{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T05:19:26Z","timestamp":1773983966005,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>As single-cell RNA-sequencing (scRNA-seq) becomes more widely used in transcriptomic research, complex experimental designs, such as paired or longitudinal studies, become increasingly feasible. Paired\/longitudinal scRNA-seq enables the study of transcriptomic changes over time within specific cell types, yet guidance on analytical approaches and resources for study planning, such as power analysis, remains limited. Data simulation is a valuable tool for evaluating analysis method performance and informing study design decisions, including sample size selection. Currently, most scRNA-seq simulation methods simulate cells for a single sample, thus ignoring the between-sample and between-subject variability inherent to paired\/longitudinal scRNA-seq data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we introduce rescueSim (REpeated measures Single Cell RNA-seqUEncing data SIMulation), a novel method that simulates paired\/longitudinal scRNA-seq data using a gamma-Poisson framework and incorporates additional variability between samples and subjects. We demonstrate our method\u2019s ability to reproduce important data properties and demonstrate its application in study planning.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>rescueSim is implemented as an R package and is available at https:\/\/github.com\/ewynn610\/rescueSim.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf442","type":"journal-article","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T15:45:36Z","timestamp":1755186336000},"source":"Crossref","is-referenced-by-count":5,"title":["Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5857-4483","authenticated-orcid":false,"given":"Elizabeth A","family":"Wynn","sequence":"first","affiliation":[{"name":"Center for Genes, Environment and Health, National Jewish Health , Denver, CO 80206,","place":["United States"]}]},{"given":"Kara J","family":"Mould","sequence":"additional","affiliation":[{"name":"Department of Medicine, National Jewish Health , Denver, CO 80206,","place":["United States"]},{"name":"Pulmonary and Critical Care Medicine, University of Colorado Anschutz Medical Campus , Aurora, CO 80045,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3772-1691","authenticated-orcid":false,"given":"Brian E","family":"Vestal","sequence":"additional","affiliation":[{"name":"Center for Genes, Environment and Health, National Jewish Health , Denver, CO 80206,","place":["United States"]},{"name":"Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO 80045,","place":["United States"]}]},{"given":"Camille M","family":"Moore","sequence":"additional","affiliation":[{"name":"Center for Genes, Environment and Health, National Jewish Health , Denver, CO 80206,","place":["United States"]},{"name":"Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO 80045,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,8,14]]},"reference":[{"key":"2025082010465655800_btaf442-B1","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2288-11-94","article-title":"Simulation methods to estimate design power: an overview for applied research","volume":"11","author":"Arnold","year":"2011","journal-title":"BMC Med Res Methodol"},{"key":"2025082010465655800_btaf442-B2","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.1093\/bioinformatics\/btaa105","article-title":"SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data","volume":"36","author":"Assefa","year":"2020","journal-title":"Bioinformatics"},{"key":"2025082010465655800_btaf442-B3","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1186\/s13059-021-02546-1","article-title":"splatPop: simulating population scale single-cell RNA sequencing data","volume":"22","author":"Azodi","year":"2021","journal-title":"Genome Biol"},{"key":"2025082010465655800_btaf442-B4","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1093\/bioinformatics\/btz752","article-title":"SPARSim single cell: a count data simulator for scRNA-seq data","volume":"36","author":"Baruzzo","year":"2020","journal-title":"Bioinformatics"},{"key":"2025082010465655800_btaf442-B5","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B Stat Methodol"},{"key":"2025082010465655800_btaf442-B6","doi-asserted-by":"crossref","first-page":"6911","DOI":"10.1038\/s41467-021-27130-w","article-title":"A benchmark study of simulation methods for single-cell RNA sequencing data","volume":"12","author":"Cao","year":"2021","journal-title":"Nat Commun"},{"key":"2025082010465655800_btaf442-B7","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/s13059-023-02904-1","article-title":"The shaky foundations of simulating single-cell