{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,13]],"date-time":"2026-09-13T23:54:54Z","timestamp":1789343694810,"version":"build-2803163510"},"reference-count":63,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["23S21901000"],"award-info":[{"award-number":["23S21901000"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013102","name":"Shanghai City Youth Science and Technology Star Project","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013102","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100019978","name":"Shanghai Pudong New Area Health Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100019978","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82174079"],"award-info":[{"award-number":["82174079"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015792","name":"Pudong New Area People's Government","doi-asserted-by":"publisher","award":["PWRd2018\\u201312"],"award-info":[{"award-number":["PWRd2018\\u201312"]}],"id":[{"id":"10.13039\/100015792","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":[[2025,12]]},"DOI":"10.1016\/j.compbiolchem.2025.108598","type":"journal-article","created":{"date-parts":[[2025,7,18]],"date-time":"2025-07-18T15:38:50Z","timestamp":1752853130000},"page":"108598","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Bioinformatics analysis combined with experiments to unveil common hub genes, pathways, and transcription factor regulatory networks in ulcerative colitis and osteoporosis"],"prefix":"10.1016","volume":"119","author":[{"given":"Kun","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianshuang","family":"Xia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liyong","family":"Lai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiqing","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiping","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianyong","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruiqing","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ti","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoqiang","family":"Yue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denghai","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7362-9972","authenticated-orcid":false,"given":"Hailiang","family":"Xin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2025.108598_bib1","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1093\/ibd\/izab174","article-title":"Characterization of skeletal phenotype and associated mechanisms with chronic intestinal inflammation in the winnie mouse model of spontaneous chronic colitis","volume":"28","author":"Al Saedi","year":"2022","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib2","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0045142","article-title":"The transcriptional profile of mesenchymal stem cell populations in primary osteoporosis is distinct and shows overexpression of osteogenic inhibitors","volume":"7","author":"Benisch","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib3","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1053\/j.gastro.2015.07.002","article-title":"Proteolytic cleavage and loss of function of biologic agents that neutralize tumor necrosis factor in the mucosa of patients with inflammatory bowel disease","volume":"149","author":"Biancheri","year":"2015","journal-title":"Gastroenterology"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib4","doi-asserted-by":"crossref","first-page":"164","DOI":"10.37349\/emd.2024.00046","article-title":"Mesenchymal stromal cells from people with osteoporosis are fewer, and defective in both osteogenic and adipogenic capacity","volume":"2","author":"Cassidy","year":"2024","journal-title":"Explor Musculoskelet. Dis."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib5","article-title":"Identification and exploration of pharmacological pyroptosis-related biomarkers of ulcerative colitis","volume":"13","author":"Chen","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib6","doi-asserted-by":"crossref","DOI":"10.1016\/j.gene.2023.147914","article-title":"What do osteoporosis and osteoarthritis have in common? An integrated study of overlapping differentially expressed genes in bone mesenchymal stem cells of osteoporosis and osteoarthritis","volume":"893","author":"Chen","year":"2024","journal-title":"Gene"},{"issue":"4","key":"10.1016\/j.compbiolchem.2025.108598_bib7","article-title":"cytoHubba: identifying hub objects and sub-networks from complex interactome","volume":"8","author":"Chin","year":"2014","journal-title":"BMC Syst. Biol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib8","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1136\/gutjnl-2014-306947","article-title":"Bone marrow Th17 TNF\u03b1 cells induce osteoclast differentiation, and link bone destruction to IBD","volume":"64","author":"Ciucci","year":"2015","journal-title":"Gut"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib9","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib10","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1093\/ibd\/izac273","article-title":"Risk variants in or near ZBTB40 AND NFATC1 increase the risk of both IBD and adverse bone health outcomes highlighting common genetic underpinnings across both diseases","volume":"29","author":"Cushing","year":"2023","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib11","doi-asserted-by":"crossref","first-page":"556","DOI":"10.3892\/ijmm.2016.2481","article-title":"Treatment with novel AP-1 and NF-\u03baB inhibitors restores the colonic endocrine cells to normal levels in rats with DSS-induced colitis","volume":"37","author":"El-Salhy","year":"2016","journal-title":"Int. J. Mol. Med."