{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T03:23:44Z","timestamp":1772249024793,"version":"3.50.1"},"reference-count":68,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T00:00:00Z","timestamp":1702944000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Comput. Neurosci."],"abstract":"<jats:p>The human brain, composed of billions of neurons and synaptic connections, is an intricate network coordinating a sophisticated balance of excitatory and inhibitory activities between brain regions. The dynamical balance between excitation and inhibition is vital for adjusting neural input\/output relationships in cortical networks and regulating the dynamic range of their responses to stimuli. To infer this balance using connectomics, we recently introduced a computational framework based on the Ising model, which was first developed to explain phase transitions in ferromagnets, and proposed a novel hybrid resting-state structural connectome (rsSC). Here, we show that a generative model based on the Kuramoto phase oscillator can be used to simulate static and dynamic functional connectomes (FC) with rsSC as the coupling weight coefficients, such that the simulated FC aligns well with the observed FC when compared with that simulated traditional structural connectome.<\/jats:p>","DOI":"10.3389\/fncom.2023.1295395","type":"journal-article","created":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T05:32:11Z","timestamp":1702963931000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Enhanced simulations of whole-brain dynamics using hybrid resting-state structural connectomes"],"prefix":"10.3389","volume":"17","author":[{"given":"Thanos","family":"Manos","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra","family":"Diaz-Pier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Igor","family":"Fortel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ira","family":"Driscoll","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Zhan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Leow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,12,19]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3389\/fninf.2013.00030","article-title":"Constructing the resting state structural connectome","author":"Ajilore","year":"2013","journal-title":"Front. Neuroinform"},{"key":"B2","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1016\/j.neuroimage.2017.05.067","article-title":"The energy landscape underpinning module dynamics in the human brain connectome","volume":"157","author":"Ashourvan","year":"2017","journal-title":"NeuroImage"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aau8535","article-title":"Cognitive chimera states in human brain networks","author":"Bansal","year":"2019","journal-title":"Sci. Adv"},{"key":"B4","doi-asserted-by":"publisher","first-page":"11167","DOI":"10.1523\/JNEUROSCI.23-35-11167.2003","article-title":"Neuronal avalanches in neocortical circuits","volume":"23","author":"Beggs","year":"2003","journal-title":"J. Neurosci"},{"key":"B5","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1002\/(SICI)1099-1492(199706\/08)10:4\/5<165::AID-NBM454>3.0.CO;2-7","article-title":"Simultaneous assessment of flow and bold signals in resting-state functional connectivity maps","volume":"10","author":"Biswal","year":"1997","journal-title":"NMR Biomed"},{"key":"B6","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1016\/j.neuroimage.2011.04.010","article-title":"Role of local network oscillations in resting-state functional connectivity","volume":"57","author":"Cabral","year":"2011","journal-title":"NeuroImage"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-05425-7","article-title":"Cognitive performance in healthy older adults relates to spontaneous switching between states of functional connectivity during rest","author":"Cabral","year":"2017","journal-title":"Scient. Rep"},{"key":"B8","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.pneurobio.2017.07.002","article-title":"Criticality in the brain: a synthesis of neurobiology, models and cognition","volume":"158","author":"Cocchi","year":"2017","journal-title":"Progr. Neurobiol"},{"key":"B9","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/j.coisb.2017.04.017","article-title":"Functional networks from inverse modeling of neural population activity","volume":"3","author":"Cocco","year":"2017","journal-title":"Curr. Opin. Syst. Biol"},{"key":"B10","doi-asserted-by":"publisher","first-page":"3366","DOI":"10.1523\/JNEUROSCI.2523-11.2012","article-title":"Ongoing cortical activity at rest: criticality, multistability, and ghost attractors","volume":"32","author":"Deco","year":"2012","journal-title":"J. Neurosci"},{"key":"B11","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/nrn2961","article-title":"Emerging concepts for the dynamical organization of resting-state activity in the brain","volume":"12","author":"Deco","year":"2011","journal-title":"Nat. Rev. Neurosci"},{"key":"B12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1000092","article-title":"The dynamic brain: From spiking neurons to neural masses and cortical