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Using data from a human cell differentiation system and an anticancer drug resistance study, we demonstrate that QUBO feature selection effectively identifies genes whose expression patterns reflect critical cell state transitions associated with differentiation and drug resistance development. Our findings indicate that quantum annealing-powered QUBO reveals complex gene expression patterns potentially missed by traditional methods, thereby enhancing scRNA-seq data analysis and interpretation.<\/jats:p>","DOI":"10.1007\/s42484-025-00312-1","type":"journal-article","created":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T10:35:09Z","timestamp":1764585309000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Quantum annealing for enhanced feature selection in single-cell RNA sequencing data analysis"],"prefix":"10.1007","volume":"7","author":[{"given":"Selim","family":"Romero","sequence":"first","affiliation":[]},{"given":"Shreyan","family":"Gupta","sequence":"additional","affiliation":[]},{"given":"Victoria","family":"Gatlin","sequence":"additional","affiliation":[]},{"given":"Robert S.","family":"Chapkin","sequence":"additional","affiliation":[]},{"given":"James J.","family":"Cai","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,12,1]]},"reference":[{"key":"312_CR1","doi-asserted-by":"publisher","first-page":"1628","DOI":"10.1038\/s41467-021-21884-z","volume":"12","author":"AF Aissa","year":"2021","unstructured":"Aissa AF, Islam A, Ariss MM, Go CC, Rader AE et al (2021) Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer. 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