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib12","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1159\/000496935","article-title":"Risk factors for low bone density in inflammatory bowel disease: use of glucocorticoids, low body mass index, and smoking","volume":"37","author":"Even Dar","year":"2019","journal-title":"Dig. Dis."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib13","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1186\/s12967-023-04449-0","article-title":"CX3CL1 promotes M1 macrophage polarization and osteoclast differentiation through NF-\u03baB signaling pathway in ankylosing spondylitis in vitro","volume":"21","author":"Feng","year":"2023","journal-title":"J. Transl. Med."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib14","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1002\/jbmr.2590","article-title":"Neonatal high bone mass with first mutation of the NF-\u03baB complex: heterozygous de novo missense (p.Asp512Ser) RELA (Rela\/p65)","volume":"31","author":"Frederiksen","year":"2016","journal-title":"J. Bone Min. Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib15","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1159\/000484979","article-title":"Alicaforsen, an antisense inhibitor of intercellular adhesion molecule-1, in the treatment for left-sided ulcerative colitis and ulcerative proctitis","volume":"36","author":"Greuter","year":"2018","journal-title":"Dig. Dis."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib16","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1001\/jama.2023.15389","article-title":"Ulcerative colitis in adults: a review","volume":"330","author":"Gros","year":"2023","journal-title":"JAMA"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib17","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/s10067-019-04771-3","article-title":"Effects of 1-year anti-TNF-\u03b1 therapies on bone mineral density and bone biomarkers in rheumatoid arthritis and ankylosing spondylitis","volume":"39","author":"Guly\u00e1s","year":"2020","journal-title":"Clin. Rheuma"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib18","article-title":"Exosome-based bone-targeting drug delivery alleviates impaired osteoblastic bone formation and bone loss in inflammatory bowel diseases","volume":"4","author":"Guo","year":"2023","journal-title":"Cell Rep. Med."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib19","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/ecco-jcc\/jjv213","article-title":"The first European evidence-based consensus on extra-intestinal manifestations in inflammatory bowel disease","volume":"10","author":"Harbord","year":"2016","journal-title":"J. Crohns Colitis"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib20","first-page":"882","article-title":"Kangfuxin alleviates ulcerative colitis in rats by inhibiting NF-\u03baB p65 activation and regulating T lymphocyte subsets","volume":"26","author":"He","year":"2023","journal-title":"Iran. J. Basic Med. Sci."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib21","article-title":"Integrative biomarker discovery and immune profiling for ulcerative colitis: a multi-methodological approach","volume":"14","author":"Jiang","year":"2024","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib22","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1002\/jbmr.3759","article-title":"Attenuation of NF-\u03baB in intestinal epithelial cells is sufficient to mitigate the bone loss comorbidity of experimental mouse colitis","volume":"34","author":"Ke","year":"2019","journal-title":"J. Bone Min. Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41540-018-0076-x","article-title":"Role of noise and parametric variation in the dynamics of gene regulatory circuits","volume":"4","author":"Kohar","year":"2018","journal-title":"npj Syst. Biol. Appl."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib24","doi-asserted-by":"crossref","first-page":"328","DOI":"10.2174\/1389450120666190927122553","article-title":"Study of intercellular adhesion molecule-1 (ICAM-1) in bone homeostasis","volume":"21","author":"Kong","year":"2020","journal-title":"Curr. Drug Targets"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib25","doi-asserted-by":"crossref","first-page":"1693","DOI":"10.1016\/j.crohns.2014.08.004","article-title":"Combination therapy with an immunomodulator and anti-TNF\u03b1 agent improves bone mineral density in IBD patients","volume":"8","author":"Krajcovicova","year":"2014","journal-title":"J. Crohns Colitis"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib26","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.phrs.2018.07.018","article-title":"Gut-derived serotonin contributes to bone deficits in colitis","volume":"140","author":"Lavoie","year":"2019","journal-title":"Pharm. Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib27","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1097\/MPG.0000000000001898","article-title":"Molecular comparison of adult and pediatric ulcerative colitis indicates broad similarity of molecular pathways in disease tissue","volume":"67","author":"Li","year":"2018","journal-title":"J. Pedia Gastroenterol. Nutr."