fields","volume":"4","author":"Deco","year":"2008","journal-title":"PLoS Computat. Biol"},{"key":"B13","doi-asserted-by":"publisher","first-page":"4436","DOI":"10.1016\/j.cub.2021.07.064","article-title":"Rare long-range cortical connections enhance human information processing","volume":"31","author":"Deco","year":"2021","journal-title":"Curr. Biol"},{"key":"B14","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1016\/j.neuroimage.2006.01.021","article-title":"An automated labeling system for subdividing the human cerebral cortex on mri scans into gyral based regions of interest","volume":"31","author":"Desikan","year":"2006","journal-title":"NeuroImage"},{"key":"B15","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/j.neuron.2013.07.036","article-title":"A predictive network model of cerebral cortical connectivity based on a distance rule","volume":"80","author":"Ercsey-Ravasz","year":"2013","journal-title":"Neuron"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-020-0774-y","article-title":"Closer to critical resting-state neural dynamics in individuals with higher fluid intelligence","author":"Ezaki","year":"2020","journal-title":"Commun. Biol"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1098\/rsta.2016.0287","article-title":"Energy landscape analysis of neuroimaging data","author":"Ezaki","year":"2017","journal-title":"Philosoph. Trans. R. Soc. A"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1038\/nn.4135","article-title":"Functional connectome fingerprinting: identifying individuals using patterns of brain connectivity","volume":"18","author":"Finn","year":"2015","journal-title":"Nat. Neurosci"},{"key":"B19","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1007\/978-3-030-32254-0_56","article-title":"\u201cBrain dynamics through the lens of statistical mechanics by unifying structure and function,\u201d","author":"Fortel","year":"2019","journal-title":"Medical Image Computing and Computer Assisted Intervention-MICCAI 2019"},{"key":"B20","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1162\/netn_a_00220","article-title":"Inferring excitation-inhibition dynamics using a maximum entropy model unifying brain structure and function","volume":"6","author":"Fortel","year":"2022","journal-title":"Netw. Neurosci"},{"key":"B21","doi-asserted-by":"publisher","first-page":"6350","DOI":"10.1093\/cercor\/bhaa190","article-title":"Connectome Signatures of hyperexcitation in cognitively intact middle-aged female APOE-\u03b54 carriers","volume":"30","author":"Fortel","year":"2020","journal-title":"Cerebral Cortex"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1449","DOI":"10.3233\/JAD-230035","article-title":"Disrupted Excitation-Inhibition balance in cognitively normal individuals at risk of alzheimer's disease","volume":"95","author":"Fortel","year":"2023","journal-title":"J. Alzheimers Dis"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1016\/S1053-8119(03)00202-7","article-title":"Dynamic causal modelling","volume":"19","author":"Friston","year":"2003","journal-title":"NeuroImage"},{"key":"B24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1000196","article-title":"Noise during rest enables the exploration of the brain's dynamic repertoire","volume":"4","author":"Ghosh","year":"2008","journal-title":"PLoS Comput. Biol"},{"key":"B25","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.jneumeth.2010.01.014","article-title":"Mr connectomics: Principles and challenges","volume":"194","author":"Hagmann","year":"2010","journal-title":"J. Neurosci. Method"},{"key":"B26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1005543","article-title":"Spontaneous cortical activity is transiently poised close to criticality","volume":"13","author":"Hahn","year":"2017","journal-title":"PLoS Computat. Biol"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.110.178101","article-title":"Brain organization into resting state networks emerges at criticality on a model of the human connectome","author":"Haimovici","year":"2013","journal-title":"Phys. Rev. Lett"},{"key":"B28","doi-asserted-by":"publisher","first-page":"119433","DOI":"10.1016\/j.neuroimage.2022.119433","article-title":"Metastability, fractal scaling, and synergistic information processing: what phase relationships reveal about intrinsic brain activity","volume":"259","author":"Hancock","year":"2022","journal-title":"NeuroImage"},{"key":"B29","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.neuroimage.2013.09.069","article-title":"The structural-functional connectome and the default mode network of the human brain","volume":"102","author":"Horn","year":"2014","journal-title":"NeuroImage"},{"key":"B30","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/j.neuroimage.2016.04.049","article-title":"The virtual epileptic patient: Individualized whole-brain models of epilepsy spread","volume":"145","author":"Jirsa","year":"2017","journal-title":"NeuroImage"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-05462-2","article-title":"Inferring structural connectivity using ising couplings in models of neuronal