{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T18:05:04Z","timestamp":1793124304887,"version":"4.5.0"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T00:00:00Z","timestamp":1774396800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T00:00:00Z","timestamp":1779062400000},"content-version":"vor","delay-in-days":54,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2021R1A2C1013554"],"award-info":[{"award-number":["2021R1A2C1013554"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003625","name":"Ministry of Health and Welfare","doi-asserted-by":"publisher","award":["RS-2025-02303065"],"award-info":[{"award-number":["RS-2025-02303065"]}],"id":[{"id":"10.13039\/501100003625","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Health & Welfare, Republic of Korea"},{"name":"Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea"},{"DOI":"10.13039\/501100003052","name":"Ministry of Trade, Industry and Energy","doi-asserted-by":"publisher","award":["S2638360"],"award-info":[{"award-number":["S2638360"]}],"id":[{"id":"10.13039\/501100003052","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea"},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Republic of Korea","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"DOI":"10.1038\/s42003-026-09906-2","type":"journal-article","created":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T13:55:57Z","timestamp":1774446957000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis"],"prefix":"10.1038","volume":"9","author":[{"given":"Cl\u00e9mentine","family":"Charton","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"So Hyun","family":"Kang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie S.","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minsu","family":"Kang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ju Hyun","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young Suk","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sang-Hoon","family":"Ahn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun-Suhk","family":"Suh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nak Jung","family":"Kwon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2402-7633","authenticated-orcid":false,"given":"Kyoung Un","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5808-912X","authenticated-orcid":false,"given":"Jieun","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9524-9981","authenticated-orcid":false,"given":"Jinho","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8916-0048","authenticated-orcid":false,"given":"Hyung-Ho","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,25]]},"reference":[{"key":"9906_CR1","first-page":"209","volume":"71","author":"H Sung","year":"2021","unstructured":"Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin. 71, 209\u2013249 (2021).","journal-title":"CA Cancer J. Clin."},{"key":"9906_CR2","doi-asserted-by":"publisher","first-page":"800","DOI":"10.1007\/s10120-021-01160-1","volume":"24","author":"WJ Koemans","year":"2021","unstructured":"Koemans, W. J. et al. Synchronous peritoneal metastases of gastric cancer origin: incidence, treatment and survival of a nationwide Dutch cohort. Gastric Cancer 24, 800\u2013809 (2021).","journal-title":"Gastric Cancer"},{"key":"9906_CR3","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2407-13-577","volume":"13","author":"J Sun","year":"2013","unstructured":"Sun, J. et al. Clinical significance of palliative gastrectomy on the survival of patients with incurable advanced gastric cancer: a systematic review and meta-analysis. BMC Cancer 13, 577 (2013).","journal-title":"BMC Cancer"},{"key":"9906_CR4","doi-asserted-by":"publisher","unstructured":"Gwee, Y. X. et al. Integration of Genomic Biology Into Therapeutic Strategies of Gastric Cancer Peritoneal Metastasis. J. Clin. Oncol. 71, https:\/\/doi.org\/10.1200\/JCO.21.02745 (2022).","DOI":"10.1200\/JCO.21.02745"},{"key":"9906_CR5","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s12957-020-01813-y","volume":"18","author":"CJ Allen","year":"2020","unstructured":"Allen, C. J. et al. Staging laparoscopy and peritoneal cytology in patients with early stage gastric adenocarcinoma. World J. Surg. Oncol. 18, 39 (2020).","journal-title":"World J. Surg. Oncol."},{"key":"9906_CR6","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1053\/j.gastro.2024.08.007","volume":"167","author":"JJ Zhao","year":"2024","unstructured":"Zhao, J. J. et al. Spatially Resolved Niche and Tumor Microenvironmental Alterations in Gastric Cancer Peritoneal Metastases. Gastroenterology 167, 1384\u20131398.e4 (2024).","journal-title":"Gastroenterology"},{"key":"9906_CR7","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1016\/j.ccell.2016.09.011","volume":"30","author":"Y Liu","year":"2016","unstructured":"Liu, Y. & Cao, X. Characteristics and Significance of the Pre-metastatic Niche. Cancer Cell 30, 668\u2013681 (2016).","journal-title":"Cancer Cell"},{"key":"9906_CR8","doi-asserted-by":"publisher","first-page":"7478","DOI":"10.3748\/wjg.v22.i33.7478","volume":"22","author":"J Wei","year":"2016","unstructured":"Wei, J., Wu, N. D. & Liu, B. R. Regional but fatal: Intraperitoneal metastasis in gastric cancer. World J. Gastroenterol. 