{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T12:02:42Z","timestamp":1763640162514,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,21]],"date-time":"2020-01-21T00:00:00Z","timestamp":1579564800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"School of Fundamental Sciences"},{"name":"New Zealand Institute for Plant and Food Research Limited Strategic Science Investment Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present sismonr, an R package for an integral generation and simulation of in silico biological systems. The package generates gene regulatory networks, which include protein-coding and non-coding genes along with different transcriptional and post-transcriptional regulations. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations but can be defined by the user to higher ploidies. A choice of stochastic simulation algorithms allows us to simulate the expression profiles of the genes in the in silico system. We illustrate the use of sismonr by simulating the anthocyanin biosynthesis regulation pathway for three genetically distinct in silico plants.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The sismonr package is implemented in R and Julia and is publicly available on the CRAN repository (https:\/\/CRAN.R-project.org\/package=sismonr). A detailed tutorial is available from GitHub at https:\/\/oliviaab.github.io\/sismonr\/.<\/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\/btaa002","type":"journal-article","created":{"date-parts":[[2020,1,17]],"date-time":"2020-01-17T12:11:30Z","timestamp":1579263090000},"page":"2938-2940","source":"Crossref","is-referenced-by-count":4,"title":["sismonr: simulation of <i>in silico<\/i> multi-omic networks with adjustable ploidy and post-transcriptional regulation in R"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7708-2919","authenticated-orcid":false,"given":"Olivia","family":"Angelin-Bonnet","sequence":"first","affiliation":[{"name":"School of Fundamental Sciences"}]},{"given":"Patrick J","family":"Biggs","sequence":"additional","affiliation":[{"name":"School of Fundamental Sciences"},{"name":"School of Veterinary Science , Massey University, Palmerston North 4442, New Zealand"}]},{"given":"Samantha","family":"Baldwin","sequence":"additional","affiliation":[{"name":"New Cultivar Innovation , The New Zealand Institute for Plant & Food Research Limited, Christchurch 8140, New Zealand"}]},{"given":"Susan","family":"Thomson","sequence":"additional","affiliation":[{"name":"New Cultivar Innovation , The New Zealand Institute for Plant & Food Research Limited, Christchurch 8140, New Zealand"}]},{"given":"Matthieu","family":"Vignes","sequence":"additional","affiliation":[{"name":"School of Fundamental Sciences"}]}],"member":"286","published-online":{"date-parts":[[2020,1,21]]},"reference":[{"key":"2023013111482451000_btaa002-B1","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1105\/tpc.113.122069","article-title":"A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots","volume":"26","author":"Albert","year":"2014","journal-title":"Plant Cell"},{"key":"2023013111482451000_btaa002-B2","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1007\/978-1-4939-8882-2_15","article-title":"Gene regulatory networks: a primer in biological processes and statistical modelling","volume":"1883","author":"Angelin-Bonnet","year":"2019","journal-title":"Methods Mol. 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