{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T02:14:13Z","timestamp":1782958453916,"version":"3.54.5"},"reference-count":109,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T00:00:00Z","timestamp":1736121600000},"content-version":"vor","delay-in-days":45,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12090052"],"award-info":[{"award-number":["12090052"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12404233"],"award-info":[{"award-number":["12404233"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12474198"],"award-info":[{"award-number":["12474198"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U24A2014"],"award-info":[{"award-number":["U24A2014"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People\u2019s Republic of China","doi-asserted-by":"publisher","award":["2021ZD0201900"],"award-info":[{"award-number":["2021ZD0201900"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Doctoral Research Startup Fund Project of Anhui Normal University","award":["762353"],"award-info":[{"award-number":["762353"]}]},{"name":"Anhui Normal University 2023 Scholarship and Supplementary Discipline Construction Project","award":["2023GFXK156"],"award-info":[{"award-number":["2023GFXK156"]}]},{"name":"Natural Science Foundation of Fujian Province of China","award":["2023J05002"],"award-info":[{"award-number":["2023J05002"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["20720230017"],"award-info":[{"award-number":["20720230017"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Aging is a complex and heterogeneous biological process at cellular, tissue, and individual levels. Despite extensive effort in scientific research, a comprehensive understanding of aging mechanisms remains lacking. This study analyzed aging-related gene networks, using single-cell RNA sequencing data from &amp;gt;15\u00a0000 cells. We constructed a gene correlation network, integrating gene expressions into the weights of network edges, and ranked gene importance using a random walk model to generate a gene importance matrix. This unsupervised method improved the clustering performance of cell types. To further quantify the complexity of gene networks during aging, we introduced network structural entropy. The findings of our study reveal that the overall network structural entropy increases in the aged cells compared to the young cells. However, network entropy changes varied greatly within different cell subtypes. Specifically, the network structural entropy among various cell types may increase, remain unchanged, or decrease. This wide range of changes may be closely related to their individual functions, highlighting the cellular heterogeneity and potential key network reconfigurations. Analyzing gene network entropy provides insights into the molecular mechanisms behind aging. This study offers new scientific evidence and theoretical support for understanding the changes in cell functions during aging.<\/jats:p>","DOI":"10.1093\/bib\/bbae698","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T04:36:26Z","timestamp":1736138186000},"source":"Crossref","is-referenced-by-count":6,"title":["The network structural entropy for single-cell RNA sequencing data during skin aging"],"prefix":"10.1093","volume":"26","author":[{"given":"Zhilong","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Physics, Xiamen University , No. 422, Siming South Road, Xiamen, Fujian, 361005 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5435-9583","authenticated-orcid":false,"given":"Hai","family":"Lin","sequence":"additional","affiliation":[{"name":"Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine , Vision and Brain Health), No. 999, Jinshi Road, Yongzhong Street, Longwan District, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, , No. 1, Jinlian Road, Longwan District, Wenzhou, Zhejiang, 325000 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Vision and Brain Health), No. 999, Jinshi Road, Yongzhong Street, Longwan District, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, , No. 1, Jinlian Road, Longwan District, Wenzhou, Zhejiang, 325000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Physics, Xiamen University , No. 422, Siming South Road, Xiamen, Fujian, 361005 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Xue","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, Cornell University , 110 Biotechnology Building, Ithaca, 14853 NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuer","family":"Lu","sequence":"additional","affiliation":[{"name":"Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine , Vision and Brain Health), No. 999, Jinshi Road, Yongzhong Street, Longwan District, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, , No. 1, Jinlian Road, Longwan District, Wenzhou, Zhejiang, 325000 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Vision and Brain Health), No. 999, Jinshi Road, Yongzhong Street, Longwan District, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, , No. 1, Jinlian Road, Longwan District, Wenzhou, Zhejiang, 325000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Physics, Anhui Normal University , No. 189 Jiuhua South Road, Wuhu, Anhui, 241002 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8712-0544","authenticated-orcid":false,"given":"Jianwei","family":"Shuai","sequence":"additional","affiliation":[{"name":"Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine , Vision and Brain Health), No. 999, Jinshi Road, Yongzhong Street, Longwan District, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, , No. 1, Jinlian Road, Longwan District, Wenzhou, Zhejiang, 325000 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Vision and Brain Health), No. 999, Jinshi Road, Yongzhong Street, Longwan District, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, , No. 1, Jinlian Road, Longwan District, Wenzhou, Zhejiang, 325000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,5]]},"reference":[{"key":"2025010601281143200_ref1","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1007\/s11427-014-4757-4","article-title":"Edge biomarkers for classification and prediction of phenotypes","volume":"57","author":"Zeng","year":"2014","journal-title":"Sci China Life Sci"},{"key":"2025010601281143200_ref2","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/nrg2918","article-title":"Network medicine: a network-based approach to human disease","volume":"12","author":"Barab\u00e1si","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2025010601281143200_ref3","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1038\/nrm2503","article-title":"Modelling and analysis of gene regulatory networks","volume":"9","author":"Karlebach","year":"2008","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025010601281143200_ref4","doi-asserted-by":"publisher","first-page":"8257","DOI":"10.1073\/pnas.1017017108","article-title":"Quantifying the Waddington landscape and biological paths for development and differentiation","volume":"108","author":"Wang","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"2025010601281143200_ref5","doi-asserted-by":"publisher","first-page":"5337","DOI":"10.1073\/pnas.1702412114","article-title":"Modeling the response of a tumor-suppressive network to mitogenic and oncogenic signals","volume":"114","author":"Tian","year":"2017","journal-title":"Proc Natl Acad Sci"},{"key":"2025010601281143200_ref6","doi-asserted-by":"publisher","first-page":"12245","DOI":"10.1073\/pnas.0813088106","article-title":"Cell fate decision mediated by p53 pulses","volume":"106","author":"Zhang","year":"2009","journal-title":"Proc Natl Acad Sci"},{"key":"2025010601281143200_ref7","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1016\/j.cell.2011.02.016","article-title":"Interactome networks and human disease","volume":"144","author":"Vidal","year":"2011","journal-title":"Cell"},{"key":"2025010601281143200_ref8","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1016\/j.cell.2018.05.051","article-title":"Common disease is more complex than implied by the core gene omnigenic model","volume":"173","author":"Wray","year":"2018","journal-title":"Cell"},{"key":"2025010601281143200_ref9","article-title":"Reveal, a general reverse engineering algorithm for inference of genetic network architectures","volume":"3","author":"Liang","year":"1998","journal-title":"Pac Symp Biocomput"},{"key":"2025010601281143200_ref10","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1093\/bioinformatics\/18.2.261","article-title":"Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks","volume":"18","author":"Shmulevich","year":"2002","journal-title":"Bioinformatics"},{"key":"2025010601281143200_ref11","doi-asserted-by":"publisher","first-page":"19033","DOI":"10.1073\/pnas.0609152103","article-title":"Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns","volume":"103","author":"Lezon","year":"2006","journal-title":"Proc Natl Acad Sci"},{"key":"2025010601281143200_ref12","doi-asserted-by":"publisher","DOI":"10.1016\/j.fmre.2024.02.009","article-title":"Incoherent feedforward loop dominates the robustness and tunability of necroptosis biphasic, emergent, and coexistent dynamics","volume":"8","author":"Xu","journal-title":"Fundamental