networks","author":"Kadirvelu","year":"2017","journal-title":"Scient. Rep"},{"key":"B32","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1038\/nphys289","article-title":"Optimal dynamical range of excitable networks at criticality","volume":"2","author":"Kinouchi","year":"2006","journal-title":"Nat. Phys"},{"key":"B33","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.neuroimage.2018.05.052","article-title":"Disrupted topology of the resting state structural connectome in middle-aged apoe \u03b54 carriers","volume":"178","author":"Korthauer","year":"2018","journal-title":"NeuroImage"},{"key":"B34","volume-title":"Chemical Oscillations, Waves, and Turbulence","author":"Kuramoto","year":"2003"},{"key":"B35","volume-title":"Elements of Applied Bifurcation Theory. Number 112 in Applied Mathematical Sciences","author":"Kuznetsov","year":"1998"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-16789-1","article-title":"Linking functional connectivity and dynamic properties of resting-state networks","author":"Lee","year":"2017","journal-title":"Scient. Rep"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1063\/1.4979043","article-title":"Balance of excitation and inhibition determines 1\/f power spectrum in neuronal networks","author":"Lombardi","year":"2017","journal-title":"Chaos"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0093616","article-title":"Information transfer and criticality in the ising model on the human connectome","volume":"9","author":"Marinazzo","year":"2014","journal-title":"PLoS ONE"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1003530","article-title":"Relating structure and function in the human brain: Relative contributions of anatomy, stationary dynamics, and non-stationarities","volume":"10","author":"Mess","year":"2014","journal-title":"PLoS Comput. Biol"},{"key":"B40","doi-asserted-by":"publisher","first-page":"12174","DOI":"10.1073\/pnas.0902071106","article-title":"Direct electrophysiological measurement of human default network areas","volume":"106","author":"Miller","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1103\/RevModPhys.90.031001","article-title":"Colloquium: Criticality and dynamical scaling in living systems","author":"Mu\u00f1oz","year":"2018","journal-title":"Rev. Mod. Phys"},{"key":"B42","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1016\/j.bpsc.2018.07.004","article-title":"Biophysical modeling of large-scale brain dynamics and applications for computational psychiatry","volume":"3","author":"Murray","year":"2018","journal-title":"Biol. Psychiat"},{"key":"B43","doi-asserted-by":"publisher","first-page":"012402","DOI":"10.1103\/PhysRevE.98.012402","article-title":"Maximum-entropy models reveal the excitatory and inhibitory correlation structures in cortical neuronal activity","volume":"98","author":"Nghiem","year":"2018","journal-title":"Phys. Rev. E"},{"key":"B44","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1126\/science.1110948","article-title":"Hemodynamic signals correlate tightly with synchronized gamma oscillations","volume":"309","author":"Niessing","year":"2005","journal-title":"Science"},{"key":"B45","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1016\/j.cub.2007.06.066","article-title":"Coupling between neuronal firing rate, gamma LfP, and bold fMRI is related to interneuronal correlations","volume":"17","author":"Nir","year":"2007","journal-title":"Curr. Biol"},{"key":"B46","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/j.neuroscience.2019.05.011","article-title":"Pairwise interactions among brain regions organize large-scale functional connectivity during execution of various tasks","volume":"412","author":"Niu","year":"2019","journal-title":"Neuroscience"},{"key":"B47","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1162\/netn_a_00146","article-title":"Synergistic information in a dynamical model implemented on the human structural connectome reveals spatially distinct associations with age","volume":"4","author":"Nuzzi","year":"2020","journal-title":"Netw. Neurosci"},{"key":"B48","doi-asserted-by":"publisher","first-page":"118201","DOI":"10.1016\/j.neuroimage.2021.118201","article-title":"Inter-subject and inter-parcellation variability of resting-state whole-brain dynamical modeling","volume":"236","author":"Popovych","year":"2021","journal-title":"NeuroImage"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.3389\/fnsys.2018.00068","article-title":"What can computational models contribute to neuroimaging data analytics?","author":"Popovych","year":"2019","journal-title":"Front. Syst. Neurosci"},{"key":"B50","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1523\/ENEURO.0283-21.2021","article-title":"Neuronal cascades shape whole-brain functional dynamics at rest","volume":"8","author":"Rabuffo","year":"2021","journal-title":"eNeuro"},{"key":"B51","doi-asserted-by":"publisher","first-page":"051915","DOI":"10.1103\/PhysRevE.79.051915","article-title":"Ising model for neural data: model quality and approximate methods for extracting functional