{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T05:09:57Z","timestamp":1793941797511,"version":"4.8.0"},"reference-count":211,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100004386","name":"Universiti Malaya","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004386","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Cancer Metastasis Rev"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The global burden of cancer is rising, with treatment failures often due to the metastatic nature of late-stage malignancies. Circulating tumour cells (CTCs) are metastatic precursors shed from primary tumours, which survive in circulation, extravasate and colonise distant organs. The advent of high-throughput single-cell RNA sequencing (scRNA-seq) has revolutionised the investigation of transcriptomic landscape at single-cell resolution, enabling deep transcriptomic profiling, re-stratifying CTC subtypes and improving the detection of rare new subpopulations. Applications extend to understanding tumour microenvironments, characterising cellular heterogeneity, uncovering metastasis molecular mechanisms and improving prognosis and diagnostic strategies. A timeline of key milestones in CTC scRNA-seq research is also provided. Nevertheless, a knowledge gap remains due to unstandardised protocols and fragmented resources in CTC scRNA-seq research. We address this gap by proposing a 12-step CTC-specific scRNA-seq workflow to overcome methodological inconsistencies. This workflow spans the entire process from enrichment, single-cell sorting and sequencing to data pre-processing and downstream analyses, with a detailed compilation of data analysis tools. An in-depth discussion of the pros and cons of commonly used scRNA-seq tools is also included, specifically evaluating their suitability for CTC research. Additionally, emerging research frontiers, including the discovery of hybrid cells\u2014fusion products of tumour and normal cells\u2014and the integration of machine learning (ML) into scRNA-seq workflows, are explored. Future research should prioritise CTC scRNA-seq workflow standardisation, integrate ML-driven analysis and investigate rare and hybrid populations to advance metastasis research. This review supports these goals by guiding methods, informing tool selection and promoting data sharing for reproducibility.<\/jats:p>","DOI":"10.1007\/s10555-025-10293-z","type":"journal-article","created":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T17:25:22Z","timestamp":1759771522000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications"],"prefix":"10.1007","volume":"44","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2504-3934","authenticated-orcid":false,"given":"Francis Yew Fu","family":"Tieng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8589-7456","authenticated-orcid":false,"given":"Learn-Han","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6914-2224","authenticated-orcid":false,"given":"Nurul-Syakima","family":"Ab Mutalib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,10,6]]},"reference":[{"key":"10293_CR1","doi-asserted-by":"publisher","first-page":"461","DOI":"10.2147\/CMAR.S506630","volume":"17","author":"W Qi","year":"2025","unstructured":"Qi, W., Tian, L., Xu, J., Li, Z., & Wang, T. (2025). Multimodal framework in lung cancer management: Integrating liquid biopsy with traditional diagnostic techniques. Cancer Management And Research, 17, 461\u2013481. https:\/\/doi.org\/10.2147\/CMAR.S506630","journal-title":"Cancer Management And Research"},{"key":"10293_CR2","doi-asserted-by":"publisher","DOI":"10.1200\/PO.24.00299","author":"P Wang","year":"2025","unstructured":"Wang, P., Yang, R. K., Jelloul, F. Z., Luthra, R., Routbort, M. J., Chen, H., Loghavi, S., Ok, C. Y., Kanagal-Shamanna, R., Roy-Chowdhuri, S., Medeiros, L. J., & Patel, K. P. (2025). Routine clinical liquid biopsy testing for solid tumors delivers the promise of minimally invasive detection of genomic variants with a faster turnaround time. JCO Precision Oncology. https:\/\/doi.org\/10.1200\/PO.24.00299","journal-title":"JCO Precision Oncology"},{"key":"10293_CR3","doi-asserted-by":"publisher","unstructured":"Liang, X., Tang, Q., Chen, J., Wei, Y. (2025). Liquid biopsy: A breakthrough technology in early cancer screening. Cancer Screening and Prevention 0 0\u20130. https:\/\/doi.org\/10.14218\/CSP.2024.00031.","DOI":"10.14218\/CSP.2024.00031"},{"key":"10293_CR4","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.43650","volume":"15","author":"T Shegekar","year":"2023","unstructured":"Shegekar, T., Vodithala, S., & Juganavar, A. (2023). The emerging role of liquid biopsies in revolutionising cancer diagnosis and therapy. Cureus, 15, Article e43650. https:\/\/doi.org\/10.7759\/cureus.43650","journal-title":"Cureus"},{"key":"10293_CR5","doi-asserted-by":"publisher","DOI":"10.1016\/j.plabm.2024.e00446","volume":"43","author":"S Pandey","year":"2025","unstructured":"Pandey, S., & Yadav, P. (2025). Liquid biopsy in cancer management: Integrating diagnostics and clinical applications. Practical Laboratory Medicine, 43, Article e00446. https:\/\/doi.org\/10.1016\/j.plabm.2024.e00446","journal-title":"Practical Laboratory Medicine"},{"key":"10293_CR6","doi-asserted-by":"publisher","DOI":"10.1016\/j.critrevonc.2025.104613","volume":"207","author":"J Song","year":"2025","unstructured":"Song, J., Ye, X., & Xiao, H. (2025). Liquid biopsy entering clinical practice: Past discoveries, current insights, and future innovations. Critical Reviews in Oncology\/Hematology, 207, Article 104613. https:\/\/doi.org\/10.1016\/j.critrevonc.2025.104613","journal-title":"Critical Reviews in Oncology\/Hematology"},{"key":"10293_CR7","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-020-00728-3","volume":"12","author":"F Castro-Giner","year":"2020","unstructured":"Castro-Giner, F., & Aceto, N. (2020). Tracking cancer progression: From circulating tumor cells to metastasis. Genome Medicine, 12, Article 31. https:\/\/doi.org\/10.1186\/s13073-020-00728-3","journal-title":"Genome Medicine"},{"key":"10293_CR8","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/978-3-319-95294-9_11","volume":"1092","author":"BL Krog","year":"2018","unstructured":"Krog, B. L., & Henry, M. D. (2018). Biomechanics of the circulating tumor cell microenvironment. Advances in Experimental Medicine and Biology, 1092, 209\u2013233. https:\/\/doi.org\/10.1007\/978-3-319-95294-9_11","journal-title":"Advances in Experimental Medicine and Biology"},{"key":"10293_CR9","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/bs.acc.2017.10.004","volume":"83","author":"LE Lowes","year":"2018","unstructured":"Lowes, L. E., & Allan, A. L. (2018). Circulating tumor cells and implications of the epithelial-to-mesenchymal transition. Advances in Clinical Chemistry, 83, 121\u2013181. https:\/\/doi.org\/10.1016\/bs.acc.2017.10.004","journal-title":"Advances in Clinical Chemistry"},{"key":"10293_CR10","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines9091242","volume":"9","author":"T Rossi","year":"2021","unstructured":"Rossi, T., Gallerani, G., Martinelli, G., Maltoni, R., & Fabbri, F. (2021). Circulating tumor cells as a tool to untangle the breast cancer heterogeneity issue. Biomedicines, 9, Article 1242. https:\/\/doi.org\/10.3390\/biomedicines9091242","journal-title":"Biomedicines"},{"key":"10293_CR11","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2021.111314","volume":"137","author":"T Yu","year":"2021","unstructured":"Yu, T., Wang, C., Xie, M., Zhu, C., Shu, Y., Tang, J., & Guan, X. (2021). Heterogeneity of CTC contributes to the organotropism of breast cancer. Biomedicine & Pharmacotherapy, 137, Article 111314. https:\/\/doi.org\/10.1016\/j.biopha.2021.111314","journal-title":"Biomedicine & Pharmacotherapy"},{"key":"10293_CR12","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-57381-8","volume":"14","author":"RM Whalen","year":"2024","unstructured":"Whalen, R. M., Anderson, A. N., Jones, J. A., Sims, Z., Chang, Y. H., Nederlof, M. A., Wong, M. H., & Gibbs, S. L. (2024). Ultra high content analyses of circulating and tumor associated hybrid cells reveal phenotypic heterogeneity. Scientific Reports, 14, Article 7350. https:\/\/doi.org\/10.1038\/s41598-024-57381-8","journal-title":"Scientific Reports"},{"key":"10293_CR13","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-017-3509-9","volume":"17","author":"D Gauck","year":"2017","unstructured":"Gauck, D., Keil, S., Niggemann, B., Z\u00e4nker, K. S., & Dittmar, T. (2017). Hybrid clone cells derived from human breast epithelial cells and human breast cancer cells exhibit properties of cancer stem\/initiating cells. BMC Cancer, 17, Article 515. https:\/\/doi.org\/10.1186\/s12885-017-3509-9","journal-title":"BMC Cancer"},{"issue":"17","key":"10293_CR14","doi-asserted-by":"publisher","DOI":"10.3390\/cancers13174496","volume":"13","author":"R Hass","year":"2021","unstructured":"Hass, R., von der Ohe, J., & Dittmar, T. (2021). Hybrid formation and fusion of cancer cells in vitro and in vivo. Cancers, 13(17), Article 4496. https:\/\/doi.org\/10.3390\/cancers13174496","journal-title":"Cancers"},{"key":"10293_CR15","doi-asserted-by":"publisher","DOI":"10.3390\/ijms241512337","volume":"24","author":"S Orrapin","year":"2023","unstructured":"Orrapin, S., Thongkumkoon, P., Udomruk, S., Moonmuang, S., Sutthitthasakul, S., Yongpitakwattana, P., Pruksakorn, D., & Chaiyawat, P. (2023). Deciphering the biology of circulating tumor cells through single-cell RNA sequencing: Implications for precision medicine in cancer. International Journal of Molecular Sciences, 24, Article 12337. https:\/\/doi.org\/10.3390\/ijms241512337","journal-title":"International Journal of Molecular Sciences"},{"key":"10293_CR16","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2020.00135","volume":"11","author":"FYF Tieng","year":"2020","unstructured":"Tieng, F. Y. F., Baharudin, R., Abu, N., Mohd Yunos, R.