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defined as genes that are expressed primarily in a single-cell type, can be identified from the single-cell transcriptome; however, such data are not always available for the many uses of marker genes, such as deconvolution of bulk tissue. Marker genes for a cell type, however, are highly correlated in bulk data, because their expression levels depend primarily on the proportion of that cell type in the samples. Therefore, when many tissue samples are analyzed, it is possible to identify these marker genes from the correlation pattern.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To capitalize on this pattern, we develop a new algorithm to detect marker genes by combining published information about likely marker genes with bulk transcriptome data in the form of a semi-supervised algorithm. The algorithm then exploits the correlation structure of the bulk data to refine the published marker genes by adding or removing genes from the list.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>We implement this method as an R package markerpen, hosted on CRAN (https:\/\/CRAN.R-project.org\/package=markerpen).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab257","type":"journal-article","created":{"date-parts":[[2021,4,24]],"date-time":"2021-04-24T15:12:58Z","timestamp":1619277178000},"page":"3228-3234","source":"Crossref","is-referenced-by-count":34,"title":["Identification of cell-type-specific marker genes from co-expression patterns in tissue samples"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0109-6692","authenticated-orcid":false,"given":"Yixuan","family":"Qiu","sequence":"first","affiliation":[{"name":"Department of Statistics and Data Science, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3828-4400","authenticated-orcid":false,"given":"Jiebiao","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA 15261, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3104-9387","authenticated-orcid":false,"given":"Jing","family":"Lei","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}]},{"given":"Kathryn","family":"Roeder","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, Carnegie Mellon University , Pittsburgh, PA 15213, USA"},{"name":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,4,27]]},"reference":[{"key":"2023051608275660900_btab257-B1","doi-asserted-by":"crossref","first-page":"e6098","DOI":"10.1371\/journal.pone.0006098","article-title":"Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus","volume":"4","author":"Abbas","year":"2009","journal-title":"PloS One"},{"key":"2023051608275660900_btab257-B2","doi-asserted-by":"crossref","first-page":"160089","DOI":"10.1038\/sdata.2016.89","article-title":"Human whole genome genotype and transcriptome data for Alzheimer\u2019s and other neurodegenerative diseases","volume":"3","author":"Allen","year":"2016","journal-title":"Sci. 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