Research"},{"key":"2025010601281143200_ref13","doi-asserted-by":"publisher","first-page":"2271","DOI":"10.1073\/pnas.1621412114","article-title":"Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells","volume":"114","author":"Bargaje","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025010601281143200_ref14","doi-asserted-by":"publisher","first-page":"e2000640","DOI":"10.1371\/journal.pbio.2000640","article-title":"Cell fate decision as high-dimensional critical state transition","volume":"14","author":"Mojtahedi","year":"2016","journal-title":"PLoS Biol"},{"key":"2025010601281143200_ref15","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1016\/j.cell.2015.10.039","article-title":"Design and analysis of single-cell sequencing experiments","volume":"163","author":"Gr\u00fcn","year":"2015","journal-title":"Cell"},{"key":"2025010601281143200_ref16","doi-asserted-by":"publisher","first-page":"4361","DOI":"10.1038\/s41467-019-12293-4","article-title":"Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells","volume":"10","author":"Hernando-Herraez","year":"2019","journal-title":"Nat Commun"},{"key":"2025010601281143200_ref17","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1093\/bioinformatics\/btq001","article-title":"A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes","volume":"26","author":"Markitsis","year":"2010","journal-title":"Bioinformatics"},{"key":"2025010601281143200_ref18","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1016\/j.gpb.2020.11.008","article-title":"scGET: predicting cell fate transition during early embryonic development by single-cell graph entropy","volume":"19","author":"Zhong","year":"2021","journal-title":"Genom Proteom Bioinform"},{"key":"2025010601281143200_ref19","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1038\/nmeth.3440","article-title":"Pathway and network analysis of cancer genomes","volume":"12","author":"Creixell","year":"2015","journal-title":"Nat Methods"},{"key":"2025010601281143200_ref20","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S1474-4422(18)30169-8","article-title":"Network imaging biomarkers: insights and clinical applications in Parkinson\u2019s disease","volume":"17","author":"Schindlbeck","year":"2018","journal-title":"Lancet Neurol"},{"key":"2025010601281143200_ref21","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1094068","article-title":"Inferring cellular networks using probabilistic graphical models","volume":"303","author":"Friedman","year":"2004","journal-title":"Science"},{"key":"2025010601281143200_ref22","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1089\/106652700750050961","article-title":"Using Bayesian networks to analyze expression data","volume":"7","author":"Friedman","year":"2000","journal-title":"J Comput Biol"},{"key":"2025010601281143200_ref23","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1093\/bioinformatics\/18.2.287","article-title":"Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling","volume":"18","author":"Toh","year":"2002","journal-title":"Bioinformatics"},{"key":"2025010601281143200_ref24","article-title":"Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements","volume":"5","author":"Butte","year":"2000","journal-title":"Pac Symp Biocomput"},{"key":"2025010601281143200_ref25","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1752-0509-4-8","article-title":"A general co-expression network-based approach to gene expression analysis: comparison and applications","volume":"4","author":"Ruan","year":"2010","journal-title":"BMC Syst Biol"},{"key":"2025010601281143200_ref26","doi-asserted-by":"publisher","first-page":"bbad129","DOI":"10.1093\/bib\/bbad129","article-title":"NSRGRN: a network structure refinement method for gene regulatory network inference","volume":"24","author":"Liu","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025010601281143200_ref27","doi-asserted-by":"publisher","first-page":"bbad227","DOI":"10.1093\/bib\/bbad227","article-title":"MPCLCDA: predicting circRNA\u2013disease associations by using automatically selected meta-path and contrastive learning","volume":"24","author":"Liu","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025010601281143200_ref28","doi-asserted-by":"publisher","first-page":"3072","DOI":"10.1109\/JBHI.2023.3260863","article-title":"Predicting CircRNA-disease associations via feature convolution learning with heterogeneous graph attention network","volume":"27","author":"Peng","year":"2023","journal-title":"IEEE J Biomed Health Inform"},{"key":"2025010601281143200_ref29","doi-asserted-by":"publisher","first-page":"bbac478","DOI":"10.1093\/bib\/bbac478","article-title":"DAESTB: inferring associations of small molecule\u2013miRNA via a scalable tree boosting model based on deep