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We use a previously developed purely theoretical algorithm built to detect nodes that can induce a state change in Boolean gene regulatory networks, and show that most genes predicted to participate in differentiation in the theoretical framework are also experimentally known to be associated with such differentiation. These results show that genes related to differentiation are associated with specific features of the genetic regulatory network. The proposed algorithm produces a better classification than simple network measures such as the nodes degree or centrality. Boolean networks were used in many previous theoretical models. Here, we show a direct application of such networks to the detection of genes and subnetworks related to differentiation. The subnetwork emerging from the genes and edges that are predicted to be associated with differentiation are the most active molecular pathways experimentally described to be involved in cell differentiation.<\/jats:p><jats:p>Availability and implementation: \u00a0http:\/\/peptibase.cs.biu.ac.il\/homepage\/Boolean_network_conversion_code.zip.<\/jats:p><jats:p>Contact: \u00a0louzouy@math.biu.ac.il<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt685","type":"journal-article","created":{"date-parts":[[2013,12,14]],"date-time":"2013-12-14T02:19:55Z","timestamp":1386987595000},"page":"406-413","source":"Crossref","is-referenced-by-count":3,"title":["Genes related to differentiation are correlated with the gene regulatory network structure"],"prefix":"10.1093","volume":"30","author":[{"given":"Matan","family":"Bodaker","sequence":"first","affiliation":[{"name":"1 Department of Cell and Developmental Biology and 2Department of Genetics, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel and 3Department of Mathematics and Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eran","family":"Meshorer","sequence":"additional","affiliation":[{"name":"1 Department of Cell and Developmental Biology and 2Department of Genetics, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel and 3Department of Mathematics and Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eduardo","family":"Mitrani","sequence":"additional","affiliation":[{"name":"1 Department of Cell and Developmental Biology and 2Department of Genetics, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel and 3Department of Mathematics and Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoram","family":"Louzoun","sequence":"additional","affiliation":[{"name":"1 Department of Cell and Developmental Biology and 2Department of Genetics, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel and 3Department of Mathematics and Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,12,12]]},"reference":[{"key":"2023012710410628600_btt685-B1","doi-asserted-by":"crossref","first-page":"e1000407","DOI":"10.1371\/journal.pcbi.1000407","article-title":"Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybrids","volume":"5","author":"Ahn","year":"2009","journal-title":"PLoS Comput. 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