{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T01:33:12Z","timestamp":1793151192644,"version":"4.5.0"},"reference-count":51,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"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":[[2026,12]]},"DOI":"10.1016\/j.compbiolchem.2026.109298","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T23:38:30Z","timestamp":1786145910000},"page":"109298","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["A topology-based framework for robust cancer-associated gene signature identification from scRNA-seq data"],"prefix":"10.1016","volume":"125","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-2948-7721","authenticated-orcid":false,"given":"Sudarshan","family":"Gogoi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2272-8935","authenticated-orcid":false,"given":"Subhajit","family":"Bandyopadhyay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3174-7786","authenticated-orcid":false,"given":"Soumen","family":"Bera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Swarup","family":"Roy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit","family":"Chakraborty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2026.109298_b1","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.mam.2017.07.002","article-title":"Identifying cell populations with scrnaseq","volume":"59","author":"Andrews","year":"2018","journal-title":"Mol. Aspects Med."},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.109298_b2","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1007\/s10844-017-0473-4","article-title":"Persistent entropy for separating topological features from noise in vietoris-rips complexes","volume":"52","author":"Atienza","year":"2019","journal-title":"J. Intell. Inf. Syst."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109298_b3","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.cell.2018.02.060","article-title":"Comprehensive characterization of cancer driver genes and mutations","volume":"173","author":"Bailey","year":"2018","journal-title":"Cell"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109298_b4","first-page":"77","article-title":"Statistical topological data analysis using persistence landscapes","volume":"16","author":"Bubenik","year":"2015","journal-title":"J. Mach. Learn. Res."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109298_b5","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1090\/S0273-0979-09-01249-X","article-title":"Topology and data","volume":"46","author":"Carlsson","year":"2009","journal-title":"Bull. Am. Math. Soc."},{"key":"10.1016\/j.compbiolchem.2026.109298_b6","doi-asserted-by":"crossref","DOI":"10.3389\/frai.2021.667963","article-title":"An introduction to topological data analysis: fundamental and practical aspects for data scientists","volume":"4","author":"Chazal","year":"2021","journal-title":"Front. Artif. Intell."},{"key":"10.1016\/j.compbiolchem.2026.109298_b7","doi-asserted-by":"crossref","unstructured":"Cohen-Steiner, David, Edelsbrunner, Herbert, Harer, John, 2005. Stability of persistence diagrams. In: Proceedings of the Twenty-First Annual Symposium on Computational Geometry. pp. 263\u2013271.","DOI":"10.1145\/1064092.1064133"},{"issue":"1\u20132","key":"10.1016\/j.compbiolchem.2026.109298_b8","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1159\/000487440","article-title":"Heterogeneity in lung cancer","volume":"85","author":"De Sousa","year":"2018","journal-title":"Pathobiology"},{"key":"10.1016\/j.compbiolchem.2026.109298_b9","doi-asserted-by":"crossref","first-page":"695","DOI":"10.3389\/fgene.2019.00695","article-title":"Identification of potential crucial genes and key pathways in breast cancer using bioinformatic analysis","volume":"10","author":"Deng","year":"2019","journal-title":"Front. Genet."},{"issue":"22","key":"10.1016\/j.compbiolchem.2026.109298_b10","doi-asserted-by":"crossref","first-page":"3279","DOI":"10.1038\/sj.onc.1210421","article-title":"MAP kinase signalling pathways in cancer","volume":"26","author":"Dhillon","year":"2007","journal-title":"Oncogene"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109298_b11","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1038\/s41588-019-0572-y","article-title":"Identification of cancer driver genes based on nucleotide context","volume":"52","author":"Dietlein","year":"2020","journal-title":"Nature Genet."},{"issue":"8","key":"10.1016\/j.compbiolchem.2026.109298_b12","doi-asserted-by":"crossref","first-page":"2628","DOI":"10.1093\/bioinformatics\/btz931","article-title":"ShinyGO: a graphical gene-set enrichment tool for animals and plants","volume":"36","author":"Ge","year":"2019","journal-title":"Bioinformatics"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109298_b13","doi-asserted-by":"crossref","first-page":"625","DOI":"10.17537\/2025.20.625","article-title":"A computational framework for cancer type classification using single-cell RNA sequencing and mathematical analysis","volume":"20","author":"Gogoi","year":"2025","journal-title":"Math. Biol. Bioinform."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109298_b14","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/s41585-020-00400-w","article-title":"Genomic and phenotypic heterogeneity in prostate cancer","volume":"18","author":"Haffner","year":"2021","journal-title":"Nat. Rev. Urol."