{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T20:18:18Z","timestamp":1788380298037,"version":"build-2803163510"},"reference-count":49,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T00:00:00Z","timestamp":1759536000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100017837","name":"Wuxi Science and Technology Association","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007956","name":"Nanjing University of Chinese Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007956","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1016\/j.compbiolchem.2025.108701","type":"journal-article","created":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T21:36:46Z","timestamp":1759009006000},"page":"108701","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"special_numbering":"P2","title":["Uncovering the therapeutic potential of Si-Miao-Yong-An decoction in abdominal aortic aneurysm: An integrative study combining network pharmacology, machine learning, molecular docking and dynamics simulation"],"prefix":"10.1016","volume":"120","author":[{"given":"Ming","family":"Xie","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiandeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guobao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haibing","family":"Hua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"2","key":"10.1016\/j.compbiolchem.2025.108701_bib1","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1093\/bioinformatics\/btm554","article-title":"Computing topological parameters of biological networks","volume":"24","author":"Assenov","year":"2008","journal-title":"Bioinformatics"},{"issue":"Database","key":"10.1016\/j.compbiolchem.2025.108701_bib2","first-page":"D991","article-title":"NCBI GEO: archive for functional genomics data sets--update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"10.1016\/j.compbiolchem.2025.108701_bib3","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1161\/ATVBAHA.117.310333","article-title":"IL-1\u03b2 (Interleukin-1\u03b2) and TNF-\u03b1 (Tumor Necrosis Factor-\u03b1) impact abdominal aortic aneurysm formation by differential effects on macrophage polarization","volume":"38","author":"Batra","year":"2018","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"issue":"12","key":"10.1016\/j.compbiolchem.2025.108701_bib4","first-page":"1616","article-title":"Isorhamnetin alleviates symptoms and inhibits oxidative stress levels in rats with pulmonary arterial hypertension","volume":"27","author":"Chen","year":"2024","journal-title":"Iran. J. Basic Med. Sci."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib5","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1007\/978-1-0716-0892-0_16","article-title":"Parameterization of large ligands for gromacs molecular dynamics simulation with LigParGen","volume":"2199","author":"Chen","year":"2021","journal-title":"Methods Mol. Biol."},{"issue":"6","key":"10.1016\/j.compbiolchem.2025.108701_bib6","first-page":"541","article-title":"Si-Miao-Yong-An decoction alleviates thromboangiitis obliterans by regulating miR-548j-5p\/IL-17A signaling pathway","volume":"22","author":"Chu","year":"2024","journal-title":"Chin. J. Nat. Med."},{"issue":"8","key":"10.1016\/j.compbiolchem.2025.108701_bib7","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock vina 1.2.0: new docking methods, expanded force field, and python bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J. Chem. Inf. Model"},{"issue":"1","key":"10.1016\/j.compbiolchem.2025.108701_bib8","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1080\/13880209.2021.1961823","article-title":"Kaempferol-induced GPER upregulation attenuates atherosclerosis via the PI3K\/AKT\/Nrf2 pathway","volume":"59","author":"Feng","year":"2021","journal-title":"Pharm. Biol."},{"issue":"12","key":"10.1016\/j.compbiolchem.2025.108701_bib9","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkx291","article-title":"Gene set selection via LASSO penalized regression (SLPR)","volume":"45","author":"Frost","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"10.1016\/j.compbiolchem.2025.108701_bib10","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1016\/j.ecl.2022.02.005","article-title":"Assessment of cardiovascular disease risk: a 2022 update","volume":"51","author":"Goldsborough","year":"2022","journal-title":"Endocrinol. Metab. Clin. North Am."