22, 7478 (2016).","journal-title":"World J. Gastroenterol."},{"key":"9906_CR9","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/S0140-6736(21)00797-2","volume":"398","author":"YY Janjigian","year":"2021","unstructured":"Janjigian, Y. Y. et al. First-line nivolumab plus chemotherapy versus chemotherapy alone for advanced gastric, gastro-oesophageal junction, and oesophageal adenocarcinoma (CheckMate 649): a randomised, open-label, phase 3 trial. Lancet 398, 27\u201340 (2021).","journal-title":"Lancet"},{"key":"9906_CR10","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1016\/S1470-2045(21)00692-6","volume":"23","author":"YK Kang","year":"2022","unstructured":"Kang, Y. K. et al. Nivolumab plus chemotherapy versus placebo plus chemotherapy in patients with HER2-negative, untreated, unresectable advanced or recurrent gastric or gastro-oesophageal junction cancer (ATTRACTION-4): a randomised, multicentre, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol. 23, 234\u2013247 (2022).","journal-title":"Lancet Oncol."},{"key":"9906_CR11","first-page":"102","volume":"54","author":"C D\u00edaz del Arco","year":"2021","unstructured":"D\u00edaz del Arco, C., Estrada Mu\u00f1oz, L., Ortega Medina, L. & Fern\u00e1ndez Ace\u00f1ero, M. J. Update on gastric cancer. New molecular classifications]. Rev. Esp. Patol. 54, 102\u2013113 (2021).","journal-title":"Rev. Esp. Patol."},{"key":"9906_CR12","doi-asserted-by":"publisher","first-page":"1127329","DOI":"10.3389\/fonc.2023.1127329","volume":"13","author":"KD Andini","year":"2023","unstructured":"Andini, K. D. et al. PMS2-associated Lynch syndrome: Past, present and future. Front Oncol. 13, 1127329 (2023).","journal-title":"Front Oncol."},{"key":"9906_CR13","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1038\/s41416-023-02338-3","volume":"129","author":"JE Lee","year":"2023","unstructured":"Lee, J. E., Kim, K. T., Shin, S. J., Cheong, J. H. & Choi, Y. Y. Genomic and evolutionary characteristics of metastatic gastric cancer by routes. Br. J. Cancer 129, 672\u2013682 (2023).","journal-title":"Br. J. Cancer"},{"key":"9906_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-020-03919-2","volume":"21","author":"S Gillis","year":"2020","unstructured":"Gillis, S. & Roth, A. PyClone-VI: scalable inference of clonal population structures using whole genome data. BMC Bioinforma. 21, 1\u201316 (2020).","journal-title":"BMC Bioinforma."},{"key":"9906_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2011-12-4-r41","volume":"12","author":"CH Mermel","year":"2011","unstructured":"Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, 1\u201314 (2011).","journal-title":"Genome Biol."},{"key":"9906_CR16","doi-asserted-by":"crossref","unstructured":"Saito-Adachi, M. et al. Oncogenic structural aberration landscape in gastric cancer genomes. Nat. Commun. 14, 1\u201313 (2023).","DOI":"10.1038\/s41467-023-39263-1"},{"key":"9906_CR17","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1007\/978-1-0716-0327-7_17","volume":"2120","author":"J Racle","year":"2020","unstructured":"Racle, J. & Gfeller, D. EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data. Methods Mol. Biol. 2120, 233\u2013248 (2020).","journal-title":"Methods Mol. Biol."},{"key":"9906_CR18","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1038\/s41587-019-0114-2","volume":"37","author":"AM Newman","year":"2019","unstructured":"Newman, A. M. et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat. Biotechnol. 37, 773\u2013782 (2019).","journal-title":"Nat. Biotechnol."},{"key":"9906_CR19","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s43018-022-00356-3","volume":"3","author":"T Chu","year":"2022","unstructured":"Chu, T., Wang, Z., Pe\u2019er, D. & Danko, C. G. Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. Nat. Cancer 3, 505\u2013517 (2022).","journal-title":"Nat. Cancer"},{"key":"9906_CR20","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1016\/j.ccell.2021.04.014","volume":"39","author":"A Bagaev","year":"2021","unstructured":"Bagaev, A. et al. Conserved pan-cancer microenvironment subtypes predict response to immunotherapy. Cancer Cell 39, 845\u2013865.e7 (2021).","journal-title":"Cancer Cell"},{"key":"9906_CR21","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1007\/s10120-018-0870-6","volume":"22","author":"HH Lee","year":"2019","unstructured":"Lee, H. H., Kim, S. Y., Jung, E. S., Yoo, J. & Kim, T. M. Mutation heterogeneity between primary gastric cancers and their matched lymph node metastases. Gastric Cancer 22, 323\u2013334 (2019).","journal-title":"Gastric Cancer"},{"key":"9906_CR22","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/s41586-023-06054-z","volume":"618","author":"F Mart\u00ednez-Jim\u00e9nez","year":"2023","unstructured":"Mart\u00ednez-Jim\u00e9nez, F. et