{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T18:27:47Z","timestamp":1772735267845,"version":"3.50.1"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2021,5,16]],"date-time":"2021-05-16T00:00:00Z","timestamp":1621123200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000377","name":"Dunhill Medical Trust","doi-asserted-by":"publisher","award":["R476\/0516"],"award-info":[{"award-number":["R476\/0516"]}],"id":[{"id":"10.13039\/501100000377","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Novo Nordisk Fonden Challenge Programme"},{"name":"Harnessing the Power of Big Data to Address the Societal Challenge of Aging","award":["NNF17OC0027812"],"award-info":[{"award-number":["NNF17OC0027812"]}]},{"DOI":"10.13039\/501100000265","name":"MRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Medical Research Council Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing","award":["MR\/R502182\/1"],"award-info":[{"award-number":["MR\/R502182\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The analysis of longitudinal datasets and construction of gene regulatory networks (GRNs) provide a valuable means to disentangle the complexity of microRNA (miRNA)\u2013mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal miRNA\u2013mRNA datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present TimiRGeN, an R package that uses time point-based differential expression results to identify miRNA\u2013mRNA interactions influencing signaling pathways of interest. miRNA\u2013mRNA interactions can be visualized in R or exported to PathVisio or Cytoscape. The output can be used for hypothesis generation and directing in vitro or further in silico work such as GRN construction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TimiRGeN is available for download on Bioconductor (https:\/\/bioconductor.org\/packages\/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer.<\/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\/btab377","type":"journal-article","created":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T19:22:57Z","timestamp":1620847377000},"page":"3604-3609","source":"Crossref","is-referenced-by-count":15,"title":["<i>TimiRGeN<\/i>: <i>R\/Bioconductor<\/i> package for time series microRNA\u2013mRNA integration and analysis"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6806-8675","authenticated-orcid":false,"given":"K","family":"Patel","sequence":"first","affiliation":[{"name":"Campus for Ageing and Vitality, Biosciences Institute, Newcastle University , Newcastle upon Tyne NE4 5PL, UK"}]},{"given":"S","family":"Chandrasegaran","sequence":"additional","affiliation":[{"name":"Campus for Ageing and Vitality, Biosciences Institute, Newcastle University , Newcastle upon Tyne NE4 5PL, UK"}]},{"given":"I M","family":"Clark","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of East Anglia , Norwich NR4 7TJ, UK"}]},{"given":"C J","family":"Proctor","sequence":"additional","affiliation":[{"name":"Campus for Ageing and Vitality, Biosciences Institute, Newcastle University , Newcastle upon Tyne NE4 5PL, UK"}]},{"given":"D A","family":"Young","sequence":"additional","affiliation":[{"name":"Life Science Centre, Biosciences Institute, Newcastle University , Newcastle upon Tyne NE1 4EP, UK"}]},{"given":"D P","family":"Shanley","sequence":"additional","affiliation":[{"name":"Campus for Ageing and Vitality, Biosciences Institute, Newcastle University , Newcastle upon Tyne NE4 5PL, UK"}]}],"member":"286","published-online":{"date-parts":[[2021,5,16]]},"reference":[{"key":"2023051609044908300_btab377-B1","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"eLife"},{"key":"2023051609044908300_btab377-B2","doi-asserted-by":"crossref","first-page":"25749","DOI":"10.1038\/srep25749","article-title":"miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis","volume":"6","author":"Andr\u00e9s-Le\u00f3n","year":"2016","journal-title":"Sci. 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