RNA sequencing data","volume":"24","author":"Crowell","year":"2023","journal-title":"Genome Biol"},{"key":"2025082010465655800_btaf442-B8","doi-asserted-by":"crossref","first-page":"6077","DOI":"10.1038\/s41467-020-19894-4","article-title":"Muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data","volume":"11","author":"Crowell","year":"2020","journal-title":"Nat Commun"},{"key":"2025082010465655800_btaf442-B9","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene expression omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2025082010465655800_btaf442-B10","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-015-0844-5","article-title":"MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data","volume":"16","author":"Finak","year":"2015","journal-title":"Genome Biol"},{"key":"2025082010465655800_btaf442-B11","doi-asserted-by":"publisher","author":"Hafner","year":"2024","DOI":"10.1101\/2024.08.01.606200,"},{"key":"2025082010465655800_btaf442-B12","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2025082010465655800_btaf442-B13","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1093\/biostatistics\/kxx053","article-title":"Missing data and technical variability in single-cell RNA-sequencing experiments","volume":"19","author":"Hicks","year":"2018","journal-title":"Biostatistics"},{"key":"2025082010465655800_btaf442-B14","doi-asserted-by":"publisher","DOI":"10.1101\/2023.03.17.533005,","article-title":"Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet","author":"Hoffman","year":"2024"},{"key":"2025082010465655800_btaf442-B15","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac286","article-title":"Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data","volume":"23","author":"Junttila","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025082010465655800_btaf442-B16","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/s41591-020-0799-2","article-title":"Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection","volume":"26","author":"Kazer","year":"2020","journal-title":"Nat Med"},{"key":"2025082010465655800_btaf442-B17","doi-asserted-by":"crossref","first-page":"109209","DOI":"10.1016\/j.clim.2022.109209","article-title":"Tracking the clonal dynamics of SARS-CoV-2-specific T cells in children and adults with mild\/asymptomatic COVID-19","volume":"246","author":"Khoo","year":"2023","journal-title":"Clin Immunol"},{"key":"2025082010465655800_btaf442-B18","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/j.cell.2018.03.041","article-title":"Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing","volume":"173","author":"Kim","year":"2018","journal-title":"Cell"},{"key":"2025082010465655800_btaf442-B19","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s13059-020-1926-6","article-title":"Eleven grand challenges in single-cell data science","volume":"21","author":"L\u00e4hnemann","year":"2020","journal-title":"Genome Biol"},{"key":"2025082010465655800_btaf442-B20","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1182\/blood-2023-187408","article-title":"A longitudinal single-cell atlas of treatment response in pediatric AML","volume":"142","author":"Lambo","year":"2023","journal-title":"Blood"},{"key":"2025082010465655800_btaf442-B21","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1186\/s12859-023-05432-8","article-title":"idesc: identifying differential expression in single-cell RNA sequencing data with multiple subjects","volume":"24","author":"Liu","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"2025082010465655800_btaf442-B22","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13059-016-0947-7","article-title":"Pooling across cells to normalize single-cell RNA sequencing data with many zero counts","volume":"17","author":"Lun","year":"2016","journal-title":"Genome Biol"},{"key":"2025082010465655800_btaf442-B23","doi-asserted-by":"crossref","first-page":"e202001004","DOI":"10.26508\/lsa.202001004","article-title":"CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data","volume":"4","author":"L\u00fctge","year":"2021","journal-title":"Life Sci Alliance"},{"key":"2025082010465655800_btaf442-B24","author":"Maechler","year":"2018"},{"key":"2025082010465655800_btaf442-B25","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1080\/01621459.1951.10500769","article-title":"The Kolmogorov\u2013Smirnov test for goodness of fit","volume":"46","author":"Massey","year":"1951","journal-title":"J Am Stat Assoc"},{"key":"2025082010465655800_btaf442-B26","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1016\/j.cell.2020.07.017","article-title":"Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing","volume":"182","author":"Maynard","year":"2020","journal-title":"Cell"},{"key":"2025082010465655800_btaf442-B27","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1164\/rccm.202005-1989OC","article-title":"Airspace