-I., Lee, L.-H., & Ab Mutalib, N.-S. (2020). Single cell transcriptome in colorectal cancer\u2014current updates on its application in metastasis, chemoresistance and the roles of circulating tumor cells. Frontiers in Pharmacology, 11, Article 135. https:\/\/doi.org\/10.3389\/fphar.2020.00135","journal-title":"Frontiers in Pharmacology"},{"key":"10293_CR17","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/s41576-020-00292-x","volume":"22","author":"E Armingol","year":"2021","unstructured":"Armingol, E., Officer, A., Harismendy, O., & Lewis, N. E. (2021). Deciphering cell\u2013cell interactions and communication from gene expression. Nature Reviews Genetics, 22, 71\u201388. https:\/\/doi.org\/10.1038\/s41576-020-00292-x","journal-title":"Nature Reviews Genetics"},{"key":"10293_CR18","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1038\/s41576-021-00370-8","volume":"22","author":"SK Longo","year":"2021","unstructured":"Longo, S. K., Guo, M. G., Ji, A. L., & Khavari, P. A. (2021). Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nature Reviews Genetics, 22, 627\u2013644. https:\/\/doi.org\/10.1038\/s41576-021-00370-8","journal-title":"Nature Reviews Genetics"},{"key":"10293_CR19","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac516","volume":"24","author":"G Meng","year":"2023","unstructured":"Meng, G., Tang, W., Huang, E., Li, Z., & Feng, H. (2023). A comprehensive assessment of cell type-specific differential expression methods in bulk data. Briefings in Bioinformatics, 24, Article bbac516. https:\/\/doi.org\/10.1093\/bib\/bbac516","journal-title":"Briefings in Bioinformatics"},{"key":"10293_CR20","doi-asserted-by":"publisher","DOI":"10.3390\/jcm9041206","volume":"9","author":"A Iyer","year":"2020","unstructured":"Iyer, A., Gupta, K., Sharma, S., Hari, K., Lee, Y. F., Ramalingam, N., Yap, Y. S., West, J., Bhagat, A. A., Subramani, B. V., Sabuwala, B., Tan, T. Z., Thiery, J. P., Jolly, M. K., Ramalingam, N., & Sengupta, D. (2020). Integrative analysis and machine learning based characterization of single circulating tumor cells. Journal of Clinical Medicine, 9, Article 1206. https:\/\/doi.org\/10.3390\/jcm9041206","journal-title":"Journal of Clinical Medicine"},{"key":"10293_CR21","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-61378-8","volume":"14","author":"K Pastuszak","year":"2024","unstructured":"Pastuszak, K., Sieczczy\u0144ski, M., Dzi\u0119gielewska, M., Wolniak, R., Drewnowska, A., Korpal, M., Zembrzuska, L., Supernat, A., & \u017baczek, A. J. (2024). Detection of circulating tumor cells by means of machine learning using Smart-Seq2 sequencing. Scientific Reports, 14, Article 11057. https:\/\/doi.org\/10.1038\/s41598-024-61378-8","journal-title":"Scientific Reports"},{"key":"10293_CR22","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1038\/nbt.2282","volume":"30","author":"D Ramsk\u00f6ld","year":"2012","unstructured":"Ramsk\u00f6ld, D., Luo, S., Wang, Y.-C., Li, R., Deng, Q., Faridani, O. R., Daniels, G. A., Khrebtukova, I., Loring, J. F., Laurent, L. C., Schroth, G. P., & Sandberg, R. (2012). Full-length mRNA-seq from single cell levels of RNA and individual circulating tumor cells. Nature Biotechnology, 30, 777\u2013782. https:\/\/doi.org\/10.1038\/nbt.2282","journal-title":"Nature Biotechnology"},{"key":"10293_CR23","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1038\/nmeth.2639","volume":"10","author":"S Picelli","year":"2013","unstructured":"Picelli, S., Bj\u00f6rklund, \u00c5. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013). Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature Methods, 10, 1096\u20131098. https:\/\/doi.org\/10.1038\/nmeth.2639","journal-title":"Nature Methods"},{"key":"10293_CR24","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/nprot.2014.006","volume":"9","author":"S Picelli","year":"2014","unstructured":"Picelli, S., Faridani, O. R., Bj\u00f6rklund, \u00c5. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014). Full-length RNA-seq from single cells using Smart-seq2. Nature Protocols, 9, 171\u2013181. https:\/\/doi.org\/10.1038\/nprot.2014.006","journal-title":"Nature Protocols"},{"key":"10293_CR25","doi-asserted-by":"publisher","first-page":"1905","DOI":"10.1016\/j.celrep.2014.08.029","volume":"8","author":"DT Ting","year":"2014","unstructured":"Ting, D. T., Wittner, B. S., Ligorio, M., Jordan, N. V., Shah, A. M., Miyamoto, D. T., Aceto, N., Bersani, F., Brannigan, B. W., Xega, K., Ciciliano, J. C., Zhu, H., MacKenzie, O. C., Trautwein, J., Arora, K. S., Shahid, M., Ellis, H. L., Qu, N., Bardeesy, N., \u2026 Haber, D. A. (2014). Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells. Cell Reports, 8, 1905\u20131918. https:\/\/doi.org\/10.1016\/j.celrep.2014.08.029","journal-title":"Cell Reports"},{"key":"10293_CR26","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14049","volume":"8","author":"GXY Zheng","year":"2017","unstructured":"Zheng, G. X. Y., Terry, J. M., Belgrader, P., Ryvkin, P., Bent, Z. W., Wilson, R., Ziraldo, S. B., Wheeler, T. D., McDermott, G. P., Zhu, J., Gregory, M. T., Shuga, J., Montesclaros, L., Underwood, J. G., Masquelier, D. A., Nishimura, S. Y., Schnall-Levin, M., Wyatt, P. W., Hindson, C. M., \u2026 Bielas, J. H. (2017). Massively parallel digital transcriptional profiling of single cells. Nature Communications, 8, Article 14049. https:\/\/doi.org\/10.1038\/ncomms14049","journal-title":"Nature Communications"},{"key":"10293_CR27","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-30047-y","volume":"8","author":"D D\u2019Avola","year":"2018","unstructured":"D\u2019Avola, D., Villacorta-Martin, C., Martins-Filho, S. N., Craig, A., Labgaa, I., von Felden, J., Kimaada, A., Bonaccorso, A., Tabrizian, P., Hartmann, B. M., Sebra, R., Schwartz, M., & Villanueva, A. (2018). High-density single cell mRNA sequencing to characterize circulating tumor cells in hepatocellular carcinoma. Scientific Reports, 8, Article 11570. https:\/\/doi.org\/10.1038\/s41598-018-30047-y","journal-title":"Scientific Reports"},{"key":"10293_CR28","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10122-2","volume":"10","author":"Y-H Cheng","year":"2019","unstructured":"Cheng, Y.-H., Chen, Y.-C., Lin, E., Brien, R., Jung, S., Chen, Y.-T., Lee, W., Hao, Z., Sahoo, S., Kang, H. M., Cong, J., Burness, M., Nagrath, S., Wicha, M. S., & Yoon, E. (2019). Hydro-seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells. Nature Communications, 10, Article 2163. https:\/\/doi.org\/10.1038\/s41467-019-10122-2","journal-title":"Nature Communications"},{"key":"10293_CR29","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-02165-7","volume":"11","author":"M Kojima","year":"2021","unstructured":"Kojima, M., Harada, T., Fukazawa, T., Kurihara, S., Saeki, I., Takahashi, S., & Hiyama, E. (2021). Single-cell DNA and RNA sequencing of circulating tumor cells. Scientific Reports, 11, Article 22864. https:\/\/doi.org\/10.1038\/s41598-021-02165-7","journal-title":"Scientific Reports"},{"key":"10293_CR30","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202000060","volume":"21","author":"F Shi","year":"2021","unstructured":"Shi, F., Jia, F., Wei, Z., Ma, Y., Fang, Z., Zhang, W., & Hu, Z. (2021). A microfluidic chip for efficient circulating tumor cells enrichment, screening, and single-cell RNA sequencing. Proteomics, 21, Article e2000060. https:\/\/doi.org\/10.1002\/pmic.202000060","journal-title":"Proteomics"},{"key":"10293_CR31","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2315168121","volume":"121","author":"Z Dong","year":"2024","unstructured":"Dong, Z., Wang, Y., Xu, G., Liu, B., Wang, Y., Reboud, J., Jajesniak, P., Yan, S., Ma, P., Liu, F., Zhou, Y., Jin, Z., Yang, K., Huang, Z., Zhuo, M., Jia, B., Fang, J., Zhang, P., Wu, N., & Chang, L. (2024). Genetic and phenotypic profiling of single living circulating tumor cells from patients with microfluidics. Proceedings of the National Academy of Sciences of the United States of America, 121, Article e2315168121. https:\/\/doi.org\/10.1073\/pnas.2315168121","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10293_CR32","unstructured":"Vasantharajan, S.S. (2024). Characterisation of circulating tumour cells isolated by a size-based method and identification of circulating tumour cell-specific transcriptomic signatures to understand colorectal cancer metastasis, University of Otago. https:\/\/ourarchive.otago.ac.nz\/esploro\/outputs\/doctoral\/Characterisation-of-circulating-tumour-cells-isolated\/9926522380201891 (Accessed November 29, 2024)."