autoencoder","volume":"23","author":"Peng","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025010601281143200_ref30","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/j.cell.2022.11.001","article-title":"Hallmarks of aging: an expanding universe","volume":"186","author":"L\u00f3pez-Ot\u00edn","year":"2023","journal-title":"Cell"},{"key":"2025010601281143200_ref31","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/s41591-023-02784-9","article-title":"Validation of biomarkers of aging","volume":"30","author":"Moqri","year":"2024","journal-title":"Nat Med"},{"key":"2025010601281143200_ref32","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/s41588-023-01627-0","article-title":"Distinguishing between driver and passenger mechanisms of aging","volume":"56","author":"Magalh\u00e3es","year":"2024","journal-title":"Nat Genet"},{"key":"2025010601281143200_ref33","doi-asserted-by":"publisher","first-page":"D900","DOI":"10.1093\/nar\/gkad927","article-title":"Human ageing genomic resources: updates on key databases in ageing research","volume":"52","author":"Magalh\u00e3es","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025010601281143200_ref34","doi-asserted-by":"publisher","first-page":"6114","DOI":"10.1093\/nar\/gkae340","article-title":"SCTC: inference of developmental potential from single-cell transcriptional complexity","volume":"52","author":"Lin","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025010601281143200_ref35","doi-asserted-by":"publisher","first-page":"1236653","DOI":"10.3389\/fmicb.2023.1236653","article-title":"Identifying SARS-CoV-2 infected cells with scVDN","volume":"14","author":"Hu","year":"2023","journal-title":"Front Microbiol"},{"key":"2025010601281143200_ref36","doi-asserted-by":"publisher","first-page":"106733","DOI":"10.1016\/j.compbiomed.2023.106733","article-title":"Gene function and cell surface protein association analysis based on single-cell multiomics data","volume":"157","author":"Hu","year":"2023","journal-title":"Comput Biol Med"},{"key":"2025010601281143200_ref37","doi-asserted-by":"crossref","first-page":"bbad005","DOI":"10.1093\/bib\/bbad005","article-title":"Modeling and analyzing single-cell multimodal data with deep parametric inference","volume":"24","author":"Hu","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025010601281143200_ref38","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1038\/s41576-023-00618-5","article-title":"Gene regulatory network inference in the era of single-cell multi-omics","volume":"24","author":"Badia-i-Mompel","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2025010601281143200_ref39","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1038\/s43587-022-00252-6","article-title":"A complex systems approach to aging biology","volume":"2","author":"Cohen","year":"2022","journal-title":"Nature Aging"},{"key":"2025010601281143200_ref40","doi-asserted-by":"publisher","first-page":"1000","DOI":"10.1016\/j.cell.2017.05.015","article-title":"Senescence in health and disease","volume":"169","author":"He","year":"2017","journal-title":"Cell"},{"key":"2025010601281143200_ref41","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbae091","article-title":"scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks","volume":"25","author":"Xu","year":"2024","journal-title":"Brief Bioinform"},{"key":"2025010601281143200_ref42","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1093\/bib\/bbad281","article-title":"Single-cell causal network inferred by cross-mapping entropy","volume":"24","author":"Li","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025010601281143200_ref43","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1016\/j.devcel.2020.11.002","article-title":"A single-cell transcriptomic atlas of human skin aging","volume":"56","author":"Zou","year":"2021","journal-title":"Dev Cell"},{"key":"2025010601281143200_ref44","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.molmed.2021.12.003","article-title":"Skin senescence: mechanisms and impact on whole-body aging","volume":"28","author":"Franco","year":"2022","journal-title":"Trends Mol Med"},{"key":"2025010601281143200_ref45","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1038\/s42003-020-0922-4","article-title":"Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming","volume":"3","author":"Sol\u00e9-Boldo","year":"2020","journal-title":"Commun Biol"},{"key":"2025010601281143200_ref46","doi-asserted-by":"publisher","first-page":"3556","DOI":"10.1016\/j.csbj.2022.06.056","article-title":"Single-cell entropy network detects the activity of immune cells based on ribosomal protein genes","volume":"20","author":"Jin","year":"2022","journal-title":"Comput Struct Biotechnol J"},{"key":"2025010601281143200_ref47","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz172","article-title":"Cell-specific