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Despite their significance, research on fungal infections continues to lag behind other infectious diseases, hindering diagnostic and treatment advances. Single-cell RNA sequencing (scRNA-seq) is a powerful tool widely used to identify biomarkers and targets of intervention in various fields, including host-pathogen research. Owing to its ability to resolve cellular heterogeneity, scRNA-seq has been successfully applied in host-viral and host-bacterial studies, providing in-depth insights into the mechanisms of pathogenesis. Recently, this method has also been increasingly adopted in fungal infection research. Here, we provide a brief overview, that summarizes key findings and offers in-depth insights into the dynamics of host\u2013fungal pathogen interactions uncovered through this approach. The review also addresses current limitations, gaps and future directions, encouraging researchers for the broader adoption of single-cell technologies in this field.<\/jats:p>","DOI":"10.1038\/s42003-026-10304-x","type":"journal-article","created":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T08:54:47Z","timestamp":1780044887000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Empowering fungal infection research with single-cell RNA sequencing"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7395-0689","authenticated-orcid":false,"given":"Renata","family":"Toth","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-5137-1668","authenticated-orcid":false,"given":"Florabelle Ruano","family":"Cabarrubias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zsolt","family":"Czimmerer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kitti","family":"Vecsernyes-Nagy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Attila","family":"Gacser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"10304_CR1","doi-asserted-by":"publisher","first-page":"e0007964","DOI":"10.1371\/journal.pntd.0007964","volume":"14","author":"ML Rodrigues","year":"2020","unstructured":"Rodrigues, M. 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