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib28","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1093\/ibd\/izad007","article-title":"Ruxolitinib alleviates inflammation, apoptosis, and intestinal barrier leakage in ulcerative colitis via STAT3","volume":"29","author":"Li","year":"2023","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib29","doi-asserted-by":"crossref","DOI":"10.1016\/j.phymed.2024.155941","article-title":"p-Hydroxy benzaldehyde, a phenolic compound from Nostoc commune, ameliorates DSS-induced colitis against oxidative stress via the Nrf2\/HO-1\/NQO-1\/NF-\u03baB\/AP-1 pathway","volume":"133","author":"Liu","year":"2024","journal-title":"Phytomedicine"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib30","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1093\/ecco-jcc\/jjaa019","article-title":"Incidence, risk factors and evaluation of osteoporosis in patients with inflammatory bowel disease: a danish population-based inception cohort with 10 years of follow-up","volume":"14","author":"Lo","year":"2020","journal-title":"J. Crohns Colitis"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib31","article-title":"TNF\u2011\u03b1 and RANKL promote osteoclastogenesis by upregulating RANK via the NF\u2011\u03baB pathway","author":"Luo","year":"2018","journal-title":"Mol. Med. Rep. 17 66056611"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib32","doi-asserted-by":"crossref","DOI":"10.1016\/j.exger.2023.112111","article-title":"Cross-sectional study and bioinformatics analysis to reveal the correlations of osteoporosis in patients with Parkinson\u2019s disease","volume":"173","author":"Ma","year":"2023","journal-title":"Exp. Gerontol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib33","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1007\/s40265-015-0391-0","article-title":"Antisense approach to inflammatory bowel disease: prospects and challenges","volume":"75","author":"Marafini","year":"2015","journal-title":"Drugs"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib34","doi-asserted-by":"crossref","first-page":"2925","DOI":"10.3389\/fimmu.2019.02925","article-title":"TNF-\u03b1 directly enhances osteocyte RANKL expression and promotes osteoclast formation","volume":"10","author":"Marahleh","year":"2019","journal-title":"Front. Immunol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib35","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/s41413-022-00206-z","article-title":"Specific inflammatory osteoclast precursors induced during chronic inflammation give rise to highly active osteoclasts associated with inflammatory bone loss","volume":"10","author":"Meirow","year":"2022","journal-title":"Bone Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib36","doi-asserted-by":"crossref","DOI":"10.1155\/2022\/3498310","article-title":"Jatrorrhizine alleviates DSS-induced ulcerative colitis by regulating the intestinal barrier function and inhibiting TLR4\/MyD88\/NF-\u03baB signaling pathway","volume":"2022","author":"Niu","year":"2022","journal-title":"Evid. Based Complement Altern. Med."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib37","article-title":"Identification of gene signatures associated with ulcerative colitis and the association with immune infiltrates in colon cancer","volume":"14","author":"Pan","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib38","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/j.jcmgh.2022.07.002","article-title":"Intestinal inflammation promotes MDL-1+ osteoclast precursor expansion to trigger osteoclastogenesis and bone loss","volume":"14","author":"Peek","year":"2022","journal-title":"Cell Mol. Gastroenterol. Hepatol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib39","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.3389\/fimmu.2018.01417","article-title":"Interleukin-35 Inhibits TNF-\u03b1-Induced Osteoclastogenesis and Promotes Apoptosis via Shifting the Activation From TNF Receptor-Associated Death Domain (TRADD)-TRAF2 to TRADD-Fas-Associated Death Domain by JAK1\/STAT1","volume":"9","author":"Peng","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib40","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1007\/s12038-021-00181-3","article-title":"IL-3 inhibits rat osteoclast differentiation induced by TNF-\u03b1 and other pro-osteoclastogenic cytokines","volume":"46","author":"Piprode","year":"2021","journal-title":"J. Biosci."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib41","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1111\/cei.13613","article-title":"Inhibitor of apoptosis-stimulating p53 protein protects against inflammatory bowel disease in mice models by inhibiting the nuclear factor kappa B signaling","volume":"205","author":"Qian","year":"2021","journal-title":"Clin. Exp. Immunol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib42","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib43","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1053\/j.gastro.2021.07.042","article-title":"Extraintestinal manifestations of inflammatory bowel disease: current concepts, treatment, and implications for disease management","volume":"161","author":"Rogler","year":"2021","journal-title":"Gastroenterology"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib44","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.3390\/nu13061863","article-title":"Associations of lifestyle factors with osteopenia and osteoporosis in polish patients with inflammatory bowel disease","volume":"13","author":"Rychter","year":"2021","journal-title":"Nutrients"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib45","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/s41467-017-02391-6","article-title":"Perturbation-response genes reveal signaling footprints in cancer gene expression","volume":"9","author":"Schubert","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib46","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.jep.2016.07.022","article-title":"Dual effect of WIN-34B on osteogenesis and osteoclastogenesis in cytokine-induced mesenchymal stem cells and bone marrow cells","volume":"193","author":"Seo","year":"2016","journal-title":"J. Ethnopharmacol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib47","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1186\/s13059-022-02835-3","article-title":"NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity","volume":"23","author":"Su","year":"2022","journal-title":"Genome Biol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib48","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib49","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1097\/MIB.0000000000000655","article-title":"Natural