},{"issue":"29","key":"10.1016\/j.compbiolchem.2025.108701_bib11","doi-asserted-by":"crossref","first-page":"2682","DOI":"10.1093\/eurheartj\/ehad386","article-title":"Pathogenesis and management of abdominal aortic aneurysm","volume":"44","author":"Golledge","year":"2023","journal-title":"Eur. Heart J."},{"issue":"10","key":"10.1016\/j.compbiolchem.2025.108701_bib12","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1002\/bjs.10964","article-title":"Predicting risk of rupture and rupture-preventing reinterventions following endovascular abdominal aortic aneurysm repair","volume":"105","author":"Grootes","year":"2018","journal-title":"Br. J. Surg."},{"issue":"2","key":"10.1016\/j.compbiolchem.2025.108701_bib13","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbad002","article-title":"A review on longitudinal data analysis with random forest","volume":"24","author":"Hu","year":"2023","journal-title":"Brief. Bioinform"},{"issue":"1","key":"10.1016\/j.compbiolchem.2025.108701_bib14","first-page":"41","article-title":"Applications of support vector machine (SVM) learning in cancer genomics","volume":"15","author":"Huang","year":"2018","journal-title":"Cancer Genom. Proteom."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/j.gene.2023.148068","article-title":"Revealing PPP1R12B and COL1A1 as piRNA pathway genes contributing to abdominal aortic aneurysm through integrated analysis and experimental validation","volume":"897","author":"Jia","year":"2024","journal-title":"Gene"},{"key":"10.1016\/j.compbiolchem.2025.108701_bib16","doi-asserted-by":"crossref","DOI":"10.3389\/fphys.2022.1034014","article-title":"Through network pharmacology and molecular docking to explore the underlying mechanism of artemisia annua L. Treating in abdominal aortic aneurysm","volume":"13","author":"Jia","year":"2022","journal-title":"Front. Physiol."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2025.108701_bib17","doi-asserted-by":"crossref","first-page":"D1388","DOI":"10.1093\/nar\/gkaa971","article-title":"PubChem in 2021: new data content and improved web interfaces","volume":"49","author":"Kim","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"10.1016\/j.compbiolchem.2025.108701_bib18","doi-asserted-by":"crossref","first-page":"D302","DOI":"10.1093\/nar\/gkj120","article-title":"The RCSB PDB information portal for structural genomics","volume":"34","author":"Kouranov","year":"2006","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"10.1016\/j.compbiolchem.2025.108701_bib19","first-page":"127","article-title":"Stigmasterol protects human brain microvessel endothelial cells against ischemia-reperfusion injury through suppressing EPHA2 phosphorylation","volume":"21","author":"Li","year":"2023","journal-title":"Chin. J. Nat. Med."},{"issue":"1","key":"10.1016\/j.compbiolchem.2025.108701_bib20","doi-asserted-by":"crossref","first-page":"5418","DOI":"10.1038\/s41467-022-33071-9","article-title":"Batch effects removal for microbiome data via conditional quantile regression","volume":"13","author":"Ling","year":"2022","journal-title":"Nat. Commun."},{"issue":"10","key":"10.1016\/j.compbiolchem.2025.108701_bib21","doi-asserted-by":"crossref","first-page":"6766","DOI":"10.1111\/jcmm.14554","article-title":"Regulatory t cells protected against abdominal aortic aneurysm by suppression of the COX-2 expression","volume":"23","author":"Liu","year":"2019","journal-title":"J. Cell. Mol. Med."},{"issue":"3","key":"10.1016\/j.compbiolchem.2025.108701_bib22","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0120259","article-title":"Isorhamnetin attenuates atherosclerosis by inhibiting macrophage apoptosis via PI3K\/AKT activation and HO-1 induction","volume":"10","author":"Luo","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.compbiolchem.2025.108701_bib23","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejphar.2023.176112","article-title":"Kaempferol protects against cardiovascular abnormalities induced by nitric oxide deficiency in rats by suppressing the TNF-alpha pathway","volume":"960","author":"Maneesai","year":"2023","journal-title":"Eur. J. Pharm."