{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T08:52:42Z","timestamp":1770367962960,"version":"3.49.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T00:00:00Z","timestamp":1768867200000},"content-version":"vor","delay-in-days":17,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100015257","name":"Northeastern University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015257","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of General Medical Sciences of the National Institutes of Health","award":["R35GM128717"],"award-info":[{"award-number":["R35GM128717"]}]},{"name":"Northeastern University Bioengineering Department Dean\u2019s Fellowship"},{"name":"On-Ramp into Research Endeavors"},{"DOI":"10.13039\/100015257","name":"Northeastern University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015257","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center for Theoretical Biological Physics at Northeastern University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The Random Circuit Perturbation (RACIPE) algorithm enables the exploration of the dynamical behaviors of gene regulatory circuits (GRCs) by simulating an ensemble of differential equation models via randomization of kinetic parameters. Here, we release sRACIPE 2.0, a major update to the R\/Bioconductor package, as a unified platform for modeling GRCs with diverse interaction types using both deterministic and stochastic simulations. The update also introduces new features for modeling perturbation, extrinsic signaling and time-corrected noise, and a new diagnostic tool to ensure proper simulations. We hope that this release will serve as a versatile modeling toolkit for the systems biology community.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The package is available on GitHub at https:\/\/github.com\/lusystemsbio\/sRACIPE under the MIT license. It is also available on Bioconductor at https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/sRACIPE.html.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag019","type":"journal-article","created":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T12:38:36Z","timestamp":1768567116000},"source":"Crossref","is-referenced-by-count":0,"title":["sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-3860-9650","authenticated-orcid":false,"given":"Aidan","family":"Tillman","sequence":"first","affiliation":[{"name":"Department of Bioengineering, Northeastern University , Boston, MA 02115,","place":["United States"]},{"name":"Center for Theoretical Biological Physics, Northeastern University , Boston, MA 02115,","place":["United 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