al. Pan-cancer whole-genome comparison of primary and metastatic solid tumours. Nature 618, 333\u2013341 (2023).","journal-title":"Nature"},{"key":"9906_CR23","doi-asserted-by":"crossref","unstructured":"Li, S. et al. Genomic landscape of paired primary and peritoneal metastatic lesions in gastric cancer highlights evolutionary dynamics and mutational drivers. J. Adv. Res. 81, 507\u2013519 (2026).","DOI":"10.1016\/j.jare.2025.05.043"},{"key":"9906_CR24","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1038\/s43018-021-00240-6","volume":"2","author":"Y Tanaka","year":"2021","unstructured":"Tanaka, Y. et al. Multi-omic profiling of peritoneal metastases in gastric cancer identifies molecular subtypes and therapeutic vulnerabilities. Nat. Cancer 2, 962\u2013977 (2021).","journal-title":"Nat. Cancer"},{"key":"9906_CR25","first-page":"1","volume":"6","author":"S Park","year":"2016","unstructured":"Park, S. et al. Clinical Relevance and Molecular Phenotypes in Gastric Cancer, of TP53 Mutations and Gene Expressions, in Combination With Other Gene Mutations. Sci. Rep. 6, 1\u201310 (2016).","journal-title":"Sci. Rep."},{"key":"9906_CR26","first-page":"1540","volume":"7","author":"S Ge","year":"2017","unstructured":"Ge, S. et al. Genomic alterations in advanced gastric cancer endoscopic biopsy samples using targeted next-generation sequencing. Am. J. Cancer Res 7, 1540 (2017).","journal-title":"Am. J. Cancer Res"},{"key":"9906_CR27","first-page":"1","volume":"8","author":"J Wang","year":"2024","unstructured":"Wang, J. et al. Large-scale analysis of CDH1 mutations defines a distinctive molecular subset with treatment implications in gastric cancer. npj Precis. Oncol. 8, 1\u201310 (2024).","journal-title":"npj Precis. Oncol."},{"key":"9906_CR28","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1136\/gutjnl-2018-318070","volume":"69","author":"R Wang","year":"2020","unstructured":"Wang, R. et al. Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response. Gut 69, 18\u201331 (2020).","journal-title":"Gut"},{"key":"9906_CR29","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2021.689139","volume":"8","author":"H Zhao","year":"2021","unstructured":"Zhao, H. et al. Overview on the Role of E-Cadherin in Gastric Cancer: Dysregulation and Clinical Implications. Front Mol. Biosci. 8, 689139 (2021).","journal-title":"Front Mol. Biosci."},{"key":"9906_CR30","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/cr.2017.34","volume":"27","author":"S Su","year":"2017","unstructured":"Su, S. et al. Blocking the recruitment of naive CD4+ T cells reverses immunosuppression in breast cancer. Cell Res. 27, 461\u2013482 (2017).","journal-title":"Cell Res."},{"key":"9906_CR31","doi-asserted-by":"crossref","unstructured":"Sugarbaker, P. Peritoneal Carcinomatosis: Principles of Management. (1996).","DOI":"10.1007\/978-1-4613-1247-5"},{"key":"9906_CR32","unstructured":"Wang H. et al. Intraperitoneal nivolumab for malignat ascites in patients with advanced gastrointestinal or pancreaticobiliary tract cancer. in ESMO Congress 2023 (2023)."},{"key":"9906_CR33","doi-asserted-by":"publisher","first-page":"3196","DOI":"10.1093\/bioinformatics\/btw389","volume":"32","author":"EA Bergmann","year":"2016","unstructured":"Bergmann, E. A., Chen, B. J., Arora, K., Vacic, V. & Zody, M. C. Conpair: concordance and contamination estimator for matched tumor-normal pairs. Bioinformatics 32, 3196\u20133198 (2016).","journal-title":"Bioinformatics"},{"key":"9906_CR34","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"9906_CR35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, 1\u20134 (2021).","journal-title":"Gigascience"},{"key":"9906_CR36","unstructured":"Van der Auwera, G., O\u2019Connor, B. & Safari. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. O\u2019Reilly Media 300 (2020)."},{"key":"9906_CR37","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","volume":"35","author":"P DI Tommaso","year":"2017","unstructured":"DI Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316\u2013319 (2017).","journal-title":"Nat. Biotechnol."},{"key":"9906_CR38","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","volume":"38","author":"PA Ewels","year":"2020","unstructured":"Ewels, P. A. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 38, 276\u2013278 (2020).","journal-title":"Nat. Biotechnol."},{"key":"9906_CR39","doi-asserted-by":"publisher","first-page":"63","DOI":"10.12688\/f1000research.16665.2","volume":"9","author":"M Garcia","year":"2020","unstructured":"Garcia, M. et al. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res 9, 63 (2020).","journal-title":"F1000Res"},{"key":"9906_CR40","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/s41592-018-0051-x","volume":"15","author":"S Kim","year":"2018","unstructured":"Kim, S. et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat. Methods 15, 591\u2013594 (2018).","journal-title":"Nat. Methods"},{"key":"9906_CR41","unstructured":"Kandoth C. mskcc\/vcf2maf: vcf2maf v1.6.18. https:\/\/github.com\/mskcc\/vcf2maf 10.5281\/zenodo.593251 (2020)."