion, Diversification and Expression Patterns

Aono, Alexandre Hild, Ricardo José Gonzaga Pimenta, Ana Letycia Basso Garcia, Fernando Henrique Correr, Guilherme Kenichi Hosaka, Marishani Marin Carrasco, Claudio Benicio Cardoso-Silva et al. "The Wild Sugarcane and Sorghum Kinomes: Insights into Expansion, Diversification and Expression Patterns." Frontiers in Plant Science 12 (2021): 589.

Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell epitope mapping

Schreibing, Felix, Monica Hannani, Fabio Ticconi, Eleanor Fewings, James Shiniti Nagai, Matthias Begemann, Christoph Kuppe et al. "Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell epitope mapping." bioRxiv (2021).

Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis

Leimkühler, N.B., Gleitz, H.F., Ronghui, L., Snoeren, I.A., Fuchs, S.N., Nagai, J.S., Banjanin, B., Lam, K.H., Vogl, T., Kuppe, C. and Stalmann, U.S., 2020. Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis. Cell Stem Cell.

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance

Aono, A.H., Costa, E.A., Rody, H.V.S., Nagai, J.S., Pimenta, R.J.G., Mancini, M.C., dos Santos, F.R.C., Pinto, L.R., de Andrade Landell, M.G., de Souza, A.P. and Kuroshu, R.M., 2020. Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance.Sci Rep 10, 20057 (2020).

A stomata classification and detection system in microscope images of maize cultivars

Aono, A.H., Nagai, J.S., da SM Dickel, G., Marinho, R.C., de Oliveira, P.E. and Faria, F.A., 2019. A stomata classification and detection system in microscope images of maize cultivars. bioRxiv, p.538165.

Gene essentiality prediction using topological features from metabolic networks

Nagai, J.S., Sousa, H., Aono, A.H., Lorena, A.C. and Kuroshu, R.M., 2018, October. Gene essentiality prediction using topological features from metabolic networks. In 2018 7th Brazilian Conference on Intelligent Systems (BRACIS) (pp. 91-96). IEEE.

A Biased Random-key Genetic Algorithm with Local Search Applied to Unsupervised Clustering of Cultural Data

Aono, A.H., de Oliveira, R.M., Franchi, B.O., Nagai, J.S., Paz, H.E.S., Chaves, A.A. and Martins, C.B., 2018. A Biased Random-key Genetic Algorithm with Local Search Applied to Unsupervised Clustering of Cultural Data Applications Track.

PluviApp: Ferramenta Web para análise e visualização de dados pluviométricos (Portuguese only)

Aono, A.H., Nagai, J.S., Santos, S.R.S., Cespedes, J.G. and da Silva, L.F., 2017. PluviApp: Ferramenta Web para análise e visualização de dados pluviométricos. Anais dos Encontros Nacionais de Engenharia e Desenvolvimento Social-ISSN 2594-7060, 14(1).

Talks

Graphlet

March 01, 2021

Talk at CostaLab, Aachen

Service and leadership

• Head of Extension Project Cinematografo from Universidade Federal de São Paulo. (2015 - 2016)
• Head of Younger Department of Japanese Society Orion de São José dos Campos. (2014 - 2016)
• Teenagers Japan Experience Fellowship of Japan International Cooperation Agency (2011)