{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T19:08:57Z","timestamp":1746126537655,"version":"3.37.3"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2022,4,28]],"date-time":"2022-04-28T00:00:00Z","timestamp":1651104000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U2C CA233291","U54 CA217450"],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P01 AI139449"],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cancer Center Support Grant","award":["P30CA068485"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,13]]},"abstract":"Abstract<\/jats:title>Motivation<\/jats:title>Intracellular communication is crucial to many biological processes, such as differentiation, development, homeostasis and inflammation. Single-cell transcriptomics provides an unprecedented opportunity for studying cell-cell communications mediated by ligand\u2013receptor interactions. Although computational methods have been developed to infer cell type-specific ligand\u2013receptor interactions from one single-cell transcriptomics profile, there is lack of approaches considering ligand and receptor simultaneously to identifying dysregulated interactions across conditions from multiple single-cell profiles.<\/jats:p><\/jats:sec>Results<\/jats:title>We developed scLR, a statistical method for examining dysregulated ligand\u2013receptor interactions between two conditions. scLR models the distribution of the product of ligands and receptors expressions and accounts for inter-sample variances and small sample sizes. scLR achieved high sensitivity and specificity in simulation studies. scLR revealed important cytokine signaling between macrophages and proliferating T cells during severe acute COVID-19 infection, and activated TGF-\u03b2 signaling from alveolar type II cells in the pathogenesis of pulmonary fibrosis.<\/jats:p><\/jats:sec>Availability and implementation<\/jats:title>scLR is freely available at https:\/\/github.com\/cyhsuTN\/scLR.<\/jats:p><\/jats:sec>Supplementary information<\/jats:title>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac294","type":"journal-article","created":{"date-parts":[[2022,4,21]],"date-time":"2022-04-21T19:17:22Z","timestamp":1650568642000},"page":"3216-3221","source":"Crossref","is-referenced-by-count":8,"title":["Dysregulated ligand\u2013receptor interactions from single-cell transcriptomics"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8892-7078","authenticated-orcid":false,"given":"Qi","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"},{"name":"Department of Biostatistics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]},{"given":"Chih-Yuan","family":"Hsu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"},{"name":"Department\u2002 of Biostatistics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]},{"given":"Jia","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"},{"name":"Department of \u2002Biostatistics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]},{"given":"Yu","family":"Shyr","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"},{"name":"Department of Biostatistics, \u2002Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,4,28]]},"reference":[{"key":"2023041408101694700_","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.coisb.2021.03.007","article-title":"The landscape of cell\u2013cell communication through single-cell transcriptomics","volume":"26","author":"Almet","year":"2021","journal-title":"Curr. 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