{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:07:17Z","timestamp":1740143237620,"version":"3.37.3"},"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T00:00:00Z","timestamp":1591228800000},"content-version":"vor","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.1007889","type":"journal-article","created":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T17:28:02Z","timestamp":1591291682000},"page":"e1007889","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Disease evolution in reaction networks: Implications for a diagnostic problem"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3650-7722","authenticated-orcid":true,"given":"Abolfazl","family":"Ramezanpour","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2157-1211","authenticated-orcid":true,"given":"Alireza","family":"Mashaghi","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,6,4]]},"reference":[{"volume-title":"Current Medical Diagnosis and Treatment, 1997","year":"1996","author":"LM Tierney","key":"pcbi.1007889.ref001"},{"key":"pcbi.1007889.ref002","doi-asserted-by":"crossref","first-page":"14344","DOI":"10.1038\/srep14344","article-title":"Integrative analysis of human protein, function and disease networks","volume":"5","author":"W Liu","year":"2015","journal-title":"Scientific reports"},{"issue":"6224","key":"pcbi.1007889.ref003","doi-asserted-by":"crossref","first-page":"1257601","DOI":"10.1126\/science.1257601","article-title":"Uncovering disease-disease relationships through the incomplete interactome","volume":"347","author":"J Menche","year":"2015","journal-title":"Science"},{"key":"pcbi.1007889.ref004","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1214\/ss\/1177013426","article-title":"Probabilistic expert systems in medicine","volume":"2","author":"DJ Spielgelharter","year":"1987","journal-title":"Stat Sci"},{"key":"pcbi.1007889.ref005","first-page":"163","volume-title":"Machine Intelligence and Pattern Recognition","author":"D Heckerman","year":"1990"},{"issue":"04","key":"pcbi.1007889.ref006","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1055\/s-0038-1634846","article-title":"Probabilistic diagnosis using a reformulation of the INTERNIST-1\/QMR knowledge base","volume":"30","author":"MA Shwe","year":"1991","journal-title":"Methods of information in Medicine"},{"issue":"1","key":"pcbi.1007889.ref007","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/0933-3657(92)90036-O","article-title":"From certainty factors to belief networks","volume":"4","author":"DE Heckerman","year":"1992","journal-title":"Artificial Intelligence in Medicine"},{"issue":"4","key":"pcbi.1007889.ref008","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1109\/69.868904","article-title":"Constructing Bayesian networks for medical diagnosis from incomplete and partially correct statistics","volume":"12","author":"D Nikovski","year":"2000","journal-title":"IEEE Transactions on Knowledge and Data Engineering"},{"issue":"2","key":"pcbi.1007889.ref009","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.physrep.2013.03.004","article-title":"Markovian dynamics on complex reaction networks","volume":"529","author":"J Goutsias","year":"2013","journal-title":"Physics reports"},{"key":"pcbi.1007889.ref010","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780198570837.001.0001","volume-title":"Information, physics, and computation","author":"M Mezard","year":"2009"},{"volume-title":"Machine learning: a probabilistic perspective","year":"2012","author":"KP Murphy","key":"pcbi.1007889.ref011"},{"issue":"12","key":"pcbi.1007889.ref012","doi-asserted-by":"crossref","first-page":"e0167490","DOI":"10.1371\/journal.pone.0167490","article-title":"Major depression as a complex dynamic system","volume":"11","author":"AO Cramer","year":"2016","journal-title":"PloS one"},{"key":"pcbi.1007889.ref013","doi-asserted-by":"crossref","DOI":"10.1201\/9780429493492","volume-title":"Lectures on phase transitions and the renormalization group","author":"N Goldenfeld","year":"2018"},{"key":"pcbi.1007889.ref014","doi-asserted-by":"crossref","first-page":"32","DOI":"10.3389\/fphy.2017.00032","article-title":"Toward First Principle Medical Diagnostics: On the Importance of Disease-Disease and Sign-Sign Interactions","volume":"5","author":"A Ramezanpour","year":"2017","journal-title":"Frontiers in Physics"},{"issue":"1","key":"pcbi.1007889.ref015","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-20826-y","article-title":"Uncovering hidden disease patterns by simulating clinical diagnostic processes","volume":"8","author":"A Ramezanpour","year":"2018","journal-title":"Scientific reports"},{"issue":"3","key":"pcbi.1007889.ref016","doi-asserted-by":"crossref","first-page":"032118","DOI":"10.1103\/PhysRevE.97.032118","article-title":"Statistical physics of medical diagnostics: Study of a probabilistic model","volume":"97","author":"A Mashaghi","year":"2018","journal-title":"Physical Review E"},{"volume-title":"Molecular Pathology and the Dynamics of Disease","year":"2018","author":"MG Mitchell","key":"pcbi.1007889.ref017"},{"volume-title":"Disease dynamics","year":"1993","author":"A Asachenkov","key":"pcbi.1007889.ref018"},{"issue":"9","key":"pcbi.1007889.ref019","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1016\/0169-5347(96)20067-9","article-title":"Resource competition and within-host disease dynamics","volume":"11","author":"VH Smith","year":"1996","journal-title":"Trends in ecology & evolution"},{"key":"pcbi.1007889.ref020","doi-asserted-by":"crossref","DOI":"10.1002\/9781118634523","volume-title":"Neural dynamics of neurological disease","author":"CA Shaw","year":"2017"},{"issue":"2","key":"pcbi.1007889.ref021","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1097\/01.CCM.0000050285.93097.52","article-title":"Physiologic data acquisition system and database for the study of disease dynamics in the intensive care unit","volume":"31","author":"B