macrophages and monocytes exist in transcriptionally distinct subsets in healthy adults","volume":"203","author":"Mould","year":"2021","journal-title":"Am J Respir Crit Care Med"},{"key":"2025082010465655800_btaf442-B28","doi-asserted-by":"crossref","first-page":"584607","DOI":"10.3389\/fonc.2020.584607","article-title":"Evolution of advanced chronic lymphoid leukemia unveiled by single-cell transcriptomics: a case report","volume":"10","author":"Ostasov","year":"2020","journal-title":"Front Oncol"},{"key":"2025082010465655800_btaf442-B29","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nrg2934","article-title":"RNA sequencing: advances, challenges and opportunities","volume":"12","author":"Ozsolak","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2025082010465655800_btaf442-B30","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1093\/mnras\/202.3.615","article-title":"Two-dimensional goodness-of-fit testing in astronomy","volume":"202","author":"Peacock","year":"1983","journal-title":"Mon Not R Astron Soc"},{"key":"2025082010465655800_btaf442-B31","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1037\/10","article-title":"Statistical power and optimal design for multisite randomized trials","volume":"5","author":"Raudenbush","year":"2000","journal-title":"Psychol Methods"},{"key":"2025082010465655800_btaf442-B32","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"Robinson","year":"2010","journal-title":"Genome Biol"},{"key":"2025082010465655800_btaf442-B33","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: a graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"Rousseeuw","year":"1987","journal-title":"J Comput Appl Math"},{"key":"2025082010465655800_btaf442-B34","doi-asserted-by":"crossref","first-page":"5692","DOI":"10.1038\/s41467-021-25960-2","article-title":"Confronting false discoveries in single-cell differential expression","volume":"12","author":"Squair","year":"2021","journal-title":"Nat Commun"},{"key":"2025082010465655800_btaf442-B35","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: the teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2025082010465655800_btaf442-B36","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2025082010465655800_btaf442-B37","doi-asserted-by":"crossref","first-page":"4860","DOI":"10.1093\/bioinformatics\/btaa607","article-title":"Simulation, power evaluation and sample size recommendation for single-cell RNA-seq","volume":"36","author":"Su","year":"2020","journal-title":"Bioinformatics"},{"key":"2025082010465655800_btaf442-B38","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1038\/s41467-023-37432-w","article-title":"A comprehensive platform for analyzing longitudinal multi-omics data","volume":"14","author":"Vasaikar","year":"2023","journal-title":"Nat Commun"},{"key":"2025082010465655800_btaf442-B39","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1186\/s12859-022-05019-9","article-title":"lmerseq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models","volume":"23","author":"Vestal","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2025082010465655800_btaf442-B40","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1186\/s13059-017-1305-0","article-title":"Splatter: simulation of single-cell RNA sequencing data","volume":"18","author":"Zappia","year":"2017","journal-title":"Genome Biol"},{"key":"2025082010465655800_btaf442-B41","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1038\/s41467-019-10500-w","article-title":"Simulating multiple faceted variability in single cell RNA sequencing","volume":"10","author":"Zhang","year":"2019","journal-title":"Nat Commun"},{"key":"2025082010465655800_btaf442-B42","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1038\/s41467-021-21038-1","article-title":"A practical solution to pseudoreplication bias in single-cell studies","volume":"12","author":"Zimmerman","year":"2021","journal-title":"Nat Commun"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf442\/64045844\/btaf442.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/8\/btaf442\/64045844\/btaf442.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/8\/btaf442\/64045844\/btaf442.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,20]],"date-time":"2025-08-20T14:47:08Z","timestamp":1755701228000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf442\/8234490"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":42,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2025,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf442","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,8]]},"published":{"date-parts":[[2025,8]]},"article-number":"btaf442"}}