{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T10:59:23Z","timestamp":1779101963217,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,9,16]],"date-time":"2020-09-16T00:00:00Z","timestamp":1600214400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100005946","name":"The Jackson Laboratory","doi-asserted-by":"publisher","award":["P30CA034196"],"award-info":[{"award-number":["P30CA034196"]}],"id":[{"id":"10.13039\/100005946","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM128717"],"award-info":[{"award-number":["R35GM128717"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009159","name":"Center for Theoretical Biological Physics","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009159","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-1427654"],"award-info":[{"award-number":["PHY-1427654"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>GeneEx is an interactive web-app that uses an ODE-based mathematical modeling approach to simulate, visualize and analyze gene regulatory circuits (GRCs) for an explicit kinetic parameter set or for a large ensemble of random parameter sets. GeneEx offers users the freedom to modify many aspects of the simulation such as the parameter ranges, the levels of gene expression noise and the GRC network topology itself. This degree of flexibility allows users to explore a variety of hypotheses by providing insight into the number and stability of attractors for a given GRC. Moreover, users have the option to upload, and subsequently compare, experimental gene expression data to simulated data generated from the analysis of a built or uploaded custom circuit. Finally, GeneEx offers a curated database that contains circuit motifs and known biological GRCs to facilitate further inquiry into these. Overall, GeneEx enables users to investigate the effects of parameter variation, stochasticity and\/or topological changes on gene expression for GRCs using a systems-biology approach.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GeneEx is available at https:\/\/geneex.jax.org. This web-app is released under the MIT license and is free and open to all users and there is no mandatory login requirement.<\/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\/btaa785","type":"journal-article","created":{"date-parts":[[2020,9,4]],"date-time":"2020-09-04T13:02:15Z","timestamp":1599224535000},"page":"1327-1329","source":"Crossref","is-referenced-by-count":5,"title":["Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1813-1597","authenticated-orcid":false,"given":"Vivek","family":"Kohar","sequence":"first","affiliation":[{"name":"The Jackson Laboratory , Bar Harbor, ME 04609, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danya","family":"Gordin","sequence":"additional","affiliation":[{"name":"The Jackson Laboratory , Bar Harbor, ME 04609, USA"},{"name":"Center for Theoretical Biological Physics"},{"name":"Department of Bioengineering"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ataur","family":"Katebi","sequence":"additional","affiliation":[{"name":"The Jackson Laboratory , Bar Harbor, ME 04609, USA"},{"name":"Center for Theoretical Biological Physics"},{"name":"Department of Bioengineering"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Herbert","family":"Levine","sequence":"additional","affiliation":[{"name":"Center for Theoretical Biological Physics"},{"name":"Department of Bioengineering"},{"name":"Department of Physics, Northeastern University , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 N","family":"Onuchic","sequence":"additional","affiliation":[{"name":"Center for Theoretical\u2002 Biological Physics"},{"name":"Department of Physics and Astronomy"},{"name":"Department of Chemistry"},{"name":"Department of Biosciences, Rice University , Houston, TX 77005, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingyang","family":"Lu","sequence":"additional","affiliation":[{"name":"The Jackson Laboratory , Bar Harbor, ME 04609, USA"},{"name":"Center for Theoretical Biological Physics"},{"name":"Department of Bioengineering"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,12,6]]},"reference":[{"key":"2023051800332160300_btaa785-B1","author":"Almende","year":"2016"},{"key":"2023051800332160300_btaa785-B2","doi-asserted-by":"crossref","DOI":"10.1201\/9781420011432","volume-title":"An Introduction to Systems Biology\u202f: Design Principles of Biological Circuits","author":"Alon","year":"2006"},{"key":"2023051800332160300_btaa785-B3","author":"Chang","year":"2016"},{"key":"2023051800332160300_btaa785-B4","author":"Dowle","year":"2017"},{"key":"2023051800332160300_btaa785-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v040.i08","article-title":"RCPP: seamless R and C++ integration","volume":"40","author":"Eddelbuettel","year":"2011","journal-title":"J. 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