Goldstein","year":"2003","journal-title":"Critical care medicine"},{"issue":"2","key":"pcbi.1007889.ref022","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0000241","article-title":"Imaging of disease dynamics during meningococcal sepsis","volume":"2","author":"H Sj\u00f6linder","year":"2007","journal-title":"PLoS One"},{"issue":"5400","key":"pcbi.1007889.ref023","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1126\/science.283.5400.381","article-title":"Emergent properties of networks of biological signaling pathways","volume":"283","author":"US Bhalla","year":"1999","journal-title":"Science"},{"issue":"4","key":"pcbi.1007889.ref024","doi-asserted-by":"crossref","first-page":"048101","DOI":"10.1103\/PhysRevLett.107.048101","article-title":"Multiplexing biochemical signals","volume":"107","author":"W de Ronde","year":"2011","journal-title":"Physical review letters"},{"issue":"1","key":"pcbi.1007889.ref025","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep11376","article-title":"Non-monotonic dynamics and crosstalk in signaling pathways and their implications for pharmacology","volume":"5","author":"R Van Wijk","year":"2015","journal-title":"Scientific reports"},{"issue":"8","key":"pcbi.1007889.ref026","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1073\/pnas.95.8.4193","article-title":"The underlying pathway structure of biochemical reaction networks","volume":"95","author":"CH Schilling","year":"1998","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"3","key":"pcbi.1007889.ref027","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1006\/mben.2000.0159","article-title":"The organization of metabolic reaction networks: a signal-oriented approach to cellular models","volume":"2","author":"A Kremling","year":"2000","journal-title":"Metabolic Engineering"},{"key":"pcbi.1007889.ref028","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1146\/annurev.physchem.012809.103457","article-title":"Functional motifs in biochemical reaction networks","volume":"61","author":"JJ Tyson","year":"2010","journal-title":"Annual review of physical chemistry"},{"issue":"4598","key":"pcbi.1007889.ref029","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1126\/science.220.4598.671","article-title":"Optimization by simulated annealing","volume":"220","author":"S Kirkpatrick","year":"1983","journal-title":"science"},{"volume-title":"Chemical reaction networks: a graph-theoretical approach","year":"1996","author":"ON Temkin","key":"pcbi.1007889.ref030"},{"volume-title":"Stochastic processes in physics and chemistry","year":"1992","author":"NG Van Kampen","key":"pcbi.1007889.ref031"},{"key":"pcbi.1007889.ref032","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1146\/annurev.physchem.58.032806.104637","article-title":"Stochastic simulation of chemical kinetics","volume":"58","author":"DT Gillespie","year":"2007","journal-title":"Annu. Rev. Phys. Chem"},{"issue":"6","key":"pcbi.1007889.ref033","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003669","article-title":"A scalable computational framework for establishing long-term behavior of stochastic reaction networks","volume":"10","author":"A Gupta","year":"2014","journal-title":"PLoS computational biology"},{"issue":"3","key":"pcbi.1007889.ref034","doi-asserted-by":"crossref","first-page":"034118","DOI":"10.1063\/1.4905196","article-title":"Adaptive hybrid simulations for multiscale stochastic reaction networks","volume":"142","author":"B Hepp","year":"2015","journal-title":"The Journal of chemical physics"},{"key":"pcbi.1007889.ref035","unstructured":"Amit DJ. Modeling Brain Function (Cambridge. Cambridge Univ. Press [2] PA Getting (1988), Neural Control of Rhythmic Movements in Vertebrates, eds, AH Cohen, S. Rossignol, 8L S. Grillner, New York: John Wiley. 1989;85:101-27."},{"key":"pcbi.1007889.ref036","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.jtbi.2011.07.027","article-title":"A thermodynamic perspective of immune capabilities","volume":"287","author":"E Agliari","year":"2011","journal-title":"Journal of theoretical biology"},{"issue":"41","key":"pcbi.1007889.ref037","doi-asserted-by":"crossref","first-page":"415003","DOI":"10.1088\/1751-8113\/46\/41\/415003","article-title":"Immune networks: multitasking capabilities near saturation","volume":"46","author":"E Agliari","year":"2013","journal-title":"Journal of Physics A: Mathematical and Theoretical"},{"issue":"2","key":"pcbi.1007889.ref038","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nrm1570","article-title":"Reconstruction of cellular signalling networks and analysis of their properties","volume":"6","author":"JA Papin","year":"2005","journal-title":"Nature reviews Molecular cell biology"},{"issue":"6","key":"pcbi.1007889.ref039","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1073\/pnas.0610772104","article-title":"Global reconstruction of the human metabolic network based on genomic and bibliomic data","volume":"104","author":"NC Duarte","year":"2007","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"pcbi.1007889.ref040","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005331","article-title":"Scalable parameter estimation for genome-scale biochemical reaction networks","volume":"13","author":"F Fr\u00f6hlich","year":"2017","journal-title":"PLoS computational biology"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007889","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T17:28:35Z","timestamp":1591291715000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007889"}},"subtitle":[],"editor":[{"given":"Benjamin","family":"Althouse","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,6,4]]},"references-count":40,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2020,6,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007889","relation":{},"ISSN":["1553-7358"],"issn-type":[{"type":"electronic","value":"1553-7358"}],"subject":[],"published":{"date-parts":[[2020,6,4]]}}}