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publications

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

Published in Encontro Nacional de Engenharia e Desenvolvimento Social, XIV Encontro Nacional de Engenharia e Desenvolvimento Social, 2017

Recommended citation: 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). http://www.eneds.net/anais/index.php/edicoes/eneds2017/paper/view/543/438

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

Published in KDMiLe – Proceedings Applications Track, 2018

Recommended citation: 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. https://www.researchgate.net/profile/Alexandre-Aono/publication/330325486_A_Biased_Random-key_Genetic_Algorithm_with_Local_Search_Applied_to_Unsupervised_Clustering_of_Cultural_Data/links/5c39205692851c22a36e4535/A-Biased-Random-key-Genetic-Algorithm-with-Local-Search-Applied-to-Unsupervised-Clustering-of-Cultural-Data.pdf

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

Published in Scientific Reports, 2020

Recommended citation: 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). https://www.nature.com/articles/s41598-020-77063-5

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

Published in Frontiers in Plant Science, 2021

Recommended citation: 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. https://www.frontiersin.org/articles/10.3389/fpls.2021.668623/abstract

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

Published in Science of The Total Enviroment, 2021

Recommended citation: 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. https://www.sciencedirect.com/science/article/abs/pii/S0048969721030163

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

Published in Development, 2022

Download paper here

Recommended citation: 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. https://journals.biologists.com/dev/article/149/9/dev200198/275303/Human-pluripotent-stem-cell-derived-kidney

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

Published in Experimental Hematology, 2022

Recommended citation: 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. https://www.sciencedirect.com/science/article/pii/S0301472X22001308

talks

Graphlet

Published:

CostaLab group meeting presentation

tools

CrossTalkeR

Published:

CrossTalkeR is a framework for network analysis and visualisation of LR networks. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterisation of changes in cellular crosstalk in disease state.

scMEGA

Published:

scMEGA Fantastic work from Zhijian Li(https://lzj1769.github.io/). scMEGA(Single-cell Multiomic Enhancer-based Gene regulAtory network inference) is a R package designed to infer gene regulatory network by using single cell multi-omics data. It is based on several popular packages for single cell RNA/ATAC-seq data analysis, particularly, Seurat, Signac, and ArchR. Picture below showed the principal of scMEGA for linking genes to TFs and building a gene regualtory network.