{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,16]],"date-time":"2025-11-16T21:11:23Z","timestamp":1763327483901,"version":"3.45.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1846216","DMS-2113754"],"award-info":[{"award-number":["DBI-1846216","DMS-2113754"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chan Zuckerberg Initiative Donor Advised Fund"},{"DOI":"10.13039\/100000923","name":"Silicon Valley Community Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Identifying differentially expressed (DE) genes along cell pseudotime is crucial for understanding dynamic biological processes captured by single-cell RNA sequencing. However, existing DE methods either produce invalid P-values by ignoring the uncertainty in pseudotime inference or struggle to scale with the growing size of modern datasets. To address these limitations, we introduce PseudotimeDE-fast, a scalable method for detecting DE genes along pseudotime with well-calibrated P-values. Through comprehensive simulations and real-data analyses, we demonstrate that PseudotimeDE-fast delivers comparable or superior performance to existing approaches while offering substantial improvements in computational efficiency.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PseudotimeDE-fast is implemented in R with Rcpp acceleration and released under the MIT license. The source code is available at: https:\/\/github.com\/dsong-lab\/PseudotimeDE.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf573","type":"journal-article","created":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T12:26:49Z","timestamp":1760617609000},"source":"Crossref","is-referenced-by-count":0,"title":["PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime"],"prefix":"10.1093","volume":"41","author":[{"given":"Yuheng","family":"Lai","sequence":"first","affiliation":[{"name":"Department of Statistics, University of Wisconsin-Madison , Madison, WI 53706,","place":["United States"]}]},{"given":"Dongyuan","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genome Sciences, University of Connecticut Health Center , Farmington, CT 06030-6403,","place":["United States"]}]},{"given":"Lucy","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of ISOM, School of Business and Management, Hong Kong University of Science and Technology , Clear Water Bay,","place":["Hong Kong"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9288-5648","authenticated-orcid":false,"given":"Jingyi Jessica","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, University of California , Los Angeles, CA 90095-1554,","place":["United States"]},{"name":"Biostatistics Program, Fred Hutchinson Cancer Center , Seattle, WA 98109,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"key":"2025111616071255400_btaf573-B1","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.3150\/13-BEJ514","article-title":"A consistent test of independence based on a sign covariance related to Kendall\u2019s 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