network constructed by single-cell RNA sequencing data","volume":"47","author":"Dai","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025010601281143200_ref48","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/j.gpb.2020.05.005","article-title":"c-CSN: single-cell RNA sequencing data analysis by conditional cell-specific network","volume":"19","author":"Li","year":"2021","journal-title":"Genom Proteom Bioinform"},{"key":"2025010601281143200_ref49","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1137\/140976649","article-title":"PageRank beyond the web","volume":"57","author":"Gleich","year":"2015","journal-title":"PageRank Beyond the Web"},{"key":"2025010601281143200_ref50","doi-asserted-by":"publisher","first-page":"9340","DOI":"10.1038\/s41598-017-09475-9","article-title":"Analysis and evaluation of the entropy indices of a static network structure","volume":"7","author":"Cai","year":"2017","journal-title":"Sci Rep"},{"key":"2025010601281143200_ref51","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/s42254-024-00720-5","article-title":"Entropy, irreversibility and inference at the foundations of statistical physics, nature reviews","volume":"6","author":"Pachter","year":"2024","journal-title":"Phys Ther"},{"key":"2025010601281143200_ref52","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1186\/s12967-024-05145-3","article-title":"Edge-based relative entropy as a sensitive indicator of critical transitions in biological systems","volume":"22","author":"Hong","year":"2024","journal-title":"J Transl Med"},{"key":"2025010601281143200_ref53","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.mad.2006.11.016","article-title":"Inflammaging and anti-inflammaging: a systemic perspective on aging and longevity emerged from studies in humans","volume":"128","author":"Franceschi","year":"2007","journal-title":"Mech Ageing Dev"},{"key":"2025010601281143200_ref54","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/s41590-017-0006-x","article-title":"The twilight of immunity: emerging concepts in aging of the immune system","volume":"19","author":"Nikolich-\u017dugich","year":"2018","journal-title":"Nat Immunol"},{"key":"2025010601281143200_ref55","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s41569-018-0064-2","article-title":"Inflammageing: chronic inflammation in ageing, cardiovascular disease, and frailty","volume":"15","author":"Ferrucci","year":"2018","journal-title":"Nat Rev Cardiol"},{"key":"2025010601281143200_ref56","doi-asserted-by":"publisher","first-page":"1508","DOI":"10.1016\/j.apsb.2024.01.008","article-title":"Macrophage senescence in health and diseases","volume":"14","author":"Wang","year":"2024","journal-title":"Acta Pharm Sin B"},{"key":"2025010601281143200_ref57","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/j.immuni.2024.01.001","article-title":"Type 2 cytokine signaling in macrophages protects from cellular senescence and organismal aging","volume":"57","author":"Zhou","year":"2024","journal-title":"Immunity"},{"key":"2025010601281143200_ref58","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1016\/j.it.2023.10.009","article-title":"Reframing macrophage diversity with network motifs","volume":"44","author":"Pizzurro","year":"2023","journal-title":"Trends Immunol"},{"key":"2025010601281143200_ref59","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1038\/s41581-022-00601-z","article-title":"Cellular senescence: the good, the bad and the unknown","volume":"18","author":"Huang","year":"2022","journal-title":"Nat Rev Nephrol"},{"key":"2025010601281143200_ref60","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/s41586-020-03160-0","article-title":"Restoring metabolism of myeloid cells reverses cognitive decline in ageing","volume":"590","author":"Minhas","year":"2021","journal-title":"Nature"},{"key":"2025010601281143200_ref61","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1038\/s41590-018-0255-3","article-title":"Macrophage de novo NAD+ synthesis specifies immune function in aging and inflammation","volume":"20","author":"Minhas","year":"2019","journal-title":"Nat Immunol"},{"key":"2025010601281143200_ref62","doi-asserted-by":"publisher","first-page":"2518","DOI":"10.4049\/jimmunol.0901022","article-title":"Age-associated decrease in TLR function in primary human dendritic cells predicts influenza vaccine response","volume":"184","author":"Panda","year":"2010","journal-title":"J Immunol"},{"key":"2025010601281143200_ref63","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1126\/science.aax0249","article-title":"Single-cell transcriptional diversity is a hallmark of developmental