},{"key":"10293_CR33","doi-asserted-by":"publisher","first-page":"107327482412515","DOI":"10.1177\/10732748241251571","volume":"31","author":"A Stucky","year":"2024","unstructured":"Stucky, A., Viet, C. T., Aouizerat, B. E., Ye, Y., Doan, C., Mundluru, T., Sedhiazadeh, P., Sinha, U. K., Chen, X., Zhang, X., Li, S. C., Cai, J., & Zhong, J. F. (2024). Single-cell molecular profiling of head and neck squamous cell carcinoma reveals five dysregulated signaling pathways associated with circulating tumor cells. Cancer Control, 31, 10732748241251572. https:\/\/doi.org\/10.1177\/10732748241251571","journal-title":"Cancer Control"},{"key":"10293_CR34","doi-asserted-by":"publisher","DOI":"10.1016\/j.jlb.2024.100276","author":"AHM Moeyersoms","year":"2024","unstructured":"Moeyersoms, A. H. M., Knechtel, K. W., Rong, A. J., Gallo, R. A., Zhang, M., Marsh, H. M., Sargi, Z. B., Leibowitz, J. M., Civantos, F. J., Weed, D. T., Dubovy, S. R., Tse, D. T., & Pelaez, D. (2024). Circulating adenoid cystic carcinoma associated MYB transcripts enable rapid and sensitive detection of metastatic disease in blood liquid biopsies. The Journal of Liquid Biopsy. https:\/\/doi.org\/10.1016\/j.jlb.2024.100276","journal-title":"The Journal of Liquid Biopsy"},{"key":"10293_CR35","doi-asserted-by":"publisher","first-page":"8725","DOI":"10.1038\/s41598-025-92542-3","volume":"15","author":"L Wu","year":"2025","unstructured":"Wu, L., Wang, Z., Zia, A., Kelley, S. O., & de Perrot, M. (2025). Mesothelioma cell heterogeneity identified by single cell RNA sequencing. Scientific Reports, 15, 8725. https:\/\/doi.org\/10.1038\/s41598-025-92542-3","journal-title":"Scientific Reports"},{"key":"10293_CR36","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1158\/2159-8290.CD-19-1500","volume":"11","author":"X Hong","year":"2021","unstructured":"Hong, X., Roh, W., Sullivan, R. J., Wong, K. H. K., Wittner, B. S., Guo, H., Dubash, T. D., Sade-Feldman, M., Wesley, B., Horwitz, E., Boland, G. M., Marvin, D. L., Bonesteel, T., Lu, C., Aguet, F., Burr, R., Freeman, S. S., Parida, L., Calhoun, K., & Haber, D. A. (2021). The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis. Cancer Discovery, 11, 678\u2013695. https:\/\/doi.org\/10.1158\/2159-8290.CD-19-1500","journal-title":"Cancer Discovery"},{"key":"10293_CR37","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/s43018-019-0020-z","volume":"1","author":"CA Stewart","year":"2020","unstructured":"Stewart, C. A., Gay, C. M., Xi, Y., Sivajothi, S., Sivakamasundari, V., Fujimoto, J., Bolisetty, M., Hartsfield, P. M., Balasubramaniyan, V., Chalishazar, M. D., Moran, C., Kalhor, N., Stewart, J., Tran, H., Swisher, S. G., Roth, J. A., Zhang, J., de Groot, J., Glisson, B., \u2026 Byers, L. A. (2020). Single-cell analyses reveal increased intratumoral heterogeneity after the onset of therapy resistance in small-cell lung cancer. Nature Cancer, 1, 423\u2013436. https:\/\/doi.org\/10.1038\/s43018-019-0020-z","journal-title":"Nature Cancer"},{"key":"10293_CR38","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.16678","volume":"12","author":"E Grigoryeva","year":"2024","unstructured":"Grigoryeva, E., Tashireva, L., Alifanov, V., Savelieva, O., Zavyalova, M., Menyailo, M., Khozyainova, A., Denisov, E. V., Bragina, O., Popova, N., Cherdyntseva, N. V., & Perelmuter, V. (2024). Integrin-associated transcriptional characteristics of circulating tumor cells in breast cancer patients. PeerJ, 12, Article e16678. https:\/\/doi.org\/10.7717\/peerj.16678","journal-title":"PeerJ"},{"key":"10293_CR39","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1101\/gr.276600.122","volume":"33","author":"S Poonia","year":"2023","unstructured":"Poonia, S., Goel, A., Chawla, S., Bhattacharya, N., Rai, P., Lee, Y. F., Yap, Y. S., West, J., Bhagat, A. A., Tayal, J., Mehta, A., Ahuja, G., Majumdar, A., Ramalingam, N., & Sengupta, D. (2023). Marker-free characterization of full-length transcriptomes of single live circulating tumor cells. Genome Research, 33, 80\u201395. https:\/\/doi.org\/10.1101\/gr.276600.122","journal-title":"Genome Research"},{"key":"10293_CR40","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-024-01984-2","volume":"23","author":"L-M Rieckmann","year":"2024","unstructured":"Rieckmann, L.-M., Spohn, M., Ruff, L., Agorku, D., Becker, L., Borchers, A., Krause, J., O\u2019Reilly, R., Hille, J., Velthaus-Rusik, J.-L., Beumer, N., G\u00fcnther, A., Willnow, L., Imbusch, C. D., Iglauer, P., Simon, R., Franzenburg, S., Winter, H., Thomas, M., \u2026 Janning, M. (2024). Diagnostic leukapheresis reveals distinct phenotypes of NSCLC circulating tumor cells. Molecular Cancer, 23, Article 93. https:\/\/doi.org\/10.1186\/s12943-024-01984-2","journal-title":"Molecular Cancer"},{"key":"10293_CR41","doi-asserted-by":"publisher","first-page":"1616","DOI":"10.1111\/cas.15707","volume":"114","author":"M Kojima","year":"2023","unstructured":"Kojima, M., Harada, T., Fukazawa, T., Kurihara, S., Touge, R., Saeki, I., Takahashi, S., & Hiyama, E. (2023). Single-cell next-generation sequencing of circulating tumor cells in patients with neuroblastoma. Cancer Science, 114, 1616\u20131624. https:\/\/doi.org\/10.1111\/cas.15707","journal-title":"Cancer Science"},{"key":"10293_CR42","doi-asserted-by":"publisher","DOI":"10.3390\/cancers13194862","volume":"13","author":"M Kozuka","year":"2021","unstructured":"Kozuka, M., Battaglin, F., Jayachandran, P., Wang, J., Arai, H., Soni, S., Zhang, W., Hirai, M., Matsusaka, S., & Lenz, H.-J. (2021). Clinical significance of circulating tumor cell induced epithelial-mesenchymal transition in patients with metastatic colorectal cancer by single-cell RNA-sequencing. Cancers, 13, Article 4862. https:\/\/doi.org\/10.3390\/cancers13194862","journal-title":"Cancers"},{"key":"10293_CR43","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.3390\/ijms21051580","volume":"21","author":"MA Zolotovskaia","year":"2020","unstructured":"Zolotovskaia, M. A., Sorokin, M. I., Petrov, I. V., Poddubskaya, E. V., Moiseev, A. A., Sekacheva, M. I., Borisov, N. M., Tkachev, V. S., Garazha, A. V., Kaprin, A. D., Shegay, P. V., Giese, A., Kim, E., Roumiantsev, S. A., & Buzdin, A. A. (2020). Disparity between inter-patient molecular heterogeneity and repertoires of target drugs used for different types of cancer in clinical oncology. International Journal of Molecular Sciences, 21, 1580. https:\/\/doi.org\/10.3390\/ijms21051580","journal-title":"International Journal of Molecular Sciences"},{"key":"10293_CR44","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1007\/s10911-023-09551-z","volume":"28","author":"B Hamelin","year":"2023","unstructured":"Hamelin, B., Obradovi\u0107, M. M. S., Sethi, A., Kloc, M., M\u00fcnst, S., Beisel, C., Eschbach, K., Kohler, H., Soysal, S., Vetter, M., Weber, W. P., Stadler, M. B., & Bentires-Alj, M. (2023). Single-cell analysis reveals inter- and intratumour heterogeneity in metastatic breast cancer. Journal of Mammary Gland Biology and Neoplasia, 28, 26. https:\/\/doi.org\/10.1007\/s10911-023-09551-z","journal-title":"Journal of Mammary Gland Biology and Neoplasia"},{"key":"10293_CR45","doi-asserted-by":"crossref","unstructured":"Goldman, S. L., MacKay, M., Afshinnekoo, E., Melnick, A. M., Wu, S., Mason, C.E. (2019). The impact of heterogeneity on single-cell sequencing, Frontiers in Genetics 10. https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2019.00008 (Accessed January 9, 2024).","DOI":"10.3389\/fgene.2019.00008"},{"key":"10293_CR46","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.246","volume":"10","author":"H Ruan","year":"2020","unstructured":"Ruan, H., Zhou, Y., Shen, J., Zhai, Y., Xu, Y., Pi, L., Huang, R., Chen, K., Li, X., Ma, W., Wu, Z., Deng, X., Wang, X., Zhang, C., & Guan, M. (2020). Circulating tumor cell characterization of lung cancer brain metastases in the cerebrospinal fluid through single-cell transcriptome analysis. Clinical and Translational Medicine, 10, Article e246. https:\/\/doi.org\/10.1002\/ctm2.246","journal-title":"Clinical and Translational Medicine"},{"key":"10293_CR47","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1002\/mc.23242","volume":"59","author":"HM Brechbuhl","year":"2020","unstructured":"Brechbuhl, H. M., Vinod-Paul, K., Gillen, A. E., Kopin, E. G., Gibney, K., Elias, A. D., Hayashi, M., Sartorius, C. A., & Kabos, P. (2020). Analysis of circulating breast cancer cell heterogeneity and interactions with peripheral blood mononuclear cells. Molecular Carcinogenesis, 59, 1129\u20131139. https:\/\/doi.org\/10.1002\/mc.23242","journal-title":"Molecular Carcinogenesis"},{"key":"10293_CR48","doi-asserted-by":"publisher","DOI":"10.3390\/cancers13194885","volume":"13","author":"CM Pauken","year":"2021","unstructured":"Pauken, C. M., Kenney, S. R., Brayer, K. J., Guo, Y., Brown-Glaberman, U. A., & Marchetti, D. (2021). Heterogeneity of circulating tumor cell neoplastic subpopulations outlined by single-cell transcriptomics. Cancers, 13, Article 4885. https:\/\/doi.org\/10.3390\/cancers13194885","journal-title":"Cancers"},{"key":"10293_CR49","doi-asserted-by":"publisher","first-page":"e0265725","DOI":"10.1371\/journal.pone.0265725","volume":"17","author":"JP Arnoletti","year":"2022","unstructured":"Arnoletti, J. P., Reza, J., Rosales, A., Monreal, A., Fanaian, N., Whisner, S., Srivastava, M., Rivera-Otero, J., Yu, G., Phanstiel, O., IV., Altomare, D. A., Tran, Q., & Litherland, S. A. (2022). Pancreatic ductal adenocarcinoma (PDAC) circulating tumor cells influence myeloid cell differentiation to support their survival and immunoresistance in portal vein circulation. PLoS One, 17, e0265725. https:\/\/doi.org\/10.1371\/journal.pone.0265725","journal-title":"PLoS One"},{"key":"10293_CR50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-55140-x","volume":"16","author":"A Mishra","year":"2025","unstructured":"Mishra, A., Huang, S.-B., Dubash, T., Burr, R., Edd, J. F., Wittner, B. S., Cunneely, Q. E., Putaturo, V. R., Deshpande, A., Antmen, E., Gopinathan, K. A., Otani, K., Miyazawa, Y., Kwak, J. E., Guay, S. Y., Kelly, J., Walsh, J., Nieman, L. T., Galler, I., \u2026 Toner, M. (2025). Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product. Nature Communications, 16, Article 32. https:\/\/doi.org\/10.1038\/s41467-024-55140-x","journal-title":"Nature Communications"},{"key":"10293_CR51","doi-asserted-by":"publisher","DOI":"10.3390\/medicina56010015","volume":"56","author":"B Arneth","year":"2019","unstructured":"Arneth, B. (2019). Tumor microenvironment. Medicina (Kaunas), 56, Article 15. https:\/\/doi.org\/10.3390\/medicina56010015","journal-title":"Medicina (Kaunas)"},{"key":"10293_CR52","doi-asserted-by":"crossref","unstructured":"Tieng, F. Y. F., Lee, L.-H., Ab Mutalib, N.