{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T05:32:33Z","timestamp":1782192753796,"version":"3.54.5"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Interferon-\u03b2 induced JAK-STAT signaling pathways contribute to mucosal immune recognition and an anti-viral state. Though the main molecular mechanisms constituting these pathways are known, neither the detailed structure of the regulatory network, nor its dynamics has yet been investigated. The objective of this work is to build a mathematical model for the pathway that would serve two purposes: (1) to reproduce experimental results in simulation of both early and late response to Interferon-\u03b2 stimulation and (2) to explain experimental phenomena generating new hypotheses about regulatory mechanisms that cannot yet be tested experimentally.<\/jats:p>\n               <jats:p>Results: Experimentally determined time dependent changes in the major components of this pathway were used to build a mathematical model describing pathway dynamics in the form of ordinary differential equations. The experimental results suggested existence of unknown negative control mechanisms that were tested numerically using the model. Together, experimental and numerical data show that the epithelial JAK-STAT pathway might be subjected to previously unknown dynamic negative control mechanisms: (1) activation of dormant phosphatases and (2) inhibition of nuclear import of IRF1.<\/jats:p>\n               <jats:p>Availability: The model, written in Matlab, is available online at www.stat.rice.edu\/~jsmieja\/IFN<\/jats:p>\n               <jats:p>Contact: \u00a0jaroslaw.smieja@polsl.pl<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn400","type":"journal-article","created":{"date-parts":[[2008,8,20]],"date-time":"2008-08-20T02:49:03Z","timestamp":1219200543000},"page":"2363-2369","source":"Crossref","is-referenced-by-count":41,"title":["Model-based analysis of interferon-\u03b2 induced signaling pathway"],"prefix":"10.1093","volume":"24","author":[{"given":"Jaroslaw","family":"Smieja","sequence":"first","affiliation":[{"name":"1 Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-101 Gliwice, Poland, 2Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555-1060 and 3Department of Statistics, Rice University, 6100 Main Street, MS-138, Houston, TX 77005, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Jamaluddin","sequence":"additional","affiliation":[{"name":"1 Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-101 Gliwice, Poland, 2Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555-1060 and 3Department of Statistics, Rice University, 6100 Main Street, MS-138, Houston, TX 77005, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allan R.","family":"Brasier","sequence":"additional","affiliation":[{"name":"1 Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-101 Gliwice, Poland, 2Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555-1060 and 3Department of Statistics, Rice University, 6100 Main Street, MS-138, Houston, TX 77005, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Kimmel","sequence":"additional","affiliation":[{"name":"1 Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-101 Gliwice, Poland, 2Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555-1060 and 3Department of Statistics, Rice University, 6100 Main Street, MS-138, Houston, TX 77005, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,8,19]]},"reference":[{"key":"2023020211252836700_B1","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nri1391","article-title":"Toll-like receptor signaling","volume":"4","author":"Akira","year":"2004","journal-title":"Nat. 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