potential","volume":"367","author":"Gulati","year":"2020","journal-title":"Science"},{"key":"2025010601281143200_ref64","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"key":"2025010601281143200_ref65","doi-asserted-by":"publisher","DOI":"10.1016\/j.patcog.2020.107522","article-title":"Spectral clustering via ensemble deep autoencoder learning (SC-EDAE)","volume":"108","author":"Affeldt","year":"2020","journal-title":"Pattern Recognition"},{"key":"2025010601281143200_ref66","doi-asserted-by":"publisher","DOI":"10.3390\/cancers11060797","article-title":"The metallophosphoesterase-domain-containing protein 2 (MPPED2) gene acts as tumor suppressor in breast cancer","volume":"11","author":"Pellecchia","year":"2019","journal-title":"Cancers (Basel)"},{"key":"2025010601281143200_ref67","doi-asserted-by":"publisher","first-page":"216848","DOI":"10.1016\/j.canlet.2024.216848","article-title":"FBXO43 promotes cell cycle progression in cancer cells through stabilizing SKP2","volume":"591","author":"Zheng","year":"2024","journal-title":"Cancer Lett"},{"key":"2025010601281143200_ref68","doi-asserted-by":"publisher","first-page":"1265","DOI":"10.1038\/s42255-020-00305-3","article-title":"Senescent cells promote tissue NAD+ decline during ageing via the activation of CD38+ macrophages","volume":"2","author":"Covarrubias","year":"2020","journal-title":"Nat Metab"},{"key":"2025010601281143200_ref69","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1038\/s41390-019-0707-y","article-title":"Identification of increased expression of activating fc receptors and novel findings regarding distinct IgE and IgM receptors in Kawasaki disease","volume":"89","author":"Chang","year":"2021","journal-title":"Pediatr Res"},{"key":"2025010601281143200_ref70","doi-asserted-by":"publisher","first-page":"2723","DOI":"10.1038\/s41467-024-46725-7","article-title":"Structure and function of semaphorin-5A glycosaminoglycan interactions","volume":"15","author":"Nagy","year":"2024","journal-title":"Nat Commun"},{"key":"2025010601281143200_ref71","doi-asserted-by":"publisher","first-page":"1461","DOI":"10.1002\/art.38425","article-title":"Secreted semaphorin 5A activates immune effector cells and is a biomarker for rheumatoid arthritis","volume":"66","author":"Gras","year":"2014","journal-title":"Arthritis Rheumatol"},{"key":"2025010601281143200_ref72","doi-asserted-by":"publisher","first-page":"97371","DOI":"10.18632\/oncotarget.22126","article-title":"Decreased long non-coding RNA MTM contributes to gastric cancer cell migration and invasion via modulating MT1F","volume":"8","author":"Lin","year":"2017","journal-title":"Oncotarget"},{"key":"2025010601281143200_ref73","doi-asserted-by":"publisher","first-page":"3509","DOI":"10.7150\/thno.86307","article-title":"RNF157 attenuates CD4(+) T cell-mediated autoimmune response by promoting HDAC1 ubiquitination and degradation","volume":"13","author":"Wang","year":"2023","journal-title":"Theranostics"},{"key":"2025010601281143200_ref74","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2023.115455","article-title":"Molecular mechanisms of thrombospondin-2 modulates tumor vasculogenic mimicry by PI3K\/AKT\/mTOR signaling pathway","volume":"167","author":"Huang","year":"2023","journal-title":"Biomed Pharmacother"},{"key":"2025010601281143200_ref75","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1016\/j.bbapap.2009.02.013","article-title":"Identification of polyubiquitin binding proteins involved in NF-\u03baB signaling using protein arrays","volume":"1794","author":"Fenner","year":"2009","journal-title":"Biochim Biophys Acta"},{"key":"2025010601281143200_ref76","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1016\/j.bbrc.2019.07.116","article-title":"The protective role of NR4A3 in acute myocardial infarction by suppressing inflammatory responses via JAK2-STAT3\/NF-\u03baB pathway","volume":"517","author":"Jiang","year":"2019","journal-title":"Biochem Biophys Res Commun"},{"key":"2025010601281143200_ref77","doi-asserted-by":"publisher","first-page":"115118","DOI":"10.1016\/j.addr.2023.115118","article-title":"Transflammation in tissue regeneration and response to injury: how cell-autonomous inflammatory signaling mediates cell plasticity","volume":"203","author":"Cooke","year":"2023","journal-title":"Adv Drug Deliv Rev"},{"key":"2025010601281143200_ref78","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/s41580-020-00314-w","article-title":"Cellular senescence in ageing: from mechanisms to therapeutic opportunities","volume":"22","author":"Di Micco","year":"2021","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025010601281143200_ref79","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1038\/s41590-021-01083-0","article-title":"Aging