{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,18]],"date-time":"2025-04-18T07:40:03Z","timestamp":1744962003014,"version":"3.40.4"},"reference-count":26,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2025,8]]},"DOI":"10.1016\/j.compbiolchem.2025.108401","type":"journal-article","created":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T17:12:28Z","timestamp":1740676348000},"page":"108401","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Single-cell transcriptomic reveals network topology changes of cancer at the individual level"],"prefix":"10.1016","volume":"117","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8336-4699","authenticated-orcid":false,"given":"Chenhui","family":"Song","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2025.108401_bib1","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1038\/s41591-020-0892-6","article-title":"Systemic dysfunction and plasticity of the immune macroenvironment in cancer models","volume":"26","author":"Allen","year":"2020","journal-title":"Nat. Med"},{"key":"10.1016\/j.compbiolchem.2025.108401_bib2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/s10142-023-01082-4","article-title":"Single-cell RNA sequencing reveals the heterogeneity and microenvironment in one adenoid cystic carcinoma sample","volume":"23","author":"An","year":"2023","journal-title":"Funct. Integr. Genom."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib3","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib4","doi-asserted-by":"crossref","first-page":"9209","DOI":"10.1073\/pnas.1201416109","article-title":"Molecular signaling network complexity is correlated with cancer patient survivability","volume":"109","author":"Breitkreutz","year":"2012","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib5","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/s41392-023-01710-2","article-title":"Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression","volume":"8","author":"Chen","year":"2023","journal-title":"Signal Transduct. Target Ther."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib6","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/s41540-024-00340-w","article-title":"Evaluation of single-sample network inference methods for precision oncology","volume":"10","author":"Deschildre","year":"2024","journal-title":"NPJ Syst. Biol. Appl."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib7","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/1752-0509-1-24","article-title":"Understanding network concepts in modules","volume":"1","author":"Dong","year":"2007","journal-title":"BMC Syst. Biol."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib8","doi-asserted-by":"crossref","first-page":"3675","DOI":"10.1038\/s41467-023-39173-2","article-title":"Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis","volume":"14","author":"Du","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib9","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.compbiolchem.2025.108401_bib10","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1016\/j.scib.2020.01.013","article-title":"SMAD7 and SERPINE1 as novel dynamic network biomarkers detect and regulate the tipping point of TGF-beta induced EMT","volume":"65","author":"Jiang","year":"2020","journal-title":"Sci. Bull."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib11","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib12","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.compbiolchem.2025.108401_bib13","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1016\/j.ccell.2023.04.011","article-title":"Remodeling of the immune and stromal cell compartment by PD-1 blockade in mismatch repair-deficient colorectal cancer","volume":"41","author":"Li","year":"2023","journal-title":"Cancer Cell"},{"key":"10.1016\/j.compbiolchem.2025.108401_bib14","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1093\/bioinformatics\/btz758","article-title":"Single-sample landscape entropy reveals the imminent phase transition during disease progression","volume":"36","author":"Liu","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2025.108401_bib15","article-title":"HdWGCNA identifies co-expression networks in high-dimensional transcriptomics data","volume":"3","author":"Morabito","year":"2023","journal-title":"Cell Rep. Methods"},{"issue":"1","key":"10.1016\/j.compbiolchem.2025.108401_bib16","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1093\/bioinformatics\/btq606","article-title":"QuACN: an R package for analyzing complex biological networks quantitatively","volume":"27","author":"Mueller","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2025.108401_bib17","doi-asserted-by":"crossref","DOI":"10.1007\/s12038-022-00253-y","article-title":"Emerging landscape of molecular interaction networks:opportunities, challenges and prospects","volume":"47","author":"Panditrao","year":"2022","journal-title":"J. Biosci."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib18","doi-asserted-by":"crossref","DOI":"10.3390\/ijms252212163","article-title":"Single-sample networks reveal intra-cytoband co-expression hotspots in breast cancer subtypes","volume":"25","author":"Ponce-Cusi","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib19","doi-asserted-by":"crossref","DOI":"10.1038\/srep12323","article-title":"Graph curvature for differentiating cancer networks","volume":"5","author":"Sandhu","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib20","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3002132","article-title":"NEW: network-enabled wisdom in biology, medicine, and health care","volume":"4","author":"Schadt","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib21","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."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib22","doi-asserted-by":"crossref","first-page":"6036","DOI":"10.1038\/s41467-022-33780-1","article-title":"Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease","volume":"13","author":"Wong","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib23","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/s12967-015-0546-5","article-title":"Unravelling personalized dysfunctional gene network of complex diseases based on differential network model","volume":"13","author":"Yu","year":"2015","journal-title":"J. Transl. Med."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib24","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1186\/s12964-023-01140-1","article-title":"Colonic stem cells from normal tissues adjacent to tumor drive inflammation and fibrosis in colorectal cancer","volume":"21","author":"Zhao","year":"2023","journal-title":"Cell Commun. Signal"},{"key":"10.1016\/j.compbiolchem.2025.108401_bib25","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41392-022-00881-8","article-title":"Single-cell transcriptomic profiling unravels the adenoma-initiation role of protein tyrosine kinases during colorectal tumorigenesis","volume":"7","author":"Zheng","year":"2022","journal-title":"Signal Transduct. Target Ther."},{"key":"10.1016\/j.compbiolchem.2025.108401_bib26","doi-asserted-by":"crossref","DOI":"10.1093\/nsr\/nwad167","article-title":"Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma","volume":"10","author":"Zhu","year":"2023","journal-title":"Natl. Sci. Rev."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927125000611?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927125000611?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,4,18]],"date-time":"2025-04-18T07:09:14Z","timestamp":1744960154000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927125000611"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":26,"alternative-id":["S1476927125000611"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2025.108401","relation":{},"ISSN":["1476-9271"],"issn-type":[{"type":"print","value":"1476-9271"}],"subject":[],"published":{"date-parts":[[2025,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Single-cell transcriptomic reveals network topology changes of cancer at the individual level","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2025.108401","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":"108401"}}