-S. (2022). Deciphering colorectal cancer immune microenvironment transcriptional landscape on single cell resolution\u2014A role for immunotherapy, Frontiers in Immunology 13. https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2022.959705 (Accessed September 5, 2022).","DOI":"10.3389\/fimmu.2022.959705"},{"key":"10293_CR53","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/s41586-019-0915-y","volume":"566","author":"BM Szczerba","year":"2019","unstructured":"Szczerba, B. M., Castro-Giner, F., Vetter, M., Krol, I., Gkountela, S., Landin, J., Scheidmann, M. C., Donato, C., Scherrer, R., Singer, J., Beisel, C., Kurzeder, C., Heinzelmann-Schwarz, V., Rochlitz, C., Weber, W. P., Beerenwinkel, N., & Aceto, N. (2019). Neutrophils escort circulating tumour cells to enable cell cycle progression. Nature, 566, 553\u2013557. https:\/\/doi.org\/10.1038\/s41586-019-0915-y","journal-title":"Nature"},{"key":"10293_CR54","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24386-0","volume":"12","author":"Y-F Sun","year":"2021","unstructured":"Sun, Y.-F., Wu, L., Liu, S.-P., Jiang, M.-M., Hu, B., Zhou, K.-Q., Guo, W., Xu, Y., Zhong, Y., Zhou, X.-R., Zhang, Z.-F., Liu, G., Liu, S., Shi, Y.-H., Ji, Y., Du, M., Li, N.-N., Li, G.-B., Zhao, Z.-K., \u2026 Yang, X.-R. (2021). Dissecting spatial heterogeneity and the immune-evasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma. Nature Communications, 12, Article 4091. https:\/\/doi.org\/10.1038\/s41467-021-24386-0","journal-title":"Nature Communications"},{"key":"10293_CR55","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1016\/j.ccell.2023.01.001","volume":"41","author":"X Liu","year":"2023","unstructured":"Liu, X., Song, J., Zhang, H., Liu, X., Zuo, F., Zhao, Y., Zhao, Y., Yin, X., Guo, X., Wu, X., Zhang, H., Xu, J., Hu, J., Jing, J., Ma, X., & Shi, H. (2023). Immune checkpoint HLA-E: CD94-NKG2A mediates evasion of circulating tumor cells from NK cell surveillance. Cancer Cell, 41, 272-287.e9. https:\/\/doi.org\/10.1016\/j.ccell.2023.01.001","journal-title":"Cancer Cell"},{"key":"10293_CR56","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2022.892177","volume":"13","author":"H-D Tang","year":"2022","unstructured":"Tang, H.-D., Wang, Y., Xie, P., Tan, S.-Y., Li, H.-F., Shen, H., Zhang, Z., Lei, Z.-Q., & Zhou, J.-H. (2022). The crosstalk between immune infiltration, circulating tumor cells, and metastasis in pancreatic cancer: Identification of HMGB3 from a multiple omics analysis. Frontiers in Genetics, 13, Article 892177. https:\/\/doi.org\/10.3389\/fgene.2022.892177","journal-title":"Frontiers in Genetics"},{"key":"10293_CR57","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002487","volume":"22","author":"T Celi\u00e0-Terrassa","year":"2024","unstructured":"Celi\u00e0-Terrassa, T., & Kang, Y. (2024). How important is EMT for cancer metastasis? PLoS Biology, 22, Article e3002487. https:\/\/doi.org\/10.1371\/journal.pbio.3002487","journal-title":"PLoS Biology"},{"key":"10293_CR58","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/s42003-021-02937-x","volume":"5","author":"R Negishi","year":"2022","unstructured":"Negishi, R., Yamakawa, H., Kobayashi, T., Horikawa, M., Shimoyama, T., Koizumi, F., Sawada, T., Oboki, K., Omuro, Y., Funasaka, C., Kageyama, A., Kanemasa, Y., Tanaka, T., Matsunaga, T., & Yoshino, T. (2022). Transcriptomic profiling of single circulating tumor cells provides insight into human metastatic gastric cancer. Communications Biology, 5, 20. https:\/\/doi.org\/10.1038\/s42003-021-02937-x","journal-title":"Communications Biology"},{"key":"10293_CR59","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1111\/1759-7714.14728","volume":"14","author":"S Pang","year":"2023","unstructured":"Pang, S., Xu, S., Wang, L., Wu, H., Chu, Y., Ma, X., Li, Y., Zou, B., Wang, S., & Zhou, G. (2023). Molecular profiles of single circulating tumor cells from early breast cancer patients with different lymph node statuses. Thoracic Cancer, 14, 156\u2013167. https:\/\/doi.org\/10.1111\/1759-7714.14728","journal-title":"Thoracic Cancer"},{"key":"10293_CR60","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1126\/science.aab0917","volume":"349","author":"DT Miyamoto","year":"2015","unstructured":"Miyamoto, D. T., Zheng, Y., Wittner, B. S., Lee, R. J., Zhu, H., Broderick, K. T., Desai, R., Fox, D. B., Brannigan, B. W., Trautwein, J., Arora, K. S., Desai, N., Dahl, D. M., Sequist, L. V., Smith, M. R., Kapur, R., Wu, C.-L., Shioda, T., Ramaswamy, S., \u2026 Haber, D. A. (2015). RNA-seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance. Science, 349, 1351\u20131356. https:\/\/doi.org\/10.1126\/science.aab0917","journal-title":"Science"},{"key":"10293_CR61","doi-asserted-by":"publisher","DOI":"10.1016\/j.canlet.2024.216757","volume":"588","author":"Q Wu","year":"2024","unstructured":"Wu, Q., Gu, Z., Shang, B., Wan, D., Zhang, Q., Zhang, X., Xie, P., Cheng, S., Zhang, W., & Zhang, K. (2024). Circulating tumor cell clustering modulates RNA splicing and polyadenylation to facilitate metastasis. Cancer Letters, 588, Article 216757. https:\/\/doi.org\/10.1016\/j.canlet.2024.216757","journal-title":"Cancer Letters"},{"key":"10293_CR62","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1007\/s10549-021-06270-z","volume":"188","author":"TK Sundaresan","year":"2021","unstructured":"Sundaresan, T. K., Dubash, T. D., Zheng, Z., Bardia, A., Wittner, B. S., Aceto, N., Silva, E. J., Fox, D. B., Liebers, M., Kapur, R., Iafrate, J., Toner, M., Maheswaran, S., & Haber, D. A. (2021). Evaluation of endocrine resistance using Esr1 genotyping of circulating tumor cells and plasma Dna. Breast Cancer Research and Treatment, 188, 43\u201352. https:\/\/doi.org\/10.1007\/s10549-021-06270-z","journal-title":"Breast Cancer Research and Treatment"},{"key":"10293_CR63","doi-asserted-by":"publisher","first-page":"2590","DOI":"10.3390\/cells12222590","volume":"12","author":"M Capuozzo","year":"2023","unstructured":"Capuozzo, M., Ferrara, F., Santorsola, M., Zovi, A., & Ottaiano, A. (2023). Circulating tumor cells as predictive and prognostic biomarkers in solid tumors. Cells, 12, 2590. https:\/\/doi.org\/10.3390\/cells12222590","journal-title":"Cells"},{"key":"10293_CR64","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1186\/s12935-021-02415-8","volume":"21","author":"X Li","year":"2021","unstructured":"Li, X., Sun, H., Liu, Q., Liu, Y., Hou, Y., & Jin, W. (2021). Conjoint analysis of circulating tumor cells and solid tumors for exploring potential prognostic markers and constructing a robust novel predictive signature for breast cancer. Cancer Cell International, 21, 708. https:\/\/doi.org\/10.1186\/s12935-021-02415-8","journal-title":"Cancer Cell International"},{"key":"10293_CR65","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2012228118","volume":"118","author":"L Yang","year":"2021","unstructured":"Yang, L., Yan, X., Chen, J., Zhan, Q., Hua, Y., Xu, S., Li, Z., Wang, Z., Dong, Y., Zuo, D., Xue, M., Tang, Y., Herschman, H. R., Lu, S., Shi, Q., & Wei, W. (2021). Hexokinase 2 discerns a novel circulating tumor cell population associated with poor prognosis in lung cancer patients. Proceedings of the National Academy of Sciences of the United States of America, 118, Article e2012228118. https:\/\/doi.org\/10.1073\/pnas.2012228118","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10293_CR66","doi-asserted-by":"publisher","first-page":"1482","DOI":"10.1002\/hep4.1900","volume":"6","author":"VL Chen","year":"2022","unstructured":"Chen, V. L., Huang, Q., Harouaka, R., Du, Y., Lok, A. S., Parikh, N. D., Garmire, L. X., & Wicha, M. S. (2022). A dual-filtration system for single-cell sequencing of circulating tumor cells and clusters in HCC. Hepatology Communications, 6, 1482\u20131491. https:\/\/doi.org\/10.1002\/hep4.1900","journal-title":"Hepatology Communications"},{"key":"10293_CR67","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1002\/cyto.a.24816","volume":"105","author":"A Abramova","year":"2023","unstructured":"Abramova, A., Rivandi, M., Yang, L., Stamm, N., Cieslik, J.-P., Honisch, E., Niederacher, D., Fehm, T., Neubauer, H., & Franken, A. (2023). A workflow for the enrichment, the identification, and the isolation of non-apoptotic single circulating tumor cells for RNA sequencing analysis. Cytometry Part A, 105, 242\u2013251. https:\/\/doi.org\/10.1002\/cyto.a.24816","journal-title":"Cytometry Part A"},{"key":"10293_CR68","doi-asserted-by":"publisher","first-page":"1468","DOI":"10.1126\/science.aay0939","volume":"367","author":"RY Ebright","year":"2020","unstructured":"Ebright, R. Y., Lee, S., Wittner, B. S., Niederhoffer, K. L., Nicholson, B. T., Bardia, A., Truesdell, S., Wiley, D. F., Wesley, B., Li, S., Mai, A., Aceto, N., Vincent-Jordan, N., Szabolcs, A., Chirn, B., Kreuzer, J., Comaills, V., Kalinich, M., Haas, W., \u2026 Micalizzi, D. S. (2020). Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis. Science, 367, 1468\u20131473. https:\/\/doi.org\/10.1126\/science.aay0939","journal-title":"Science"},{"key":"10293_CR69","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.ab.2014.10.011","volume":"471","author":"H Matsunaga","year":"2015","unstructured":"Matsunaga, H., Goto, M., Arikawa, K., Shirai, M., Tsunoda, H., Huang, H., & Kambara, H. (2015). A highly sensitive and accurate gene expression analysis by sequencing (\u201cbead-seq\u201d) for a single cell. Analytical Biochemistry, 471, 9\u201316. https:\/\/doi.org\/10.1016\/j.ab.2014.10.011","journal-title":"Analytical Biochemistry"},{"key":"10293_CR70","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-023-01753-7","volume":"22","author":"HD Huh","year":"2023","unstructured":"Huh, H. D., Sub, Y., Oh, J., Kim, Y. E., Lee, J. Y., Kim, H.-R., Lee, S., Lee, H., Pak, S., Amos, S. E., Vahala, D., Park, J. H., Shin, J. E., Park, S. Y., Kim, H. S., Roh, Y. H., Lee, H.-W., Guan, K.