disrupts circadian gene regulation and function in macrophages","volume":"23","author":"Blacher","year":"2022","journal-title":"Nat Immunol"},{"key":"2025010601281143200_ref80","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1038\/s43587-023-00436-8","article-title":"Reduced mitochondrial calcium uptake in macrophages is a major driver of inflammaging","volume":"3","author":"Seegren","year":"2023","journal-title":"Nature Aging"},{"key":"2025010601281143200_ref81","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1016\/j.stem.2023.09.014","article-title":"Decoding aging-dependent regenerative decline across tissues at single-cell resolution","volume":"30","author":"Cai","year":"2023","journal-title":"Cell Stem Cell"},{"key":"2025010601281143200_ref82","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/s43587-021-00043-5","article-title":"Healthy aging and the blood\u2013brain barrier","volume":"1","author":"Banks","year":"2021","journal-title":"Nature Aging"},{"key":"2025010601281143200_ref83","doi-asserted-by":"publisher","first-page":"2144","DOI":"10.1101\/gad.192294.112","article-title":"Age-associated inflammation inhibits epidermal stem cell function","volume":"26","author":"Doles","year":"2012","journal-title":"Genes Dev"},{"key":"2025010601281143200_ref84","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/j.cell.2022.12.027","article-title":"Loss of epigenetic information as a cause of mammalian aging","volume":"186","author":"Yang","year":"2023","journal-title":"Cell"},{"key":"2025010601281143200_ref85","doi-asserted-by":"publisher","first-page":"3208","DOI":"10.1038\/s41467-023-38842-6","article-title":"Senescent immune cells accumulation promotes brown adipose tissue dysfunction during aging","volume":"14","author":"Feng","year":"2023","journal-title":"Nat Commun"},{"key":"2025010601281143200_ref86","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1038\/s41392-023-01502-8","article-title":"Inflammation and aging: signaling pathways and intervention therapies","volume":"8","author":"Li","year":"2023","journal-title":"Signal Transduct Target Ther"},{"key":"2025010601281143200_ref87","doi-asserted-by":"publisher","first-page":"e57925","DOI":"10.15252\/embr.202357925","article-title":"Excessive apoptosis of Rip1-deficient T cells leads to premature aging","volume":"24","author":"Wang","year":"2023","journal-title":"EMBO Rep"},{"key":"2025010601281143200_ref88","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1038\/s41556-021-00740-8","article-title":"Human melanocyte development and melanoma dedifferentiation at single-cell resolution","volume":"23","author":"Belote","year":"2021","journal-title":"Nat Cell Biol"},{"key":"2025010601281143200_ref89","doi-asserted-by":"publisher","first-page":"800","DOI":"10.1111\/pcmr.12994","article-title":"Alterations of the pigmentation system in the aging process","volume":"34","author":"Kang","year":"2021","journal-title":"Pigment Cell Melanoma Res"},{"key":"2025010601281143200_ref90","doi-asserted-by":"publisher","first-page":"5717","DOI":"10.3390\/en7095717","article-title":"The Gouy-Stodola theorem in bioenergetic analysis of living systems (irreversibility in bioenergetics of living systems)","volume":"7","author":"Lucia","year":"2014","journal-title":"Energies"},{"key":"2025010601281143200_ref91","doi-asserted-by":"publisher","DOI":"10.3390\/ijms18122672","article-title":"Of energy and entropy: the ineluctable impact of aging in old age dementia","volume":"18","author":"Boccardi","year":"2017","journal-title":"Int J Mol Sci"},{"key":"2025010601281143200_ref92","doi-asserted-by":"publisher","first-page":"e14163","DOI":"10.1111\/acel.14163","article-title":"Methylation entropy landscape of Chinese long-lived individuals reveals lower epigenetic noise related to human healthy aging","volume":"23","author":"Wang","year":"2024","journal-title":"Aging Cell"},{"key":"2025010601281143200_ref93","doi-asserted-by":"publisher","first-page":"1696","DOI":"10.1038\/s41593-019-0491-3","article-title":"Single-cell transcriptomic profiling of the aging mouse brain","volume":"22","author":"Ximerakis","year":"2019","journal-title":"Nat Neurosci"},{"key":"2025010601281143200_ref94","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1016\/j.tcb.2018.02.001","article-title":"Hallmarks of cellular senescence","volume":"28","author":"Hernandez-Segura","year":"2018","journal-title":"Trends Cell Biol"},{"key":"2025010601281143200_ref95","doi-asserted-by":"publisher","first-page":"6398","DOI":"10.1038\/s41467-024-50559-8","article-title":"Aging drives cerebrovascular network remodeling and functional changes in the mouse brain","volume":"15","author":"Bennett","year":"2024","journal-title":"Nat