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib24","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.989933","article-title":"Immune and inflammatory mechanisms of abdominal aortic aneurysm","volume":"13","author":"Marquez-Sanchez","year":"2022","journal-title":"Front. Immunol."},{"issue":"2","key":"10.1016\/j.compbiolchem.2025.108701_bib25","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.tips.2021.11.004","article-title":"Network pharmacology: curing causal mechanisms instead of treating symptoms","volume":"43","author":"Nogales","year":"2022","journal-title":"Trends Pharmacol. Sci."},{"issue":"15","key":"10.1016\/j.compbiolchem.2025.108701_bib26","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1042\/CS20220795","article-title":"Novel pharmacological approaches in abdominal aortic aneurysm","volume":"137","author":"Puertas-Umbert","year":"2023","journal-title":"Clin. Sci. (Lond. )."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib27","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/1471-2105-12-77","article-title":"pROC: an open-source package for r and S+ to analyze and compare ROC curves","volume":"12","author":"Robin","year":"2011","journal-title":"BMC Bioinforma."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib28","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1758-2946-6-13","article-title":"TCMSP: a database of systems pharmacology for drug discovery from herbal medicines","volume":"6","author":"Ru","year":"2014","journal-title":"J. Chemin.."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib29","doi-asserted-by":"crossref","first-page":"33","DOI":"10.3389\/fcvm.2018.00033","article-title":"Chinese herbal Medicine as a potential treatment of abdominal aortic aneurysm","volume":"5","author":"Seto","year":"2018","journal-title":"Front. Cardiovasc. Med."},{"issue":"11","key":"10.1016\/j.compbiolchem.2025.108701_bib30","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"issue":"3","key":"10.1016\/j.compbiolchem.2025.108701_bib31","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1165\/rcmb.2020-0105OC","article-title":"Increased MAO-A activity promotes progression of pulmonary arterial hypertension","volume":"64","author":"Sun","year":"2021","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2025.108701_bib32","doi-asserted-by":"crossref","first-page":"D607","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"10.1016\/j.compbiolchem.2025.108701_bib33","doi-asserted-by":"crossref","first-page":"3454","DOI":"10.1093\/bioinformatics\/btw488","article-title":"NCMine: Core-peripheral based functional module detection using near-clique mining","volume":"32","author":"Tadaka","year":"2016","journal-title":"Bioinformatics"},{"issue":"D1","key":"10.1016\/j.compbiolchem.2025.108701_bib34","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"UniProt","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.compbiolchem.2025.108701_bib35","article-title":"Quercetin downregulates Cyclooxygenase-2 expression and HIF-1alpha\/VEGF Signaling-Related angiogenesis in a mouse model of abdominal aortic aneurysm. Biomed res. Int","volume":"2020","author":"Wang","year":"2020"},{"key":"10.1016\/j.compbiolchem.2025.108701_bib36","article-title":"Identification of a biomarker and immune infiltration in perivascular adipose tissue of abdominal aortic aneurysm","volume":"13","author":"Wang","year":"2022","journal-title":"Front. Physiol."},{"issue":"5","key":"10.1016\/j.compbiolchem.2025.108701_bib37","doi-asserted-by":"crossref","DOI":"10.1016\/j.bbadis.2024.167224","article-title":"Pentamethylquercetin attenuates angiotensin II-induced abdominal aortic aneurysm formation by blocking nuclear translocation of C\/EBPbeta at Lys253","volume":"1870","author":"Wu","year":"2024","journal-title":"Biochim. Biophys. Acta Mol. Basis Dis."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib38","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.3389\/fphar.2018.01059","article-title":"Luteolin inhibits vascular smooth muscle cell proliferation and migration by inhibiting TGFBR1 signaling","volume":"9","author":"Wu","year":"2018","journal-title":"Front. Pharm."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib39","article-title":"Exploring the effect and mechanism of Si-Miao-Yong-An decoction on abdominal aortic aneurysm based on mice experiment and bioinformatics analysis","volume":"2022","author":"Xu","year":"2022","journal-title":"Evid. Based Complement. Altern. Med."