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Research

Table of Contents

Selected Publications

*Equal contribution. Please check all my publications at Google Scholar, ORCID or ResearchGate profile.

  • Bojović I.*, Sousa A.G.G.*, Junttila S., Elo L.L. (2025). Sketching T cell atlases in the single‐cell era: challenges and recommendations. Immunology & Cell Biology. https://doi.org/10.1111/imcb.70040

  • Figueiredo A., Rastogi S.T., Ramos S., Nogueira F., De Villiers K., Sousa A.G.G., Votborg-Novél L., von Wedel C., Tober-Lau P., Jentho E., Pagnotta S., Mesquita M., Cardoso S., Bortolussi G., Muro A.F., Tranfield E.M., Thibaud J., Duarte D., Sousa A.L., Pinto S.N., Kitoko J., Mombo-Ngoma G., Mischlinger J., Junttila S., Alenquer M., Amorim M.J., Vasavda C., Bosma P.J., Violante S., Drotleff B., Paixão T., Portugal S., Kurth F., Elo L.L., Paul B.D., Martins R., Soares M.P. (2025). A metabolite-based resistance mechanism against malaria. Science. https://doi.org/10.1126/science.adq6741

  • Kleino I.*, Perk M.*, Sousa A.G.G.*, Linden M.*, Mathlin J., Giesel D., Frolovaite P., Pietilä S., Junttila S., Suomi T., Elo L.L. (2025). CellRomeR: an R package for clustering cell migration phenotypes from microscopy data. Bioinformatics Advances. https://doi.org/10.1093/bioadv/vbaf069

  • Sousa A.G.G., Smolander J., Junttila S., Elo L.L. (2025). Coralysis enables sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration. bioRxiv. https://doi.org/10.1101/2025.02.07.637023

  • Sousa A.G.G., Smolander J., Junttila S., Elo L.L. (2024). Inferring Tree-Shaped Single-Cell Trajectories with Totem. In Transcriptome Data Analysis (Vol. 2812, pp. 169–191). Humana Press. https://doi.org/10.1007/978-1-0716-3886-6_9

  • Jentho E.*, Sousa A.G.G.*, Ramos S., Ademolue T.W., Sobral J., Costa J., Brito D., Manteiro M., Leite R.B., Lilue J., Soares M.P. (2023). Single-cell RNA sequencing and analysis of rodent blood stage Plasmodium. STAR Protocols. https://doi.org/10.1016/j.xpro.2023.102491

  • Ramos S., Ademolue T.W., Jentho E., Wu Q., Guerra J., Martins R., Pires G., Weis S., Carlos A.R., Mahú I., Seixas E., Duarte D., Rajas F., Cardoso S., Sousa A.G.G., Lilue J., Paixão T., Mithieux G., Nogueira F., Soares M.P. (2022). A hypometabolic defense strategy against malaria. Cell Metabolism. https://doi.org/10.1016/j.cmet.2022.06.011

  • Paiva R.A., Sousa A.G.G., Ramos C.V., Ávila M., Lilue J., Paixão T., Martins V.C. (2021). Self-renewal of double-negative 3 early thymocytes enables thymus autonomy but compromises the β-selection checkpoint. Cell Reports. https://doi.org/10.1016/j.celrep.2021.108967

  • Santos J.P., Sousa A.G.G., Ribeiro H., Magalhães C. (2020). The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2020.574815

  • Sousa A.G.G., Tomasino M.P., Duarte P., Fernández-Méndez M., Assmy P., Ribeiro H., Surkont J., Leite R.B., Pereira-Leal J.B., Torgo L., Magalhães C. (2019). Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. Microbial Ecology. https://doi.org/10.1007/s00248-018-01314-2

Software & Resources

Below is a list of software and resources I helped develop.

Coralysis

  • R/Bioconductor package for sensitive integration, reference-mapping, and cell state identification in single-cell data

    GitHub | Bioconductor | publication

    Developer/Maintainer

CellRomeR

  • R package for phenotypic clustering of cells from microscopy images

    GitHub | publication

    Author/Contributor

Totem’s protocols

  • User-friendly protocols for inferring tree-shaped single-cell trajectories with Totem

    Website | GitHub | publication

    Developer

Press & Media

  • Researchers elucidate the role of jaundice during malaria as a metabolic response against Plasmodium infection [link]