{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T12:53:00Z","timestamp":1779367980684,"version":"3.53.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T00:00:00Z","timestamp":1676419200000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The gene regulatory process resembles a logic system in which a target gene is regulated by a logic gate among its regulators. While various computational techniques are developed for a gene regulatory network (GRN) reconstruction, the study of logical relationships has received little attention. Here, we propose a novel tool called wpLogicNet that simultaneously infers both the directed GRN structures and logic gates among genes or transcription factors (TFs) that regulate their target genes, based on continuous steady-state gene expressions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>wpLogicNet proposes a framework to infer the logic gates among any number of regulators, with a low time-complexity. This distinguishes wpLogicNet from the existing logic-based models that are limited to inferring the gate between two genes or TFs. Our method applies a Bayesian mixture model to estimate the likelihood of the target gene profile and to infer the logic gate a posteriori. Furthermore, in structure-aware mode, wpLogicNet reconstructs the logic gates in TF\u2013gene or gene\u2013gene interaction networks with known structures. The predicted logic gates are validated on simulated datasets of TF\u2013gene interaction networks from Escherichia coli. For the directed-edge inference, the method is validated on datasets from E.coli and DREAM project. The results show that compared to other well-known methods, wpLogicNet is more precise in reconstructing the network and logical relationships among genes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The datasets and R package of wpLogicNet are available in the github repository, https:\/\/github.com\/CompBioIPM\/wpLogicNet.<\/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\/btad072","type":"journal-article","created":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T12:39:38Z","timestamp":1676464778000},"source":"Crossref","is-referenced-by-count":18,"title":["wpLogicNet: logic gate and structure inference in gene regulatory networks"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3525-3548","authenticated-orcid":false,"given":"Seyed Amir","family":"Malekpour","sequence":"first","affiliation":[{"name":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryam","family":"Shahdoust","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosa","family":"Aghdam","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5746, Iran"},{"name":"Wisconsin Institute for Discovery, University of Wisconsin-Madison , Madison, WI 53715, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mehdi","family":"Sadeghi","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology , Tehran 1497716316, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,2,15]]},"reference":[{"key":"2023051718071359800_btad072-B1","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1039\/C4MB00413B","article-title":"CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test","volume":"11","author":"Aghdam","year":"2015","journal-title":"Mol. 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