nuclear factor kappa beta inhibitors: safe therapeutic options for inflammatory bowel disease","volume":"22","author":"Tambuwala","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib50","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.biosystems.2014.11.005","article-title":"CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks","volume":"127","author":"Tang","year":"2015","journal-title":"Biosystems"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10787-011-0104-6","article-title":"Targeting leukocyte migration and adhesion in Crohn\u2019s disease and ulcerative colitis","volume":"20","author":"Thomas","year":"2012","journal-title":"Inflammopharmacology"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib52","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1111\/j.1365-2036.2011.04667.x","article-title":"Review article: the effects of antitumour necrosis factor-\u03b1 on bone metabolism in inflammatory bowel disease","volume":"33","author":"Veerappan","year":"2011","journal-title":"Aliment Pharm. Ther."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib53","doi-asserted-by":"crossref","first-page":"1715","DOI":"10.1016\/j.clnu.2023.07.022","article-title":"Eicosapentaenoic acid supplementation modulates the osteoblast\/osteoclast balance in inflammatory environments and protects against estrogen deficiency-induced bone loss in mice","volume":"42","author":"Wang","year":"2023","journal-title":"Clin. Nutr."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib54","doi-asserted-by":"crossref","first-page":"336","DOI":"10.4248\/BR201304004","article-title":"Mice Deficient in NF-\u03baB p50 and p52 or RANK have defective growth plate formation and post-natal dwarfism","volume":"1","author":"Xing","year":"2013","journal-title":"Bone Res"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib55","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-023-50488-4","article-title":"Identification of neutrophil extracellular traps and crosstalk genes linking inflammatory bowel disease and osteoporosis by integrated bioinformatics analysis and machine learning","volume":"13","author":"Xu","year":"2023","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib56","doi-asserted-by":"crossref","DOI":"10.1016\/j.phrs.2019.104381","article-title":"MOTS-c inhibits Osteolysis in the Mouse Calvaria by affecting osteocyte-osteoclast crosstalk and inhibiting inflammation","volume":"147","author":"Yan","year":"2019","journal-title":"Pharm. Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib57","first-page":"1738","article-title":"Apoptotic extracellular vesicles alleviate Pg-LPS induced inflammatory responses of macrophages via AMPK\/SIRT1\/NF-\u03baB pathway and inhibit osteoclast formation","volume":"93","author":"Ye","year":"2022","journal-title":"J. Periodo"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib58","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.biopha.2018.03.080","article-title":"TNF-\u03b1 contributes to postmenopausal osteoporosis by synergistically promoting RANKL-induced osteoclast formation","volume":"102","author":"Zha","year":"2018","journal-title":"Biomed. Pharm."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib59","doi-asserted-by":"crossref","DOI":"10.1530\/EC-22-0461","article-title":"Systemic immune-inflammation index is associated with decreased bone mass density and osteoporosis in postmenopausal women but not in premenopausal women","volume":"12","author":"Zhang","year":"2023","journal-title":"Endocr. Connect"},{"key":"10.1016\/j.compbiolchem.2025.108598_bib60","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/j.jgr.2025.02.001","article-title":"Ginsenoside Rg2, a principal effective ingredient of Panax ginseng, attenuates DSS-induced ulcerative colitis through NF-\u03baB\/NLRP3 pathway","volume":"49","author":"Zhang","year":"2025","journal-title":"J. Ginseng Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib61","doi-asserted-by":"crossref","first-page":"3201","DOI":"10.2147\/JIR.S507269","article-title":"Osteoclast activation and inflammatory bone diseases: focusing on receptors in osteoclasts","volume":"18","author":"Zhao","year":"2025","journal-title":"J. Inflamm. Res."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib62","doi-asserted-by":"crossref","DOI":"10.3389\/fendo.2022.1052721","article-title":"Revealing oxidative stress-related genes in osteoporosis and advanced structural biological study for novel natural material discovery regarding MAPKAPK2","volume":"13","author":"Zhao","year":"2022","journal-title":"Front. Endocrinol."},{"key":"10.1016\/j.compbiolchem.2025.108598_bib63","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s40169-020-00270-0","article-title":"Bone mineral density is negatively correlated with ulcerative colitis: a systematic review and meta-analysis","volume":"9","author":"Zhou","year":"2020","journal-title":"Clin. Transl. Med."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927125002592?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927125002592?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T10:41:25Z","timestamp":1779446485000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927125002592"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":63,"alternative-id":["S1476927125002592"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2025.108598","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Bioinformatics analysis combined with experiments to unveil common hub genes, pathways, and transcription factor regulatory networks in ulcerative colitis and osteoporosis","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2025.108598","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"108598"}}