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.109298_b15","doi-asserted-by":"crossref","first-page":"bbac405","DOI":"10.1093\/bib\/bbac405","article-title":"DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network","volume":"23","author":"He","year":"2022","journal-title":"Brief. Bioinform."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.109298_b16","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1093\/biostatistics\/kxx053","article-title":"Missing data and technical variability in single-cell RNA-sequencing experiments","volume":"19","author":"Hicks","year":"2018","journal-title":"Biostatistics"},{"issue":"D1","key":"10.1016\/j.compbiolchem.2026.109298_b17","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gkaa970","article-title":"KEGG: integrating viruses and cellular organisms","volume":"49","author":"Kanehisa","year":"2020","journal-title":"Nucleic Acids Res."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109298_b18","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002375","article-title":"Ten years of pathway analysis: current approaches and outstanding challenges","volume":"8","author":"Khatri","year":"2012","journal-title":"PLoS Comput. Biol."},{"issue":"5","key":"10.1016\/j.compbiolchem.2026.109298_b19","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1093\/bioinformatics\/btz772","article-title":"Cancer classification of single-cell gene expression data by neural network","volume":"36","author":"Kim","year":"2020","journal-title":"Bioinformatics"},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.109298_b20","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/j.molcel.2015.04.005","article-title":"The technology and biology of single-cell RNA sequencing","volume":"58","author":"Kolodziejczyk","year":"2015","journal-title":"Mol. Cell"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109298_b21","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s13059-020-1926-6","article-title":"Eleven grand challenges in single-cell data science","volume":"21","author":"L\u00e4hnemann","year":"2020","journal-title":"Genome Biol."},{"issue":"10","key":"10.1016\/j.compbiolchem.2026.109298_b22","article-title":"Thymosin \u03b11 reverses oncolytic adenovirus-induced M2 polarization of macrophages to improve antitumor immunity and therapeutic efficacy","volume":"5","author":"Liu","year":"2024","journal-title":"Cell Rep. Med."},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.109298_b23","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109298_b24","doi-asserted-by":"crossref","DOI":"10.1016\/j.ygeno.2022.01.001","article-title":"PanClassif: Improving pan cancer classification of single cell RNA-seq gene expression data using machine learning","volume":"114","author":"Mahin","year":"2022","journal-title":"Genomics"},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.109298_b25","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/nrc2602","article-title":"Cell cycle, CDKs and cancer: a changing paradigm","volume":"9","author":"Malumbres","year":"2009","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.compbiolchem.2026.109298_b26","series-title":"International Congress on Mathematical Software","first-page":"167","article-title":"The gudhi library: Simplicial complexes and persistent homology","author":"Maria","year":"2014"},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.109298_b27","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1038\/ng.3984","article-title":"Computational correction of copy number effect improves specificity of CRISPR\u2013Cas9 essentiality screens in cancer cells","volume":"49","author":"Meyers","year":"2017","journal-title":"Nature Genet."},{"issue":"17","key":"10.1016\/j.compbiolchem.2026.109298_b28","doi-asserted-by":"crossref","first-page":"7265","DOI":"10.1073\/pnas.1102826108","article-title":"Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival","volume":"108","author":"Nicolau","year":"2011","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109298_b29","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1140\/epjds\/s13688-017-0109-5","article-title":"A roadmap for the computation of persistent homology","volume":"6","author":"Otter","year":"2017","journal-title":"EPJ Data Sci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109298_b30","doi-asserted-by":"crossref","first-page":"3808","DOI":"10.1038\/s41467-020-17659-7","article-title":"Identification of relevant genetic alterations in cancer using topological data analysis","volume":"11","author":"Rabad\u00e1n","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.compbiolchem.2026.109298_b31","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbi.2019.103357","article-title":"A topological approach for cancer subtyping from gene expression data","volume":"102","author":"Rafique","year":"2020","journal-title":"J. Biomed. Inform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109298_b32","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"Edger: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.109298_b33","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1161\/ATVBAHA.123.319283","article-title":"Single-cell RNA sequencing reveals that adaptation of human aortic endothelial cells to antiproliferative therapies is modulated by flow-induced shear stress","volume":"43","author":"Salazar-Mart\u00edn","year":"2023","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"issue":"5","key":"10.1016\/j.compbiolchem.2026.109298_b34","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nature Biotechnol."