{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T03:55:11Z","timestamp":1772855711416,"version":"3.50.1"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,4,20]],"date-time":"2025-04-20T00:00:00Z","timestamp":1745107200000},"content-version":"vor","delay-in-days":50,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004826","name":"Beijing Natural Science Foundation","doi-asserted-by":"publisher","award":["7254340"],"award-info":[{"award-number":["7254340"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82372897"],"award-info":[{"award-number":["82372897"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-cell RNA sequencing (scRNA-seq) has enabled the dissection of complex tumor ecosystems. Recognition of malignant cells as an essential step has a profound impact on downstream interpretation. However, most existing computational strategies are based on prior knowledge of canonical cell-type markers. We have developed a marker-free approach, the Seed-Cluster based Approach for NEoplastic cells Recognition (SCANER), to identify malignant cells based on significant gene expression variations caused by genomic instability. Upon analyzing different cancer types, SCANER achieved superior accuracy and robustness in identifying malignant cells, effectively addressing dropout events and tumor purity variations. Besides, SCANER can significantly detect copy number variations (CNVs) in malignant cells compared to nonmalignant cells, which is further confirmed through the paired whole exome sequencing data. In conclusion, SCANER has the potential to facilitate the biological exploration of the tumor ecosystem by accurately identifying malignant cells and it is applicable across various solid cancer types regardless of prior knowledge. SCANER is available at https:\/\/github.com\/woolingxiang\/SCANER.<\/jats:p>","DOI":"10.1093\/bib\/bbaf175","type":"journal-article","created":{"date-parts":[[2025,4,20]],"date-time":"2025-04-20T14:58:41Z","timestamp":1745161121000},"source":"Crossref","is-referenced-by-count":1,"title":["SCANER: robust and sensitive identification of malignant cells from the scRNA-seq profiled tumor ecosystem"],"prefix":"10.1093","volume":"26","author":[{"given":"Peng","family":"Xia","sequence":"first","affiliation":[{"name":"School of Biological Science & Medical Engineering, Southeast University , 8 Dongnandaxue Road, Jiangning District, Nanjing 211189 , Jiangsu,","place":["China"]},{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Wei","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Biological Science & Medical Engineering, Southeast University , 8 Dongnandaxue Road, Jiangning District, Nanjing 211189 , Jiangsu,","place":["China"]},{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Quanzhong","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Bin","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Biological Science & Medical Engineering, Southeast University , 8 Dongnandaxue Road, Jiangning District, Nanjing 211189 , Jiangsu,","place":["China"]},{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Min","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Zihan","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Mengyan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Miao","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Ying","family":"Qu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Kening","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Lingxiang","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University , 119 South 4th Ring West Road, Fengtai District, Beijing 100070 ,","place":["China"]}]},{"given":"Ruohan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]}]},{"given":"Qianghu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Biological Science & Medical Engineering, Southeast University , 8 Dongnandaxue Road, Jiangning District, Nanjing 211189, Jiangsu ,","place":["China"]},{"name":"Department of Bioinformatics, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu ,","place":["China"]},{"name":"The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research , 42 Baiziting Road, Xuanwu District, Nanjing 210009, Jiangsu ,","place":["China"]},{"name":"Department of Pathology, Jiangsu Province Hospital and the First Affiliated Hospital of Nanjing Medical University , 300 Guangzhou Road, Gulou District, Nanjing 210029, Jiangsu ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,4,20]]},"reference":[{"key":"2025042010583800300_ref1","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1016\/j.molcel.2015.05.005","article-title":"Advances and applications of single-cell sequencing technologies","volume":"58","author":"Wang","year":"2015","journal-title":"Mol Cell"},{"key":"2025042010583800300_ref2","doi-asserted-by":"publisher","first-page":"1499","DOI":"10.1101\/gr.191098.115","article-title":"The first five years of single-cell cancer genomics and beyond","volume":"25","author":"Navin","year":"2015","journal-title":"Genome Res"},{"key":"2025042010583800300_ref3","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1038\/s41581-018-0021-7","article-title":"Single-cell RNA sequencing for the study of development, 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