-L., Choi, Y. S., \u2026 Park, H. W. (2023). Reprogramming anchorage dependency by adherent-to-suspension transition promotes metastatic dissemination. Molecular Cancer, 22, Article 63. https:\/\/doi.org\/10.1186\/s12943-023-01753-7","journal-title":"Molecular Cancer"},{"key":"10293_CR71","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1186\/s12943-023-01838-3","volume":"22","author":"HD Huh","year":"2023","unstructured":"Huh, H. D., Sub, Y., Oh, J., Kim, Y. E., Lee, J. Y., Kim, H., Lee, S., Lee, H., Pak, S., Amos, S. E., Vahala, D., Park, J. H., Shin, J. E., Park, S. Y., Kim, H. S., Roh, Y. H., Lee, H., Guan, K., Choi, Y. S., \u2026 Park, H. W. (2023). Reprogramming anchorage dependency by adherent-to-suspension transition promotes metastatic dissemination. Molecular Cancer, 22, 135. https:\/\/doi.org\/10.1186\/s12943-023-01838-3","journal-title":"Molecular Cancer"},{"key":"10293_CR72","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.cell.2018.11.046","volume":"176","author":"S Gkountela","year":"2019","unstructured":"Gkountela, S., Castro-Giner, F., Szczerba, B. M., Vetter, M., Landin, J., Scherrer, R., Krol, I., Scheidmann, M. C., Beisel, C., Stirnimann, C. U., Kurzeder, C., Heinzelmann-Schwarz, V., Rochlitz, C., Weber, W. P., & Aceto, N. (2019). Circulating tumor cell clustering shapes DNA methylation to enable metastasis seeding. Cell, 176, 98-112.e14. https:\/\/doi.org\/10.1016\/j.cell.2018.11.046","journal-title":"Cell"},{"key":"10293_CR73","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1158\/1541-7786.MCR-17-0480","volume":"16","author":"N Aceto","year":"2018","unstructured":"Aceto, N., Bardia, A., Wittner, B. S., Donaldson, M. C., O\u2019Keefe, R., Engstrom, A., Bersani, F., Zheng, Y., Comaills, V., Niederhoffer, K., Zhu, H., Mackenzie, O., Shioda, T., Sgroi, D., Kapur, R., Ting, D. T., Moy, B., Ramaswamy, S., Toner, M., \u2026 Maheswaran, S. (2018). AR expression in breast cancer CTCs associates with bone metastases. Molecular Cancer Research, 16, 720\u2013727. https:\/\/doi.org\/10.1158\/1541-7786.MCR-17-0480","journal-title":"Molecular Cancer Research"},{"key":"10293_CR74","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1016\/j.cell.2014.07.013","volume":"158","author":"N Aceto","year":"2014","unstructured":"Aceto, N., Bardia, A., Miyamoto, D. T., Donaldson, M. C., Wittner, B. S., Spencer, J. A., Yu, M., Pely, A., Engstrom, A., Zhu, H., Brannigan, B. W., Kapur, R., Stott, S. L., Shioda, T., Ramaswamy, S., Ting, D. T., Lin, C. P., Toner, M., Haber, D. A., & Maheswaran, S. (2014). Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell, 158, 1110\u20131122. https:\/\/doi.org\/10.1016\/j.cell.2014.07.013","journal-title":"Cell"},{"key":"10293_CR75","doi-asserted-by":"publisher","DOI":"10.1016\/j.xpro.2023.102539","volume":"4","author":"X Liu","year":"2023","unstructured":"Liu, X., Song, J., Liu, X., Zhang, H., Wang, X., Li, Y., Yang, Z., Jing, J., Ma, X., & Shi, H. (2023). Protocol for identifying immune checkpoint on circulating tumor cells of human pancreatic ductal adenocarcinoma by single-cell RNA sequencing. Star Protocols, 4, Article 102539. https:\/\/doi.org\/10.1016\/j.xpro.2023.102539","journal-title":"Star Protocols"},{"key":"10293_CR76","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.1158\/1535-7163.MCT-19-1166","volume":"19","author":"S Dimitrov-Markov","year":"2020","unstructured":"Dimitrov-Markov, S., Perales-Pat\u00f3n, J., Bockorny, B., Dopazo, A., Mu\u00f1oz, M., Ba\u00f1os, N., Bonilla, V., Menendez, C., Duran, Y., Huang, L., Perea, S., Muthuswamy, S. K., Al-Shahrour, F., Lopez-Casas, P. P., & Hidalgo, M. (2020). Discovery of new targets to control metastasis in pancreatic cancer by single-cell transcriptomics analysis of circulating tumor cells. Molecular Cancer Therapeutics, 19, 1751\u20131760. https:\/\/doi.org\/10.1158\/1535-7163.MCT-19-1166","journal-title":"Molecular Cancer Therapeutics"},{"key":"10293_CR77","doi-asserted-by":"publisher","first-page":"3303","DOI":"10.1038\/s41467-020-17150-3","volume":"11","author":"JW Franses","year":"2020","unstructured":"Franses, J. W., Philipp, J., Missios, P., Bhan, I., Liu, A., Yashaswini, C., Tai, E., Zhu, H., Ligorio, M., Nicholson, B., Tassoni, E. M., Desai, N., Kulkarni, A. S., Szabolcs, A., Hong, T. S., Liss, A. S., Fernandez-del Castillo, C., Ryan, D. P., Maheswaran, S., \u2026 Ting, D. T. (2020). Pancreatic circulating tumor cell profiling identifies LIN28B as a metastasis driver and drug target. Nature communications, 11, 3303. https:\/\/doi.org\/10.1038\/s41467-020-17150-3","journal-title":"Nature communications"},{"key":"10293_CR78","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2009.236","volume":"5","author":"F Tang","year":"2010","unstructured":"Tang, F., Barbacioru, C., Nordman, E., Xu, N., Bashkirov, V. I., Lao, K., & Surani, M. A. (2010). RNA-seq analysis to capture the transcriptome landscape of a single cell. Nature Protocols, 5, Article 10.1038\/nprot.2009.236. https:\/\/doi.org\/10.1038\/nprot.2009.236","journal-title":"Nature Protocols"},{"key":"10293_CR79","doi-asserted-by":"publisher","DOI":"10.3390\/cancers12123774","volume":"12","author":"L Zhu","year":"2020","unstructured":"Zhu, L., Kan, K.-J., Gr\u00fcn, J. L., Hissa, B., Yang, C., Gy\u0151rffy, B., Loges, S., Rei\u00dffelder, C., & Sch\u00f6lch, S. (2020). GAS2L1 is a potential biomarker of circulating tumor cells in pancreatic cancer. Cancers, 12, Article E3774. https:\/\/doi.org\/10.3390\/cancers12123774","journal-title":"Cancers"},{"key":"10293_CR80","doi-asserted-by":"publisher","DOI":"10.1038\/s41419-023-05823-y","volume":"14","author":"M Chen","year":"2023","unstructured":"Chen, M., Li, H., Xu, X., Bao, X., Xue, L., Ai, X., Xu, J., Xu, M., Shi, Y., Zhen, T., Li, J., Yang, Y., Ji, Y., Fu, Z., Xing, K., Qing, T., Wang, Q., Zhong, P., & Zhu, S. (2023). Identification of RAC1 in promoting brain metastasis of lung adenocarcinoma using single-cell transcriptome sequencing. Cell Death & Disease, 14, Article 330. https:\/\/doi.org\/10.1038\/s41419-023-05823-y","journal-title":"Cell Death & Disease"},{"key":"10293_CR81","doi-asserted-by":"publisher","DOI":"10.3390\/cancers14143446","volume":"14","author":"SS Vasantharajan","year":"2022","unstructured":"Vasantharajan, S. S., Barnett, E., Gray, E. S., McCall, J. L., Rodger, E. J., Eccles, M. R., Munro, F., Pattison, S., & Chatterjee, A. (2022). Assessment of a size-based method for enriching circulating tumour cells in colorectal cancer. Cancers, 14, Article 3446. https:\/\/doi.org\/10.3390\/cancers14143446","journal-title":"Cancers"},{"key":"10293_CR82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41392-022-00881-8","volume":"7","author":"X Zheng","year":"2022","unstructured":"Zheng, X., Song, J., Yu, C., Zhou, Z., Liu, X., Yu, J., Xu, G., Yang, J., He, X., Bai, X., Luo, Y., Bao, Y., Li, H., Yang, L., Xu, M., Song, N., Su, X., Xu, J., Ma, X., & Shi, H. (2022). Single-cell transcriptomic profiling unravels the adenoma-initiation role of protein tyrosine kinases during colorectal tumorigenesis. Signal Transduction and Targeted Therapy, 7, 1\u201314. https:\/\/doi.org\/10.1038\/s41392-022-00881-8","journal-title":"Signal Transduction and Targeted Therapy"},{"key":"10293_CR83","doi-asserted-by":"publisher","DOI":"10.3390\/cancers14194921","volume":"14","author":"R Fankhauser","year":"2022","unstructured":"Fankhauser, R., Chang, M., Garrison, Z., Berryman, R., Lucero, O. M., Fuiten, A., DePatie, N., Seifert, H., & Kulkarni, R. P. (2022). Single-cell identification of melanoma biomarkers in circulating tumor cells. Cancers, 14, Article 4921. https:\/\/doi.org\/10.3390\/cancers14194921","journal-title":"Cancers"},{"key":"10293_CR84","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1016\/j.cell.2018.10.038","volume":"175","author":"M Sade-Feldman","year":"2018","unstructured":"Sade-Feldman, M., Yizhak, K., Bjorgaard, S. L., Ray, J. P., de Boer, C. G., Jenkins, R. W., Lieb, D. J., Chen, J. H., Frederick, D. T., Barzily-Rokni, M., Freeman, S. S., Reuben, A., Hoover, P. J., Villani, A.-C., Ivanova, E., Portell, A., Lizotte, P. H., Aref, A. R., Eliane, J.-P., \u2026 Hacohen, N. (2018). Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell, 175, 998-1013.e20. https:\/\/doi.org\/10.1016\/j.cell.2018.10.038","journal-title":"Cell"},{"key":"10293_CR85","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1038\/s41551-023-01023-3","volume":"7","author":"Z Wang","year":"2023","unstructured":"Wang, Z., Ahmed, S., Labib, M., Wang, H., Wu, L., Bavaghar-Zaeimi, F., Shokri, N., Blanco, S., Karim, S., Czarnecka-Kujawa, K., Sargent, E. H., McGray, A. J. R., de Perrot, M., & Kelley, S. O. (2023). Isolation of tumour-reactive lymphocytes from peripheral blood via microfluidic immunomagnetic cell sorting. Nature Biomedical Engineering, 7, 1188\u20131203. https:\/\/doi.org\/10.1038\/s41551-023-01023-3","journal-title":"Nature Biomedical Engineering"},{"key":"10293_CR86","doi-asserted-by":"publisher","first-page":"5553","DOI":"10.1038\/s41388-020-1379-0","volume":"39","author":"D Green","year":"2020","unstructured":"Green, D., Eyre, H., Singh, A., Taylor, J. T., Chu, J., Jeys, L., Sumathi, V., Coonar, A., Rassl, D., Babur, M., Forster, D., Alzabin, S., Ponthan, F., McMahon, A., Bigger, B., Reekie, T., Kassiou, M., Williams, K., Dalmay, T., \u2026 Finegan, K. G. (2020). Targeting the MAPK7\/MMP9 axis for metastasis in primary bone cancer. Oncogene, 39, 5553\u20135569. https:\/\/doi.org\/10.1038\/s41388-020-1379-0","journal-title":"Oncogene"},{"key":"10293_CR87","doi-asserted-by":"publisher","unstructured":"Hayes, D. F., Smerage, J. B. (2010). Circulating tumor cells, in: Progress in molecular biology and translational science, Elsevier pp. 95\u2013112. https:\/\/doi.org\/10.1016\/B978-0-12-385071-3.00005-8.","DOI":"10.1016\/B978-0-12-385071-3.00005-8"},{"key":"10293_CR88","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1177\/1758834010378414","volume":"2","author":"MG Krebs","year":"2010","unstructured":"Krebs, M. G., Hou, J.