},{"key":"9906_CR42","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1093\/annonc\/mdu479","volume":"26","author":"F Favero","year":"2014","unstructured":"Favero, F. et al. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann. Oncol. 26, 64 (2014).","journal-title":"Ann. Oncol."},{"key":"9906_CR43","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","volume":"500","author":"LB Alexandrov","year":"2013","unstructured":"Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415\u2013421 (2013).","journal-title":"Nature"},{"key":"9906_CR44","doi-asserted-by":"publisher","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","volume":"28","author":"T Rausch","year":"2012","unstructured":"Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333 (2012).","journal-title":"Bioinformatics"},{"key":"9906_CR45","doi-asserted-by":"publisher","first-page":"1349","DOI":"10.1093\/bioinformatics\/btv003","volume":"31","author":"S Malikic","year":"2015","unstructured":"Malikic, S., McPherson, A. W., Donmez, N. & Sahinalp, C. S. Clonality inference in multiple tumor samples using phylogeny. Bioinformatics 31, 1349\u20131356 (2015).","journal-title":"Bioinformatics"},{"key":"9906_CR46","unstructured":"Smith, M. timescape: Patient Clonal Timescapes. https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/timescape.html (2025)."},{"key":"9906_CR47","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10\u201312 (2011).","journal-title":"EMBnet J."},{"key":"9906_CR48","doi-asserted-by":"publisher","unstructured":"Patel, H. et al. nf-core\/rnaseq: nf-core\/rnaseq v3.18.0 - Lithium Lynx. https:\/\/doi.org\/10.5281\/ZENODO.14537300.","DOI":"10.5281\/ZENODO.14537300"},{"key":"9906_CR49","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"9906_CR50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li, B. & Dewey, C. N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12, 1\u201316 (2011).","journal-title":"BMC Bioinform."},{"key":"9906_CR51","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/ncomms3612","volume":"4","author":"K Yoshihara","year":"2013","unstructured":"Yoshihara, K. et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun.4, 1\u201311 (2013).","journal-title":"Nat. Commun."},{"key":"9906_CR52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1\u201321 (2014).","journal-title":"Genome Biol."},{"key":"9906_CR53","volume":"2","author":"T Wu","year":"2021","unstructured":"Wu, T. et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation 2, 100141 (2021).","journal-title":"Innovation"},{"key":"9906_CR54","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","volume":"1","author":"A Liberzon","year":"2015","unstructured":"Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417\u2013425 (2015).","journal-title":"Cell Syst."},{"key":"9906_CR55","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1158\/2159-8290.CD-21-0683","volume":"12","author":"V Kumar","year":"2022","unstructured":"Kumar, V. et al. Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer. Cancer Discov. 12, 670\u2013691 (2022).","journal-title":"Cancer Discov."},{"key":"9906_CR56","doi-asserted-by":"crossref","unstructured":"Jiang, H. et al. Revealing the transcriptional heterogeneity of organ-specific metastasis in human gastric cancer using single-cell RNA Sequencing. Clin. Transl. Med. 12, (2022).","DOI":"10.1002\/ctm2.730"},{"key":"9906_CR57","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"Y Hao","year":"2021","unstructured":"Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573\u20133587.e29 (2021).","journal-title":"Cell"},{"key":"9906_CR58","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"9906_CR59","doi-asserted-by":"publisher","first-page":"5482","DOI":"10.1016\/j.cell.2021.09.014","volume":"184","author":"BA Luca","year":"2021","unstructured":"Luca, B. A. et al. Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell 184, 5482\u20135496.e28 (2021).","journal-title":"Cell"},{"key":"9906_CR60","doi-asserted-by":"publisher","unstructured":"Proks, M. et al. nf-core\/rnafusion: nf-core\/rnafusion:1.2.0. https:\/\/doi.org\/10.5281\/ZENODO.3946477.","DOI":"10.5281\/ZENODO.3946477"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-09906-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-09906-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-09906-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T00:04:45Z","timestamp":1779062685000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-09906-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,25]]},"references-count":60,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["9906"],"URL":"https:\/\/doi.org\/10.1038\/s42003-026-09906-2","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,25]]},"assertion":[{"value":"21 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 March 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 March 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"666"}}