{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T04:35:30Z","timestamp":1781152530520,"version":"3.54.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000},"content-version":"vor","delay-in-days":36,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012359","name":"DBT","doi-asserted-by":"publisher","award":["IC-12044(12)\/4\/2022-ICD-DBT"],"award-info":[{"award-number":["IC-12044(12)\/4\/2022-ICD-DBT"]}],"id":[{"id":"10.13039\/100012359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001411","name":"Indian Council of Medical Research","doi-asserted-by":"publisher","award":["EMDR\/IG\/16\/2024-01-01321"],"award-info":[{"award-number":["EMDR\/IG\/16\/2024-01-01321"]}],"id":[{"id":"10.13039\/501100001411","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["CRG\/2022\/007706"],"award-info":[{"award-number":["CRG\/2022\/007706"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The complexity of scRNA-sequencing datasets highlights the urgent need for enhanced clustering and visualization methods. Here, we propose Stardust, an iterative, force-directed graph layout algorithm that enables the simultaneous embedding of cells and marker genes. Stardust, for the first time, allows a single-stop visualization of cells and marker genes on a single 2D map. While Stardust provides its own visualization pipeline, it can be plugged in with state-of-the-art methods such as Uniform Manifold Approximation and Projection (UMAP) and t-Distributed Stochastic Neighbor Embedding (t-SNE). We benchmarked Stardust against popular visualization and clustering tools on both scRNA-seq and spatial transcriptomics datasets. In all cases, Stardust performs competitively in identifying and visualizing cell types in an accurate and spatially coherent manner.<\/jats:p>","DOI":"10.1093\/bib\/bbaf537","type":"journal-article","created":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T17:48:34Z","timestamp":1759772914000},"source":"Crossref","is-referenced-by-count":1,"title":["Network based simultaneous embedding of cells and marker genes from scRNA-seq studies"],"prefix":"10.1093","volume":"26","author":[{"given":"Namrata","family":"Bhattacharya","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) , Okhla Industrial Estate, Phase III, New Delhi \u2013 110020, Delhi,","place":["India"]},{"name":"Australian Prostate Cancer Research Centre-Queensland , Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove Campus, 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New Delhi \u2013 110020, Delhi,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3390-9494","authenticated-orcid":false,"given":"Krishan","family":"Gupta","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Boston Children's Hospital in Harvard Medical School , 300 Longwood Avenue, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aayushi","family":"Mittal","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) , Okhla Industrial Estate, Phase III, New Delhi \u2013 110020, Delhi,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debajyoti","family":"Sinha","sequence":"additional","affiliation":[{"name":"Centre de Recherche en Transplantation et Immunologie, Inserm, CHU Nantes, UMR1064, ITUN, Universit\u00e9 de Nantes , Chem. de la 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