{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T16:18:25Z","timestamp":1782836305505,"version":"3.54.5"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,10,9]],"date-time":"2022-10-09T00:00:00Z","timestamp":1665273600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000288","name":"The Royal Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Diabetes UK early-career grants","award":["20\/0006187"],"award-info":[{"award-number":["20\/0006187"]}]},{"name":"European Union\u2019s Horizon 2020","award":["101016072"],"award-info":[{"award-number":["101016072"]}]},{"name":"Personal Chair Awards","award":["CH\/15\/1\/31199"],"award-info":[{"award-number":["CH\/15\/1\/31199"]}]},{"name":"British Heart Foundation Programme Grant","award":["RG\/15\/5\/31446"],"award-info":[{"award-number":["RG\/15\/5\/31446"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single-cell\/nuclei RNA-sequencing (scRNA-seq) technologies can simultaneously quantify gene expression in thousands of cells across the genome. However, the majority of the noncoding RNAs, such as microRNAs (miRNAs), cannot currently be profiled at the same scale. MiRNAs are a class of small noncoding RNAs and play an important role in gene regulation. MiRNAs originate from the processing of primary transcripts, known as primary-microRNAs (pri-miRNAs). The pri-miRNA transcripts, independent of their cognate miRNAs, can also function as long noncoding RNAs, code for micropeptides or even interact with DNA, acting like enhancers. Therefore, it is apparent that the significance of scRNA-seq pri-miRNA profiling expands beyond using pri-miRNA as proxies of mature miRNAs. However, there are no computational methods that allow profiling and quantification of pri-miRNAs at the single-cell-type resolution.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a simple yet effective computational framework to profile pri-MiRNAs from single-cell RNA-sequencing datasets (PPMS). Based on user input, PPMS can profile pri-miRNAs at cell-type resolution. PPMS can be applied to both newly produced and publicly available datasets obtained via single cell or single-nuclei RNA-seq. It allows users to (i) investigate the distribution of pri-miRNAs across cell types and cell states and (ii) establish a relationship between the number of cells\/reads sequenced and the detection of pri-miRNAs. Here, to demonstrate its efficacy, we have applied PPMS to publicly available scRNA-seq data generated from (i) individual chambers (ventricles and atria) of the human heart, (ii) human pluripotent stem cells during their differentiation into cardiomyocytes (the heart beating cells) and (iii) hiPSCs-derived cardiomyocytes infected with severe acute respiratory syndrome\u00a0coronavirus 2.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbac419","type":"journal-article","created":{"date-parts":[[2022,10,9]],"date-time":"2022-10-09T13:26:06Z","timestamp":1665321966000},"source":"Crossref","is-referenced-by-count":10,"title":["PPMS: A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets"],"prefix":"10.1093","volume":"23","author":[{"given":"Jiahui","family":"Ji","sequence":"first","affiliation":[{"name":"National Heart and Lung Institute, Imperial College London , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryam","family":"Anwar","sequence":"additional","affiliation":[{"name":"National Heart and Lung Institute, Imperial College London , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrico","family":"Petretto","sequence":"additional","affiliation":[{"name":"London Institute of Medical Sciences , MRC, UK"},{"name":"Duke-NUS Medical School , Singapore"},{"name":"Institute of Big Data and Artificial Intelligence, China Pharmaceutical University (CPU) , 211198 Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Costanza","family":"Emanueli","sequence":"additional","affiliation":[{"name":"National Heart and Lung Institute, Imperial College London , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1454-5493","authenticated-orcid":false,"given":"Prashant Kumar","family":"Srivastava","sequence":"additional","affiliation":[{"name":"National Heart and Lung Institute, Imperial College London , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,8]]},"reference":[{"key":"2022112111120401100_ref1","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1161\/CIRCULATIONAHA.119.042474","article-title":"Regulatory RNAs in heart failure","volume":"141","author":"Gomes","year":"2020","journal-title":"Circulation"},{"key":"2022112111120401100_ref2","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1161\/ATVBAHA.112.300139","article-title":"Intercellular transport of microRNAs","volume":"33","author":"Boon","year":"2013","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"2022112111120401100_ref3","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nsmb.2982","article-title":"Microprocessor mediates transcriptional termination in long noncoding microRNA 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