connectivity","volume":"79","author":"Roudi","year":"2009","journal-title":"Phys. Rev. E"},{"key":"B52","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.neuroimage.2015.01.002","article-title":"Mathematical framework for large-scale brain network modeling in the virtual brain","volume":"111","author":"Sanz-Leon","year":"2015","journal-title":"NeuroImage"},{"key":"B53","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1038\/nature04701","article-title":"Weak pairwise correlations imply strongly correlated network states in a neural population","volume":"440","author":"Schneidman","year":"2006","journal-title":"Nature"},{"key":"B54","doi-asserted-by":"publisher","first-page":"10238","DOI":"10.1073\/pnas.0913110107","article-title":"Neural basis of global resting-state fMRI activity","volume":"107","author":"Sch\u00f6lvinck","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"B55","doi-asserted-by":"publisher","first-page":"15595","DOI":"10.1523\/JNEUROSCI.3864-09.2009","article-title":"Neuronal avalanches imply maximum dynamic range in cortical networks at criticality","volume":"29","author":"Shew","year":"2009","journal-title":"J. Neurosci"},{"key":"B56","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1523\/JNEUROSCI.4637-10.2011","article-title":"Information capacity and transmission are maximized in balanced cortical networks with neuronal avalanches","volume":"31","author":"Shew","year":"2011","journal-title":"J. Neurosci"},{"key":"B57","doi-asserted-by":"publisher","first-page":"8254","DOI":"10.1523\/JNEUROSCI.1282-06.2006","article-title":"The structure of multi-neuron firing patterns in primate retina","volume":"26","author":"Shlens","year":"2006","journal-title":"J. Neurosci"},{"key":"B58","volume-title":"Critical Phenomena in Natural Sciences: Chaos, Fractals, Selforganization, and Disorder: Concepts and Tools","author":"Sornette","year":"2004"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0010042","article-title":"The human connectome: a structural description of the human brain","author":"Sporns","year":"2005","journal-title":"PLoS Comput. Biol"},{"key":"B60","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.concog.2017.08.008","article-title":"The signatures of conscious access and its phenomenology are consistent with large-scale brain communication at criticality","volume":"55","author":"Tagliazucchi","year":"2017","journal-title":"Consc. Cogn"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2012.00015","article-title":"Criticality in large-scale brain fmri dynamics unveiled by a novel point process analysis","author":"Tagliazucchi","year":"2012","journal-title":"Front. Physiol"},{"key":"B62","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1016\/j.neunet.2021.07.028","article-title":"Commpool: an interpretable graph pooling framework for hierarchical graph representation learning","volume":"143","author":"Tang","year":"2021","journal-title":"Neural Netw"},{"key":"B63","doi-asserted-by":"publisher","first-page":"11508","DOI":"10.1073\/pnas.1514188112","article-title":"Thermodynamics and signatures of criticality in a network of neurons","volume":"112","author":"Tkacik","year":"2015","journal-title":"Proc. Natl. Acad. Sci"},{"key":"B64","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1016\/j.neuroimage.2015.05.042","article-title":"Effects of lesions on synchrony and metastability in cortical networks","volume":"118","author":"V\u00e1\u010da","year":"2015","journal-title":"NeuroImage"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms2388","article-title":"A pairwise maximum entropy model accurately describes resting-state human brain networks","author":"Watanabe","year":"2013","journal-title":"Nat. Commun"},{"key":"B66","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.conb.2019.08.002","article-title":"25 years of criticality in neuroscience\u2013established results, open controversies, novel concepts","volume":"58","author":"Wilting","year":"2019","journal-title":"Curr. Opin. Neurobiol"},{"key":"B67","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1007\/s10955-019-02483-1","article-title":"Towards a mathematical model of the brain","volume":"180","author":"Young","year":"2020","journal-title":"J. Statist. Phys"},{"key":"B68","doi-asserted-by":"publisher","first-page":"3251","DOI":"10.1002\/cne.24274","article-title":"The significance of negative correlations in brain connectivity","volume":"525","author":"Zhan","year":"2017","journal-title":"J. Compar. Neurol"}],"container-title":["Frontiers in Computational Neuroscience"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fncom.2023.1295395\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T05:32:15Z","timestamp":1702963935000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fncom.2023.1295395\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,19]]},"references-count":68,"alternative-id":["10.3389\/fncom.2023.1295395"],"URL":"https:\/\/doi.org\/10.3389\/fncom.2023.1295395","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.02.16.528836","asserted-by":"object"}]},"ISSN":["1662-5188"],"issn-type":[{"value":"1662-5188","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,19]]},"article-number":"1295395"}}