Commun"},{"key":"2025010601281143200_ref96","doi-asserted-by":"publisher","first-page":"3873","DOI":"10.1038\/s41467-024-48118-2","article-title":"Repression of developmental transcription factor networks triggers aging-associated gene expression in human glial progenitor cells","volume":"15","author":"Mariani","year":"2024","journal-title":"Nat Commun"},{"key":"2025010601281143200_ref97","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1038\/s43587-024-00607-1","article-title":"Spatiotemporal transcriptomic changes of human ovarian aging and the regulatory role of FOXP1","volume":"4","author":"Wu","year":"2024","journal-title":"Nature Aging"},{"key":"2025010601281143200_ref98","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1038\/s43587-024-00696-y","article-title":"Loss of coordination between basic cellular processes in human aging","volume":"4","author":"Leote","year":"2024","journal-title":"Nature Aging"},{"key":"2025010601281143200_ref99","doi-asserted-by":"publisher","DOI":"10.1038\/s43587-024-00762-5","article-title":"Molecular and genetic insights into human ovarian aging from single-nuclei multi-omics analyses","author":"Jin","year":"2024","journal-title":"Nature Aging"},{"key":"2025010601281143200_ref100","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1016\/S0092-8674(00)81872-3","article-title":"Oncoprotein networks","volume":"88","author":"Hunter","year":"1997","journal-title":"Cell"},{"key":"2025010601281143200_ref101","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.cell.2017.11.011","article-title":"Single-cell genomics: a stepping stone for future immunology discoveries","volume":"172","author":"Giladi","year":"2018","journal-title":"Cell"},{"key":"2025010601281143200_ref102","doi-asserted-by":"publisher","first-page":"e2308879","DOI":"10.1002\/advs.202308879","article-title":"Quantifying landscape-flux via single-cell transcriptomics uncovers the underlying mechanism of cell cycle","volume":"11","author":"Zhu","year":"2024","journal-title":"Adv Sci"},{"key":"2025010601281143200_ref103","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/s41587-024-02215-1","article-title":"Startups probe hidden viruses in the \u2018dark genome\u2019 to treat disease","volume":"42","author":"Eisenstein","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2025010601281143200_ref104","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/s41556-018-0067-6","article-title":"Deconstructing the pluripotency gene regulatory network","volume":"20","author":"Li","year":"2018","journal-title":"Nat Cell Biol"},{"key":"2025010601281143200_ref105","doi-asserted-by":"publisher","first-page":"012415","DOI":"10.1103\/PhysRevE.103.012415","article-title":"Statistical complexity is maximized close to criticality in cortical dynamics","volume":"103","author":"Lotfi","year":"2021","journal-title":"Phys Rev E"},{"key":"2025010601281143200_ref106","doi-asserted-by":"publisher","first-page":"3039","DOI":"10.1038\/srep03039","article-title":"Cellular network entropy as the energy potential in Waddington\u2019s differentiation landscape","volume":"3","author":"Banerji","year":"2013","journal-title":"Sci Rep"},{"key":"2025010601281143200_ref107","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1186\/1752-0509-4-104","article-title":"Increased entropy of signal transduction in the cancer metastasis phenotype","volume":"4","author":"Teschendorff","year":"2010","journal-title":"BMC Syst Biol"},{"key":"2025010601281143200_ref108","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1016\/j.ymeth.2014.03.013","article-title":"Signalling entropy: a novel network-theoretical framework for systems analysis and interpretation of functional omic data","volume":"67","author":"Teschendorff","year":"2014","journal-title":"Methods"},{"key":"2025010601281143200_ref109","doi-asserted-by":"publisher","first-page":"2258","DOI":"10.1038\/s41467-024-45889-6","article-title":"Charting cellular differentiation trajectories with Ricci flow","volume":"15","author":"Baptista","year":"2024","journal-title":"Nat Commun"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbae698\/61330894\/bbae698.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbae698\/61330894\/bbae698.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T04:36:41Z","timestamp":1736138201000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae698\/7942792"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,22]]},"references-count":109,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,11,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae698","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,11,22]]},"article-number":"bbae698"}}