},{"issue":"15","key":"10.1016\/j.compbiolchem.2026.109298_b35","doi-asserted-by":"crossref","first-page":"8505","DOI":"10.1093\/nar\/gkab632","article-title":"RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data","volume":"49","author":"Schmidt","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2026.109298_b36","series-title":"GeneLit: PubMed literature status app","author":"Subhajit Bandyopadhyay","year":"2025"},{"issue":"43","key":"10.1016\/j.compbiolchem.2026.109298_b37","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.109298_b38","first-page":"209","article-title":"Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA: Cancer J. Clin."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.109298_b39","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0079217","article-title":"A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity","volume":"8","author":"Tarca","year":"2013","journal-title":"PLoS One"},{"issue":"50","key":"10.1016\/j.compbiolchem.2026.109298_b40","doi-asserted-by":"crossref","first-page":"14330","DOI":"10.1073\/pnas.1616440113","article-title":"Evaluating the evaluation of cancer driver genes","volume":"113","author":"Tokheim","year":"2016","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"7793","key":"10.1016\/j.compbiolchem.2026.109298_b41","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/s41586-020-1969-6","article-title":"Pan-cancer analysis of whole genomes","volume":"578","author":"Underwood","year":"2020","journal-title":"Nature"},{"issue":"6127","key":"10.1016\/j.compbiolchem.2026.109298_b42","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1126\/science.1235122","article-title":"Cancer genome landscapes","volume":"339","author":"Vogelstein","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.compbiolchem.2026.109298_b43","article-title":"Arsenic trioxide-based nanoparticles for enhance chemotherapy by activating pyroptosis","author":"Wang","year":"2025","journal-title":"Acta Pharm. Sin. B"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109298_b44","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/1756-9966-30-87","article-title":"Apoptosis in cancer: from pathogenesis to treatment","volume":"30","author":"Wong","year":"2011","journal-title":"J. Exp. Clin. Cancer Res."},{"key":"10.1016\/j.compbiolchem.2026.109298_b45","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2022.105697","article-title":"Evaluating the performance of dropout imputation and clustering methods for single-cell RNA sequencing data","volume":"146","author":"Xu","year":"2022","journal-title":"Comput. Biol. Med."},{"issue":"16","key":"10.1016\/j.compbiolchem.2026.109298_b46","doi-asserted-by":"crossref","first-page":"32366","DOI":"10.1109\/JIOT.2025.3576735","article-title":"Blockchain-based verifiable decentralized identity for intelligent flexible manufacturing","volume":"12","author":"Xu","year":"2025","journal-title":"IEEE Internet Things J."},{"key":"10.1016\/j.compbiolchem.2026.109298_b47","article-title":"A novel GSH depletor for simultaneous ferroptosis and cuproptosis activation in hepatocellular carcinoma","author":"Yang","year":"2025","journal-title":"Biochem. Pharmacol."},{"key":"10.1016\/j.compbiolchem.2026.109298_b48","doi-asserted-by":"crossref","first-page":"8553","DOI":"10.12659\/MSM.910364","article-title":"Nucleolar and spindle associated protein 1 (NUSAP1) inhibits cell proliferation and enhances susceptibility to epirubicin in invasive breast cancer cells by regulating cyclin d kinase (CDK1) and DLGAP5 expression","volume":"24","author":"Zhang","year":"2018","journal-title":"Med. Sci. Monit.: Int. Med. J. Exp. Clin. Res."},{"issue":"7","key":"10.1016\/j.compbiolchem.2026.109298_b49","doi-asserted-by":"crossref","first-page":"4188","DOI":"10.21037\/tcr-19-2829","article-title":"Key genes involved in cell cycle arrest and DNA damage repair identified in anaplastic thyroid carcinoma using integrated bioinformatics analysis","volume":"9","author":"Zhang","year":"2020","journal-title":"Transl. Cancer Res."},{"key":"10.1016\/j.compbiolchem.2026.109298_b50","doi-asserted-by":"crossref","DOI":"10.1016\/j.jep.2024.119126","article-title":"Chrysotoxine regulates ferroptosis and the PI3K\/AKT\/mTOR pathway to prevent cervical cancer","volume":"338","author":"Zhou","year":"2025","journal-title":"J. Ethnopharmacol."},{"key":"10.1016\/j.compbiolchem.2026.109298_b51","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2023.106873","article-title":"Mlspatial: a machine-learning method to reconstruct the spatial distribution of cells from scRNA-seq by extracting spatial features","volume":"159","author":"Zhu","year":"2023","journal-title":"Comput. Biol. Med."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126004251?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126004251?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T00:44:45Z","timestamp":1793148285000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927126004251"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,12]]},"references-count":51,"alternative-id":["S1476927126004251"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109298","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2026,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A topology-based framework for robust cancer-associated gene signature identification from scRNA-seq data","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109298","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"109298"}}