},{"key":"10.1016\/j.compbiolchem.2025.108701_bib40","doi-asserted-by":"crossref","first-page":"49","DOI":"10.2147\/OTT.S486300","article-title":"Integrated network pharmacology, machine learning and experimental validation to identify the key targets and compounds of TiaoShenGongJian for the treatment of breast cancer","volume":"18","author":"Ying","year":"2025","journal-title":"Onco Targets Ther."},{"issue":"5","key":"10.1016\/j.compbiolchem.2025.108701_bib41","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"Clusterprofiler: an r package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"issue":"4","key":"10.1016\/j.compbiolchem.2025.108701_bib42","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/btu684","article-title":"DOSE: an R\/Bioconductor package for disease ontology semantic and enrichment analysis","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"},{"issue":"6","key":"10.1016\/j.compbiolchem.2025.108701_bib43","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1016\/j.joim.2024.09.001","article-title":"Luteolin protects against myocardial ischemia\/reperfusion injury by reducing oxidative stress and apoptosis through the p53 pathway","volume":"22","author":"Zhai","year":"2024","journal-title":"J. Integr. Med."},{"issue":"1","key":"10.1016\/j.compbiolchem.2025.108701_bib44","doi-asserted-by":"crossref","first-page":"57","DOI":"10.2174\/1386207326666230703150803","article-title":"Exploring the mechanism of Si-miao-yong-an decoction in the treatment of coronary heart disease based on network pharmacology and experimental verification","volume":"27","author":"Zhang","year":"2024","journal-title":"Comb. Chem. High. Throughput Screen"},{"key":"10.1016\/j.compbiolchem.2025.108701_bib45","doi-asserted-by":"crossref","first-page":"5423","DOI":"10.1016\/j.csbj.2023.10.052","article-title":"Comprehensive bioinformatics analysis revealed potential key genes and pathways underlying abdominal aortic aneurysm","volume":"21","author":"Zhang","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"issue":"1","key":"10.1016\/j.compbiolchem.2025.108701_bib46","doi-asserted-by":"crossref","DOI":"10.3390\/nu17010071","article-title":"The potential mechanism of alpiniae oxyphyllae fructus against hyperuricemia: an integration of network pharmacology, molecular docking, molecular dynamics simulation, and in vitro experiments","volume":"17","author":"Zhang","year":"2024","journal-title":"Nutrients"},{"issue":"5","key":"10.1016\/j.compbiolchem.2025.108701_bib47","first-page":"1209","article-title":"Exploration on origin of simiao yong'an decoction","volume":"45","author":"Zhao","year":"2020","journal-title":"Zhongguo Zhong Yao Za Zhi"},{"key":"10.1016\/j.compbiolchem.2025.108701_bib48","doi-asserted-by":"crossref","DOI":"10.1016\/j.jep.2023.116306","article-title":"Network pharmacology, a promising approach to reveal the pharmacology mechanism of Chinese Medicine formula","volume":"309","author":"Zhao","year":"2023","journal-title":"J. Ethnopharmacol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2025.108701_bib49","doi-asserted-by":"crossref","DOI":"10.1080\/07853890.2023.2218105","article-title":"Network pharmacology-based approach to research the effect and mechanism of Si-Miao-Yong-An decoction against thromboangiitis obliterans","volume":"55","author":"Zou","year":"2023","journal-title":"Ann. Med."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927125003627?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927125003627?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T15:39:12Z","timestamp":1773157152000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927125003627"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":49,"alternative-id":["S1476927125003627"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2025.108701","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2026,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Uncovering the therapeutic potential of Si-Miao-Yong-An decoction in abdominal aortic aneurysm: An integrative study combining network pharmacology, machine learning, molecular docking and dynamics simulation","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2025.108701","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"108701"}}