{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:23:19Z","timestamp":1764688999363},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T00:00:00Z","timestamp":1415232000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003916","type":"journal-article","created":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T19:08:14Z","timestamp":1415300894000},"page":"e1003916","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks"],"prefix":"10.1371","volume":"10","author":[{"given":"Ricardo","family":"Pinho","sequence":"first","affiliation":[]},{"given":"Victor","family":"Garcia","sequence":"additional","affiliation":[]},{"given":"Manuel","family":"Irimia","sequence":"additional","affiliation":[]},{"given":"Marcus W.","family":"Feldman","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,11,6]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1126\/science.1090005","article-title":"Evolution at two levels in humans and chimpanzees","volume":"188","author":"M-C King","year":"1975","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"e245","DOI":"10.1371\/journal.pbio.0030245","article-title":"Evolution at two levels: on genes and form","volume":"3","author":"SB Carroll","year":"2005","journal-title":"PLoS Biol"},{"key":"ref3","doi-asserted-by":"crossref","unstructured":"Davidson EH (2006) The regulatory genome: gene regulatory networks in development and evolution. Academic Press.","DOI":"10.1016\/B978-012088563-3.50022-5"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/35036627","article-title":"The large-scale organization of metabolic networks","volume":"407","author":"H Jeong","year":"2000","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1126\/science.298.5594.824","article-title":"Network motifs: simple building blocks of complex networks","volume":"298","author":"R Milo","year":"2002","journal-title":"Science"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1038\/43199","article-title":"Robustness in simple biochemical networks","volume":"387","author":"N Barkai","year":"1997","journal-title":"Nature"},{"key":"ref7","first-page":"967","article-title":"Perspective: Complex Adaptations and the Evolution of Evolvability","volume":"50","author":"GP Wagner","year":"1996","journal-title":"Evolution (N Y)"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1073\/pnas.94.3.814","article-title":"Stochastic mechanisms in gene expression","volume":"94","author":"HH McAdams","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/35014651","article-title":"Engineering stability in gene networks by autoregulation","volume":"405","author":"A Becskei","year":"2000","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/ng881","article-title":"Network motifs in the transcriptional regulation network of Escherichia coli","volume":"31","author":"SS Shen-Orr","year":"2002","journal-title":"Nat Genet"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1075090","article-title":"Transcriptional Regulatory Networks in Saccharomyces cerevisiae","volume":"298","author":"TI Lee","year":"2002","journal-title":"Science"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e255","DOI":"10.1371\/journal.pbio.0060255","article-title":"Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system","volume":"6","author":"DJ Hogan","year":"2008","journal-title":"PLoS Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1007\/978-3-642-81703-8_24","article-title":"On the Relation Between the Logical Structure of Systems and Their Ability to Generate Multiple Steady States or Sustained Oscillations","volume":"9","author":"R Thomas","year":"1981","journal-title":"Numer methods study Crit Phenom"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/BF02460618","article-title":"Dynamical behaviour of biological regulatory networks\u2014I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state","volume":"57","author":"R Thomas","year":"1995","journal-title":"Bull Math Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/S0079-6603(08)60892-2","article-title":"Autoregulation of eukaryotic transcription factors","volume":"60","author":"E Bateman","year":"1998","journal-title":"Prog Nucleic Acid Res Mol Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1578","DOI":"10.1126\/science.8128244","article-title":"Negative feedback defining a circadian clock: autoregulation of the clock gene frequency","volume":"263","author":"B Aronson","year":"1994","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/nrg2102","article-title":"Network motifs: theory and experimental approaches","volume":"8","author":"U Alon","year":"2007","journal-title":"Nat Rev Genet"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1007\/BF02460695","article-title":"Logical identification of all steady states: The concept of feedback loop characteristic states","volume":"55","author":"EH Snoussi","year":"1993","journal-title":"Bull Math Biol"},{"key":"ref19","first-page":"479","article-title":"Laws for the dynamics of regulatory networks","volume":"42","author":"R Thomas","year":"1998","journal-title":"Int J Dev Biol"},{"key":"ref20","article-title":"On Circuit Functionality in Boolean Networks","author":"J-P Comet","year":"2013","journal-title":"Bull Math Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/BF02478259","article-title":"A logical calculus of the ideas immanent in nervous activity","volume":"5","author":"WS McCulloch","year":"1943","journal-title":"Bull Math Biophys"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"2554","DOI":"10.1073\/pnas.79.8.2554","article-title":"Neural networks and physical systems with emergent collective computational abilities","volume":"79","author":"JJ Hopfield","year":"1982","journal-title":"PNAS"},{"key":"ref23","first-page":"1008","article-title":"Does evolutionary plasticity evolve?","volume":"50","author":"A Wagner","year":"1996","journal-title":"Evolution (N Y)"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/0022-5193(69)90015-0","article-title":"Metabolic stability and epigenesis in randomly constructed genetic nets","volume":"22","author":"SA Kauffman","year":"1969","journal-title":"J Theor Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"L615","DOI":"10.1088\/0305-4470\/21\/11\/009","article-title":"Correspondence between neural threshold networks and Kauffman Boolean cellular automata","volume":"21","author":"KE Kurten","year":"1988","journal-title":"J Phys A Math Gen"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1103\/PhysRevLett.95.048701","article-title":"Dynamics of critical Kauffman networks under asynchronous stochastic update","volume":"95","author":"F Greil","year":"2005","journal-title":"Phys Rev Lett"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1088\/1367-2630\/9\/10\/373","article-title":"Critical