{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T04:01:41Z","timestamp":1770350501092,"version":"3.49.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,3,21]],"date-time":"2025-03-21T00:00:00Z","timestamp":1742515200000},"content-version":"vor","delay-in-days":20,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Scientific Foundation of the Spanish Association Against Cancer","award":["PERME224336TARA"],"award-info":[{"award-number":["PERME224336TARA"]}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["AC22\/00058"],"award-info":[{"award-number":["AC22\/00058"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As multi-omics sequencing technologies advance, the need for simulation tools capable of generating realistic and diverse (bulk and single-cell) multi-omics datasets for method testing and benchmarking becomes increasingly important. We present MOSim, an R package that simulates both bulk (via mosim function) and single-cell (via sc_mosim function) multi-omics data. The mosim function generates bulk transcriptomics data (RNA-seq) and additional regulatory omics layers (ATAC-seq, miRNA-seq, ChIP-seq, Methyl-seq, and transcription factors), while sc_mosim simulates single-cell transcriptomics data (scRNA-seq) with scATAC-seq and transcription factors as regulatory layers. The tool supports various experimental designs, including simulation of gene co-expression patterns, biological replicates, and differential expression between conditions. MOSim enables users to generate quantification matrices for each simulated omics data type, capturing the heterogeneity and complexity of bulk and single-cell multi-omics datasets. Furthermore, MOSim provides differentially abundant features within each omics layer and elucidates the active regulatory relationships between regulatory omics and gene expression data at both bulk and single-cell levels. By leveraging MOSim, researchers will be able to generate realistic and customizable bulk and single-cell multi-omics datasets to benchmark and validate analytical methods specifically designed for the integrative analysis of diverse regulatory omics data.<\/jats:p>","DOI":"10.1093\/bib\/bbaf110","type":"journal-article","created":{"date-parts":[[2025,3,23]],"date-time":"2025-03-23T08:49:50Z","timestamp":1742719790000},"source":"Crossref","is-referenced-by-count":4,"title":["MOSim: bulk and single-cell multilayer regulatory network simulator"],"prefix":"10.1093","volume":"26","author":[{"given":"Carolina","family":"Monz\u00f3","sequence":"first","affiliation":[{"name":"Genomics of Gene Expression Lab, Institute for Integrative Systems Biology, Spanish National Research Council (CSIC-UV) , C\/ Catedr\u00e0tic Agust\u00edn Escardino Benlloch, Paterna 46980 ,","place":["Spain"]}]},{"given":"Maider","family":"Aguerralde-Martin","sequence":"additional","affiliation":[{"name":"Applied Statistics, Operational Research and Quality Department, Universitat Polit\u00e8cnica de Val\u00e8ncia , Cam\u00ed de Vera s\/n, Val\u00e8ncia 46022 ,","place":["Spain"]}]},{"given":"Carlos","family":"Mart\u00ednez-Mira","sequence":"additional","affiliation":[{"name":"Biobam Bioinformatics S.L. , Marina de Valencia Base 5, BioHub, C\/ de la Traves\u00eda, s\/n, Sector Puerto 14 E, Val\u00e8ncia 46024 ,","place":["Spain"]}]},{"given":"\u00c1ngeles","family":"Arzalluz-Luque","sequence":"additional","affiliation":[{"name":"Genomics of Gene Expression Lab, Institute for Integrative Systems Biology, Spanish National Research Council (CSIC-UV) , C\/ Catedr\u00e0tic Agust\u00edn Escardino Benlloch, Paterna 46980 ,","place":["Spain"]},{"name":"Applied Statistics, Operational Research and Quality Department, Universitat Polit\u00e8cnica de Val\u00e8ncia , Cam\u00ed de Vera s\/n, Val\u00e8ncia 46022 ,","place":["Spain"]}]},{"given":"Ana","family":"Conesa","sequence":"additional","affiliation":[{"name":"Genomics of Gene Expression Lab, Institute for Integrative Systems Biology, Spanish National Research Council (CSIC-UV) , C\/ Catedr\u00e0tic Agust\u00edn Escardino Benlloch, Paterna 46980 ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5346-1407","authenticated-orcid":false,"given":"Sonia","family":"Tarazona","sequence":"additional","affiliation":[{"name":"Applied Statistics, Operational Research and Quality Department, Universitat Polit\u00e8cnica de Val\u00e8ncia , Cam\u00ed de Vera s\/n, Val\u00e8ncia 46022 ,","place":["Spain"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,21]]},"reference":[{"key":"2025032119021603000_ref1","doi-asserted-by":"publisher","first-page":"e1011254","DOI":"10.1371\/journal.pcbi.1011254","article-title":"From time-series transcriptomics to gene regulatory networks: a review on inference 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