{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T21:29:34Z","timestamp":1784755774538,"version":"3.55.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3007,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u00a0In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene\u2013gene, protein\u2013protein and gene\u2013protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes.<\/jats:p>\n               <jats:p>Results: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software.<\/jats:p>\n               <jats:p>Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1\u2013Th2 cellular differentiation process.<\/jats:p>\n               <jats:p>Availability: The software binaries for Windows and Linux platforms can be downloaded from http:\/\/si2.epfl.ch\/~garg\/genysis.html.<\/jats:p>\n               <jats:p>Contact: \u00a0abhishek.garg@epfl.ch<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn336","type":"journal-article","created":{"date-parts":[[2008,7,10]],"date-time":"2008-07-10T00:25:55Z","timestamp":1215649555000},"page":"1917-1925","source":"Crossref","is-referenced-by-count":244,"title":["Synchronous versus asynchronous modeling of gene regulatory networks"],"prefix":"10.1093","volume":"24","author":[{"given":"Abhishek","family":"Garg","sequence":"first","affiliation":[{"name":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, 2Merck Serono, Geneva, 3Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland and 4Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9exico, M\u00e9xico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Di Cara","sequence":"additional","affiliation":[{"name":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, 2Merck Serono, Geneva, 3Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland and 4Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9exico, M\u00e9xico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[{"name":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, 2Merck Serono, Geneva, 3Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland and 4Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9exico, M\u00e9xico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Mendoza","sequence":"additional","affiliation":[{"name":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, 2Merck Serono, Geneva, 3Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland and 4Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9exico, M\u00e9xico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"De Micheli","sequence":"additional","affiliation":[{"name":"1 Ecole Polytechnique Federale de Lausanne, Station 14, 1015 Lausanne, 2Merck Serono, Geneva, 3Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland and 4Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9exico, M\u00e9xico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,7,9]]},"reference":[{"key":"2023020211085359600_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(03)00035-3","article-title":"The topology of the regulatory interactions predicts the expression pattern of the Drosophila segment polarity genes","volume":"223","author":"Albert","year":"2003","journal-title":"J. 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