Kauffman networks under deterministic asynchronous update","volume":"9","author":"F Greil","year":"2007","journal-title":"New J Phys"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1103\/PhysRevE.72.055101","article-title":"Stable and unstable attractors in Boolean networks","volume":"72","author":"K Klemm","year":"2005","journal-title":"Phys Rev E"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"10528","DOI":"10.1073\/pnas.102303999","article-title":"Waddington's canalization revisited: developmental stability and evolution","volume":"99","author":"ML Siegal","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e34285","DOI":"10.1371\/journal.pone.0034285","article-title":"Most Networks in Wagner's Model Are Cycling","volume":"7","author":"R Pinho","year":"2012","journal-title":"PLoS One"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1002\/j.1538-7305.1950.tb00463.x","article-title":"Error detecting and error correcting codes","volume":"29","author":"RW Hamming","year":"1950","journal-title":"Bell Syst Tech J"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1745-6150-3-49","article-title":"Activating and inhibiting connections in biological network dynamics","volume":"3","author":"D McDonald","year":"2008","journal-title":"Biol Direct"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1371\/journal.pcbi.0030015","article-title":"Robustness can evolve gradually in complex regulatory gene networks with varying topology","volume":"3","author":"S Ciliberti","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"4781","DOI":"10.1073\/pnas.0305937101","article-title":"The yeast cell-cycle network is robustly designed","volume":"101","author":"F Li","year":"2004","journal-title":"PNAS"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e1672","DOI":"10.1371\/journal.pone.0001672","article-title":"Boolean network model predicts cell cycle sequence of fission yeast","volume":"3","author":"MI Davidich","year":"2008","journal-title":"PLoS One"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e124","DOI":"10.1093\/bioinformatics\/btl210","article-title":"Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle","volume":"22","author":"A Faur\u00e9","year":"2006","journal-title":"Bioinformatics"},{"key":"ref37","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 segment polarity genes in Drosophila melanogaster","volume":"223","author":"R Albert","year":"2003","journal-title":"J Theor Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/15.7.593","article-title":"Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis","volume":"15","author":"L Mendoza","year":"1999","journal-title":"Bioinformatics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"2923","DOI":"10.1105\/tpc.104.021725","article-title":"A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles","volume":"16","author":"C Espinosa-Soto","year":"2004","journal-title":"Plant Cell"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1104\/pp.103.022780","article-title":"Light- and carbon-signaling pathways. Modeling circuits of interactions","volume":"132","author":"KE Thum","year":"2003","journal-title":"Plant Physiol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"e3210","DOI":"10.1371\/journal.pone.0003210","article-title":"Transcriptional autoregulatory loops are highly conserved in vertebrate evolution","volume":"3","author":"SM Kie\u0142basa","year":"2008","journal-title":"PLoS One"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.cell.2013.03.035","article-title":"Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes","volume":"153","author":"WA Whyte","year":"2013","journal-title":"Cell"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1016\/j.cell.2011.01.032","article-title":"Control of the embryonic stem cell state","volume":"144","author":"RA Young","year":"2011","journal-title":"Cell"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.cell.2008.01.015","article-title":"Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming","volume":"132","author":"R Jaenisch","year":"2008","journal-title":"Cell"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"D203","DOI":"10.1093\/nar\/gks1201","article-title":"RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more","volume":"41","author":"H Salgado","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"e1002992","DOI":"10.1371\/journal.pcbi.1002992","article-title":"Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids","volume":"9","author":"AJ Stewart","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/msb.2008.52","article-title":"Survival of the sparsest: robust gene networks are parsimonious","volume":"4","author":"RD Leclerc","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1534\/genetics.104.027334","article-title":"Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster","volume":"167","author":"J Jaeger","year":"2004","journal-title":"Genetics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nature04488","article-title":"Sexual reproduction selects for robustness and negative epistasis in artificial gene networks","volume":"440","author":"RBR Azevedo","year":"2006","journal-title":"Nature"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1038\/nrg1633","article-title":"Circadian rhythms from multiple oscillators: lessons from diverse organisms","volume":"6","author":"D Bell-Pedersen","year":"2005","journal-title":"Nat Rev Genet"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"2005.0013","DOI":"10.1038\/msb4100018","article-title":"Extension of a genetic network model by iterative experimentation and mathematical analysis","volume":"1","author":"JCW Locke","year":"2005","journal-title":"Mol Syst Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"i80","DOI":"10.1093\/bioinformatics\/btt243","article-title":"Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model","volume":"29","author":"N Bonzanni","year":"2013","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"D750","DOI":"10.1093\/nar\/gkn887","article-title":"SpBase: the sea urchin genome database and web site","volume":"37","author":"RA Cameron","year":"2009","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003916","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,17]],"date-time":"2023-07-17T23:29:16Z","timestamp":1689636556000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003916"}},"subtitle":[],"editor":[{"given":"Marcel","family":"Salath\u00e9","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,11,6]]},"references-count":53,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2014,11,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003916","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,6]]}}}