-M., Ward, T. H., Blackhall, F. H., & Dive, C. (2010). Circulating tumour cells: Their utility in cancer management and predicting outcomes. Therapeutic Advances in Medical Oncology, 2, 351\u2013365. https:\/\/doi.org\/10.1177\/1758834010378414","journal-title":"Therapeutic Advances in Medical Oncology"},{"key":"10293_CR89","doi-asserted-by":"publisher","DOI":"10.1155\/2010\/617421","author":"MC Miller","year":"2010","unstructured":"Miller, M. C., Doyle, G. V., & Terstappen, L. W. M. M. (2010). Significance of circulating tumor cells detected by the CellSearch system in patients with metastatic breast colorectal and prostate cancer. Journal Of Oncology. https:\/\/doi.org\/10.1155\/2010\/617421","journal-title":"Journal Of Oncology"},{"key":"10293_CR90","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1016\/j.molonc.2015.12.002","volume":"10","author":"KC Andree","year":"2016","unstructured":"Andree, K. C., van Dalum, G., & Terstappen, L. W. M. M. (2016). Challenges in circulating tumor cell detection by the Cell Search System. Molecular Oncology, 10, 395\u2013407. https:\/\/doi.org\/10.1016\/j.molonc.2015.12.002","journal-title":"Molecular Oncology"},{"key":"10293_CR91","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.11191","volume":"7","author":"EE van der Toom","year":"2016","unstructured":"van der Toom, E. E., Verdone, J. E., Gorin, M. A., & Pienta, K. J. (2016). Technical challenges in the isolation and analysis of circulating tumor cells. Oncotarget, 7, Article 62754\u201362766. https:\/\/doi.org\/10.18632\/oncotarget.11191","journal-title":"Oncotarget"},{"key":"10293_CR92","doi-asserted-by":"publisher","first-page":"335","DOI":"10.20892\/j.issn.2095-3941.2018.0256","volume":"15","author":"D Zou","year":"2018","unstructured":"Zou, D., & Cui, D. (2018). Advances in isolation and detection of circulating tumor cells based on microfluidics. Cancer Biology & Medicine, 15, 335\u2013353. https:\/\/doi.org\/10.20892\/j.issn.2095-3941.2018.0256","journal-title":"Cancer Biology & Medicine"},{"key":"10293_CR93","first-page":"146","volume":"14","author":"TR Ashworth","year":"1869","unstructured":"Ashworth, T. R. (1869). A case of cancer in which cells similar to those in the tumors were seen in the blood after death. Australasian Medical Journal, 14, 146\u2013149.","journal-title":"Australasian Medical Journal"},{"key":"10293_CR94","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1038\/s41467-017-01705-y","volume":"8","author":"KHK Wong","year":"2017","unstructured":"Wong, K. H. K., Tessier, S. N., Miyamoto, D. T., Miller, K. L., Bookstaver, L. D., Carey, T. R., Stannard, C. J., Thapar, V., Tai, E. C., Vo, K. D., Emmons, E. S., Pleskow, H. M., Sandlin, R. D., Sequist, L. V., Ting, D. T., Haber, D. A., Maheswaran, S., Stott, S. L., & Toner, M. (2017). Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells. Nature Communications, 8, 1733. https:\/\/doi.org\/10.1038\/s41467-017-01705-y","journal-title":"Nature Communications"},{"key":"10293_CR95","doi-asserted-by":"publisher","unstructured":"Miller, M., Robinson, P., Wagner, C., O\u2019Shannessy, D. (2018). The ParsortixTM cell separation system\u2014A versatile liquid biopsy platform, Cytometry Part A 93. https:\/\/doi.org\/10.1002\/cyto.a.23571.","DOI":"10.1002\/cyto.a.23571"},{"key":"10293_CR96","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics11112136","volume":"11","author":"FYF Tieng","year":"2021","unstructured":"Tieng, F. Y. F., Abu, N., Nasir, S. N., Lee, L.-H., & Ab Mutalib, N.-S. (2021). Liquid biopsy-based colorectal cancer screening via surface markers of circulating tumor cells. Diagnostics, 11, Article 2136. https:\/\/doi.org\/10.3390\/diagnostics11112136","journal-title":"Diagnostics"},{"key":"10293_CR97","doi-asserted-by":"publisher","first-page":"R31","DOI":"10.1186\/gb-2013-14-4-r31","volume":"14","author":"Y Sasagawa","year":"2013","unstructured":"Sasagawa, Y., Nikaido, I., Hayashi, T., Danno, H., Uno, K. D., Imai, T., & Ueda, H. R. (2013). Quartz-Seq: A highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biology, 14, R31. https:\/\/doi.org\/10.1186\/gb-2013-14-4-r31","journal-title":"Genome Biology"},{"key":"10293_CR98","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/s13059-018-1407-3","volume":"19","author":"Y Sasagawa","year":"2018","unstructured":"Sasagawa, Y., Danno, H., Takada, H., Ebisawa, M., Tanaka, K., Hayashi, T., Kurisaki, A., & Nikaido, I. (2018). Quartz-seq2: A high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads. Genome Biology, 19, 29. https:\/\/doi.org\/10.1186\/s13059-018-1407-3","journal-title":"Genome Biology"},{"key":"10293_CR99","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1038\/s41587-020-0497-0","volume":"38","author":"M Hagemann-Jensen","year":"2020","unstructured":"Hagemann-Jensen, M., Ziegenhain, C., Chen, P., Ramsk\u00f6ld, D., Hendriks, G.-J., Larsson, A. J. M., Faridani, O. R., & Sandberg, R. (2020). Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nature Biotechnology, 38, 708\u2013714. https:\/\/doi.org\/10.1038\/s41587-020-0497-0","journal-title":"Nature Biotechnology"},{"key":"10293_CR100","doi-asserted-by":"crossref","unstructured":"Bageritz, J., & Raddi, G. (2019). Single-cell RNA sequencing with Drop-Seq. In V. Proserpio (Ed.),","DOI":"10.1007\/978-1-4939-9240-9_6"},{"key":"10293_CR101","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","volume":"161","author":"EZ Macosko","year":"2015","unstructured":"Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., Trombetta, J. J., Weitz, D. A., Sanes, J. R., Shalek, A. K., Regev, A., & McCarroll, S. A. (2015). Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 161, 1202\u20131214. https:\/\/doi.org\/10.1016\/j.cell.2015.05.002","journal-title":"Cell"},{"key":"10293_CR102","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1016\/j.molcel.2017.01.023","volume":"65","author":"C Ziegenhain","year":"2017","unstructured":"Ziegenhain, C., Vieth, B., Parekh, S., Reinius, B., Guillaumet-Adkins, A., Smets, M., Leonhardt, H., Heyn, H., Hellmann, I., & Enard, W. (2017). Comparative analysis of single-cell RNA sequencing methods. Molecular Cell, 65, 631-643.e4. https:\/\/doi.org\/10.1016\/j.molcel.2017.01.023","journal-title":"Molecular Cell"},{"key":"10293_CR103","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-07874-1","volume":"12","author":"O Shomroni","year":"2022","unstructured":"Shomroni, O., Sitte, M., Schmidt, J., Parbin, S., Ludewig, F., Yigit, G., Zelarayan, L. C., Streckfuss-B\u00f6meke, K., Wollnik, B., & Salinas, G. (2022). A novel single-cell RNA-sequencing approach and its applicability connecting genotype to phenotype in ageing disease. Scientific Reports, 12, Article 4091. https:\/\/doi.org\/10.1038\/s41598-022-07874-1","journal-title":"Scientific Reports"},{"key":"10293_CR104","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1007\/978-981-13-6037-4_5","volume":"1129","author":"EY Shum","year":"2019","unstructured":"Shum, E. Y., Walczak, E. M., Chang, C., & Christina Fan, H. (2019). Quantitation of mRNA transcripts and proteins using the BD RhapsodyTM single-cell analysis system. Advances in Experimental Medicine and Biology, 1129, 63\u201379. https:\/\/doi.org\/10.1007\/978-981-13-6037-4_5","journal-title":"Advances in Experimental Medicine and Biology"},{"key":"10293_CR105","doi-asserted-by":"publisher","first-page":"70","DOI":"10.3389\/fbioe.2016.00070","volume":"4","author":"N Ramalingam","year":"2016","unstructured":"Ramalingam, N., Fowler, B., Szpankowski, L., Leyrat, A. A., Hukari, K., Maung, M. T., Yorza, W., Norris, M., Cesar, C., Shuga, J., Gonzales, M. L., Sanada, C. D., Wang, X., Yeung, R., Hwang, W., Axsom, J., Devaraju, N. S. G. K., Angeles, N. D., Greene, C., \u2026 West, J. A. A. (2016). Fluidic logic used in a systems approach to enable integrated single-cell functional analysis. Front Bioeng Biotechnol, 4, 70. https:\/\/doi.org\/10.3389\/fbioe.2016.00070","journal-title":"Front Bioeng Biotechnol"},{"key":"10293_CR106","unstructured":"LaMar, D. (2015). FastQC, https:\/\/qubeshub.org\/resources\/fastqc."},{"key":"10293_CR107","unstructured":"Krueger, F. (2015). Trim Galore!: A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data, Babraham Institute. https:\/\/cir.nii.ac.jp\/crid\/1370294643762929691 (Accessed March 30, 2025)."},{"key":"10293_CR108","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114\u20132120. https:\/\/doi.org\/10.1093\/bioinformatics\/btu170","journal-title":"Bioinformatics"},{"key":"10293_CR109","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.15931.2","volume":"7","author":"SW Wingett","year":"2018","unstructured":"Wingett, S. W., & Andrews, S. (2018). FastQ screen: A tool for multi-genome mapping and quality control. F1000Research, 7, Article 1338. https:\/\/doi.org\/10.12688\/f1000research.15931.2","journal-title":"F1000Research"},{"key":"10293_CR110","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15\u201321. https:\/\/doi.org\/10.1093\/bioinformatics\/bts635","journal-title":"Bioinformatics"},{"key":"10293_CR111","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods, 14, 417\u2013419. https:\/\/doi.org\/10.1038\/nmeth.4197","journal-title":"Nature Methods"},{"issue":"3","key":"10293_CR112","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nbt.3519","volume":"34","author":"NL Bray","year":"2016","unstructured":"Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34(3), 525\u2013527. https:\/\/doi.org\/10.1038\/nbt.3519","journal-title":"Nature Biotechnology"},{"key":"10293_CR113","doi-asserted-by":"publisher","first-page":"2943","DOI":"10.1093\/bioinformatics\/btac166","volume":"38","author":"GH Putri","year":"2022","unstructured":"Putri, G. H., Anders, S., Pyl, P. T., Pimanda, J. E., & Zanini, F. (2022). Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, 38, 2943\u20132945. https:\/\/doi.org\/10.1093\/bioinformatics\/btac166","journal-title":"Bioinformatics"},{"key":"10293_CR114","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K., & Shi, W. (2014). FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923\u2013930. https:\/\/doi.org\/10.1093\/bioinformatics\/btt656","journal-title":"Bioinformatics"},{"key":"10293_CR115","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","volume":"8","author":"SL Wolock","year":"2019","unstructured":"Wolock, S. L., Lopez, R., & Klein, A. M. (2019). Scrublet: Computational identification of cell doublets in single-cell transcriptomic data. Cell Systems, 8, 281-291.e9. https:\/\/doi.org\/10.1016\/j.cels.2018.11.005","journal-title":"Cell Systems"},{"key":"10293_CR116","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","volume":"8","author":"CS McGinnis","year":"2019","unstructured":"McGinnis, C. S., Murrow, L. M., & Gartner, Z. J. (2019). DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Systems, 8, 329-337.e4. https:\/\/doi.org\/10.1016\/j.cels.2019.03.003","journal-title":"Cell Systems"},{"key":"10293_CR117","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02584-9","volume":"23","author":"S Choudhary","year":"2022","unstructured":"Choudhary, S., & Satija, R. (2022). Comparison and evaluation of statistical error models for scRNA-seq. Genome Biology, 23, Article 27. https:\/\/doi.org\/10.1186\/s13059-021-02584-9","journal-title":"Genome Biology"},{"key":"10293_CR118","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","volume":"20","author":"C Hafemeister","year":"2019","unstructured":"Hafemeister, C., & Satija, R. (2019). Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biology, 20, 296. https:\/\/doi.org\/10.1186\/s13059-019-1874-1","journal-title":"Genome Biology"},{"key":"10293_CR119","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1038\/nbt.4091","volume":"36","author":"L Haghverdi","year":"2018","unstructured":"Haghverdi, L., Lun, A. T. L., Morgan, M. D., & Marioni, J. C. (2018). Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nature Biotechnology, 36, 421\u2013427. https:\/\/doi.org\/10.1038\/nbt.4091","journal-title":"Nature Biotechnology"},{"key":"10293_CR120","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41587-019-0113-3","volume":"37","author":"B Hie","year":"2019","unstructured":"Hie, B., Bryson, B., & Berger, B. (2019). Efficient integration of heterogeneous single-cell transcriptomes using Scanorama. Nature Biotechnology, 37, 685\u2013691. https:\/\/doi.org\/10.1038\/s41587-019-0113-3","journal-title":"Nature Biotechnology"},{"key":"10293_CR121","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/nbt.3102","volume":"33","author":"F Buettner","year":"2015","unstructured":"Buettner, F., Natarajan, K. N., Casale, F. P., Proserpio, V., Scialdone, A., Theis, F. J., Teichmann, S. A., Marioni, J. C., & Stegle, O. (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature Biotechnology, 33, 155\u2013160. https:\/\/doi.org\/10.1038\/nbt.3102","journal-title":"Nature Biotechnology"},{"key":"10293_CR122","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1038\/s41467-018-03405-7","volume":"9","author":"WV Li","year":"2018","unstructured":"Li, W. V., & Li, J. J. (2018). An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nature Communications, 9, 997. https:\/\/doi.org\/10.1038\/s41467-018-03405-7","journal-title":"Nature Communications"},{"key":"10293_CR123","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/0098-3004(93)90090-R","volume":"19","author":"A Ma\u0107kiewicz","year":"1993","unstructured":"Ma\u0107kiewicz, A., & Ratajczak, W. (1993). Principal components analysis (PCA). Computers & Geosciences, 19, 303\u2013342. https:\/\/doi.org\/10.1016\/0098-3004(93)90090-R","journal-title":"Computers & Geosciences"},{"key":"10293_CR124","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s43586-024-00363-x","volume":"4","author":"J Healy","year":"2024","unstructured":"Healy, J., & McInnes, L. (2024). Uniform manifold approximation and projection. Nature Reviews Methods Primers, 4, 1\u201315. https:\/\/doi.org\/10.1038\/s43586-024-00363-x","journal-title":"Nature Reviews Methods Primers"},{"key":"10293_CR125","doi-asserted-by":"publisher","unstructured":"McInnes, L., Healy, J., Melville, J. (2020). UMAP: Uniform manifold approximation and projection for dimension reduction. https:\/\/doi.org\/10.48550\/arXiv.1802.03426.","DOI":"10.48550\/arXiv.1802.03426"},{"key":"10293_CR126","doi-asserted-by":"publisher","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","volume":"2008","author":"VD Blondel","year":"2008","unstructured":"Blondel, V. D., Guillaume, J.-L., Lambiotte, R., & Lefebvre, E. (2008). Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment, 2008, Article P10008. https:\/\/doi.org\/10.1088\/1742-5468\/2008\/10\/P10008","journal-title":"Journal of Statistical Mechanics: Theory and Experiment"},{"key":"10293_CR127","doi-asserted-by":"publisher","first-page":"2212","DOI":"10.1093\/bioinformatics\/btaa956","volume":"37","author":"M Tang","year":"2021","unstructured":"Tang, M., Kaymaz, Y., Logeman, B. L., Eichhorn, S., Liang, Z. S., Dulac, C., & Sackton, T. B. (2021). Evaluating single-cell cluster stability using the Jaccard similarity index. Bioinformatics, 37, 2212\u20132214. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa956","journal-title":"Bioinformatics"},{"key":"10293_CR128","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/nbt.2859","volume":"32","author":"C Trapnell","year":"2014","unstructured":"Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014). The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology, 32, 381\u2013386. https:\/\/doi.org\/10.1038\/nbt.2859","journal-title":"Nature Biotechnology"},{"key":"10293_CR129","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","volume":"20","author":"D Aran","year":"2019","unstructured":"Aran, D., Looney, A. P., Liu, L., Wu, E., Fong, V., Hsu, A., Chak, S., Naikawadi, R. P., Wolters, P. J., Abate, A. R., Butte, A. J., & Bhattacharya, M. (2019). Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nature Immunology, 20, 163\u2013172. https:\/\/doi.org\/10.1038\/s41590-018-0276-y","journal-title":"Nature Immunology"},{"key":"10293_CR130","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1038\/ng.3818","volume":"49","author":"H Li","year":"2017","unstructured":"Li, H., Courtois, E. T., Sengupta, D., Tan, Y., Chen, K. H., Goh, J. J. L., Kong, S. L., Chua, C., Hon, L. K., Tan, W. S., Wong, M., Choi, P. J., Wee, L. J. K., Hillmer, A. M., Tan, I. B., Robson, P., & Prabhakar, S. (2017). Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nature Genetics, 49, 708\u2013718. https:\/\/doi.org\/10.1038\/ng.3818","journal-title":"Nature Genetics"},{"key":"10293_CR131","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.9501.2","volume":"5","author":"ATL Lun","year":"2016","unstructured":"Lun, A. T. L., McCarthy, D. J., & Marioni, J. C. (2016). A step-by-step workflow for low-level analysis of single-cell RNA-seq data with bioconductor. F1000research, 5, Article 2122. https:\/\/doi.org\/10.12688\/f1000research.9501.2","journal-title":"F1000research"},{"key":"10293_CR132","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"ME Ritchie","year":"2015","unstructured":"Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015). Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43, Article e47. https:\/\/doi.org\/10.1093\/nar\/gkv007","journal-title":"Nucleic Acids Research"},{"key":"10293_CR133","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012). ClusterProfiler: An R package for comparing biological themes among gene clusters. Omics\u202f: A Journal of Integrative Biology, 16, 284\u2013287. https:\/\/doi.org\/10.1089\/omi.2011.0118","journal-title":"Omics : A Journal of Integrative Biology"},{"key":"10293_CR134","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li, B., & Dewey, C. N. (2011). Rsem: Accurate transcript quantification from rna-seq data with or without a reference genome. Bmc Bioinformatics, 12, 323. https:\/\/doi.org\/10.1186\/1471-2105-12-323","journal-title":"Bmc Bioinformatics"},{"key":"10293_CR135","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-14-7","volume":"14","author":"S H\u00e4nzelmann","year":"2013","unstructured":"H\u00e4nzelmann, S., Castelo, R., & Guinney, J. (2013). GSVA: Gene set variation analysis for microarray and RNA-Seq data. Bmc Bioinformatics, 14, 7. https:\/\/doi.org\/10.1186\/1471-2105-14-7","journal-title":"Bmc Bioinformatics"},{"key":"10293_CR136","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1039\/c5mb00663e","volume":"12","author":"G Yu","year":"2016","unstructured":"Yu, G., & He, Q.-Y. (2016). ReactomePA: An R\/Bioconductor package for reactome pathway analysis and visualization. Molecular Biosystems, 12, 477\u2013479. https:\/\/doi.org\/10.1039\/c5mb00663e","journal-title":"Molecular Biosystems"},{"key":"10293_CR137","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","volume":"15","author":"M Efremova","year":"2020","unstructured":"Efremova, M., Vento-Tormo, M., Teichmann, S. A., & Vento-Tormo, R. (2020). Cell PhoneDB: Inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes. Nature Protocols, 15, 1484\u20131506. https:\/\/doi.org\/10.1038\/s41596-020-0292-x","journal-title":"Nature Protocols"},{"key":"10293_CR138","doi-asserted-by":"publisher","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","volume":"111","author":"S Shen","year":"2014","unstructured":"Shen, S., Park, J. W., Lu, Z., Lin, L., Henry, M. D., Wu, Y. N., Zhou, Q., & Xing, Y. (2014). rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proceedings of the National Academy of Sciences, 111, E5593\u2013E5601. https:\/\/doi.org\/10.1073\/pnas.1419161111","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"10293_CR139","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.molcel.2017.06.003","volume":"67","author":"Y Song","year":"2017","unstructured":"Song, Y., Botvinnik, O. B., Lovci, M. T., Kakaradov, B., Liu, P., Xu, J. L., & Yeo, G. W. (2017). Single-cell alternative splicing analysis with expedition reveals splicing dynamics during neuron differentiation. Molecular Cell, 67, 148-161.e5. https:\/\/doi.org\/10.1016\/j.molcel.2017.06.003","journal-title":"Molecular Cell"},{"key":"10293_CR140","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","volume":"566","author":"J Cao","year":"2019","unstructured":"Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., Trapnell, C., & Shendure, J. (2019). The single-cell transcriptional landscape of mammalian organogenesis. Nature, 566, 496\u2013502. https:\/\/doi.org\/10.1038\/s41586-019-0969-x","journal-title":"Nature"},{"key":"10293_CR141","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nbt.3192","volume":"33","author":"R Satija","year":"2015","unstructured":"Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nature Biotechnology, 33, 495\u2013502. https:\/\/doi.org\/10.1038\/nbt.3192","journal-title":"Nature Biotechnology"},{"key":"10293_CR142","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1186\/s13059-015-0844-5","volume":"16","author":"G Finak","year":"2015","unstructured":"Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., Slichter, C. K., Miller, H. W., McElrath, M. J., Prlic, M., Linsley, P. S., & Gottardo, R. (2015). MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biology, 16, 278. https:\/\/doi.org\/10.1186\/s13059-015-0844-5","journal-title":"Genome Biology"},{"key":"10293_CR143","doi-asserted-by":"publisher","first-page":"2953","DOI":"10.1016\/j.csbj.2020.10.007","volume":"18","author":"Y Zhang","year":"2020","unstructured":"Zhang, Y., Ma, Y., Huang, Y., Zhang, Y., Jiang, Q., Zhou, M., & Su, J. (2020). Benchmarking algorithms for pathway activity transformation of single-cell RNA-seq data. Computational and Structural Biotechnology Journal, 18, 2953\u20132961. https:\/\/doi.org\/10.1016\/j.csbj.2020.10.007","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"10293_CR144","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s12859-021-04528-3","volume":"23","author":"H Feng","year":"2022","unstructured":"Feng, H., Lin, L., & Chen, J. (2022). ScDIOR: Single cell RNA-seq data IO software. BMC Bioinformatics, 23, 16. https:\/\/doi.org\/10.1186\/s12859-021-04528-3","journal-title":"BMC Bioinformatics"},{"key":"10293_CR145","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","volume":"28","author":"L Wang","year":"2012","unstructured":"Wang, L., Wang, S., & Li, W. (2012). RSeQC: Quality control of RNA-seq experiments. Bioinformatics, 28, 2184\u20132185. https:\/\/doi.org\/10.1093\/bioinformatics\/bts356","journal-title":"Bioinformatics"},{"key":"10293_CR146","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1093\/bioinformatics\/btw777","volume":"33","author":"DJ McCarthy","year":"2017","unstructured":"McCarthy, D. J., Campbell, K. R., Lun, A. T. L., & Wills, Q. F. (2017). Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics, 33, 1179\u20131186. https:\/\/doi.org\/10.1093\/bioinformatics\/btw777","journal-title":"Bioinformatics"},{"key":"10293_CR147","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/gix120","volume":"7","author":"Y Chen","year":"2018","unstructured":"Chen, Y., Chen, Y., Shi, C., Huang, Z., Zhang, Y., Li, S., Li, Y., Ye, J., Yu, C., Li, Z., Zhang, X., Wang, J., Yang, H., Fang, L., & Chen, Q. (2018). SOAPnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience, 7, Article gix120. https:\/\/doi.org\/10.1093\/gigascience\/gix120","journal-title":"Gigascience"},{"key":"10293_CR148","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. Gigascience, 10, Article giab008. https:\/\/doi.org\/10.1093\/gigascience\/giab008","journal-title":"Gigascience"},{"key":"10293_CR149","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels, P., Magnusson, M., Lundin, S., & K\u00e4ller, M. (2016). MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32, 3047\u20133048. https:\/\/doi.org\/10.1093\/bioinformatics\/btw354","journal-title":"Bioinformatics"},{"key":"10293_CR150","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1101\/gr.209601.116","volume":"27","author":"T Smith","year":"2017","unstructured":"Smith, T., Heger, A., & Sudbery, I. (2017). UMI-tools: Modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Research, 27, 491\u2013499. https:\/\/doi.org\/10.1101\/gr.209601.116","journal-title":"Genome Research"},{"key":"10293_CR151","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giy059","volume":"7","author":"S Parekh","year":"2018","unstructured":"Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018). zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs. Gigascience, 7, Article giy059. https:\/\/doi.org\/10.1093\/gigascience\/giy059","journal-title":"Gigascience"},{"key":"10293_CR152","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1186\/s12859-019-2797-2","volume":"20","author":"Z Wang","year":"2019","unstructured":"Wang, Z., Hu, J., Johnson, W. E., & Campbell, J. D. (2019). Scruff: An R\/Bioconductor package for preprocessing single-cell RNA-sequencing data. Bmc Bioinformatics, 20, 222. https:\/\/doi.org\/10.1186\/s12859-019-2797-2","journal-title":"Bmc Bioinformatics"},{"key":"10293_CR153","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","volume":"14","author":"D Kim","year":"2013","unstructured":"Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013). Tophat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14, R36. https:\/\/doi.org\/10.1186\/gb-2013-14-4-r36","journal-title":"Genome Biology"},{"key":"10293_CR154","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","volume":"25","author":"C Trapnell","year":"2009","unstructured":"Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat. Bioinformatics, 25, 1105\u20131111. https:\/\/doi.org\/10.1093\/bioinformatics\/btp120","journal-title":"Bioinformatics"},{"key":"10293_CR155","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25. https:\/\/doi.org\/10.1186\/gb-2009-10-3-r25","journal-title":"Genome Biology"},{"key":"10293_CR156","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357\u2013359. https:\/\/doi.org\/10.1038\/nmeth.1923","journal-title":"Nature Methods"},{"key":"10293_CR157","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37, 907\u2013915. https:\/\/doi.org\/10.1038\/s41587-019-0201-4","journal-title":"Nature Biotechnology"},{"key":"10293_CR158","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx828","volume":"45","author":"SH Yip","year":"2017","unstructured":"Yip, S. H., Wang, P., Kocher, J.-P.A., Sham, P. C., & Wang, J. (2017). Linnorm: Improved statistical analysis for single cell RNA-seq expression data. Nucleic Acids Research, 45, Article e179. https:\/\/doi.org\/10.1093\/nar\/gkx828","journal-title":"Nucleic Acids Research"},{"key":"10293_CR159","first-page":"2579","volume":"9","author":"L van der Maaten","year":"2008","unstructured":"van der Maaten, L., & Hinton, G. (2008). Viualizing data using t-SNE. Journal of Machine Learning Research, 9, 2579\u20132605.","journal-title":"Journal of Machine Learning Research"},{"key":"10293_CR160","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1038\/s41467-017-02554-5","volume":"9","author":"D Risso","year":"2018","unstructured":"Risso, D., Perraudeau, F., Gribkova, S., Dudoit, S., & Vert, J.-P. (2018). A general and flexible method for signal extraction from single-cell RNA-seq data. Nature Communications, 9, 284. https:\/\/doi.org\/10.1038\/s41467-017-02554-5","journal-title":"Nature Communications"},{"key":"10293_CR161","doi-asserted-by":"publisher","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","volume":"9","author":"VA Traag","year":"2019","unstructured":"Traag, V. A., Waltman, L., & van Eck, N. J. (2019). From Louvain to Leiden: Guaranteeing well-connected communities. Scientific Reports, 9, 5233. https:\/\/doi.org\/10.1038\/s41598-019-41695-z","journal-title":"Scientific Reports"},{"key":"10293_CR162","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1038\/nmeth.4236","volume":"14","author":"VY Kiselev","year":"2017","unstructured":"Kiselev, V. Y., Kirschner, K., Schaub, M. T., Andrews, T., Yiu, A., Chandra, T., Natarajan, K. N., Reik, W., Barahona, M., Green, A. R., & Hemberg, M. (2017). SC3: Consensus clustering of single-cell RNA-seq data. Nature Methods, 14, 483\u2013486. https:\/\/doi.org\/10.1038\/nmeth.4236","journal-title":"Nature Methods"},{"key":"10293_CR163","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1038\/s41592-020-0820-1","volume":"17","author":"H Heaton","year":"2020","unstructured":"Heaton, H., Talman, A. M., Knights, A., Imaz, M., Gaffney, D. J., Durbin, R., Hemberg, M., & Lawniczak, M. K. N. (2020). Souporcell: Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Nature Methods, 17, 615\u2013620. https:\/\/doi.org\/10.1038\/s41592-020-0820-1","journal-title":"Nature Methods"},{"key":"10293_CR164","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1038\/s41587-021-00859-x","volume":"39","author":"Y Liu","year":"2021","unstructured":"Liu, Y., Wang, T., Zhou, B., & Zheng, D. (2021). Robust integration of multiple single-cell RNA sequencing datasets using a single reference space. Nature Biotechnology, 39, 877\u2013884. https:\/\/doi.org\/10.1038\/s41587-021-00859-x","journal-title":"Nature Biotechnology"},{"key":"10293_CR165","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I., Millard, N., Fan, J., Slowikowski, K., Zhang, F., Wei, K., Baglaenko, Y., Brenner, M., Loh, P.-R., & Raychaudhuri, S. (2019). Fast, sensitive and accurate integration of single-cell data with harmony. Nature Methods, 16, 1289\u20131296. https:\/\/doi.org\/10.1038\/s41592-019-0619-0","journal-title":"Nature Methods"},{"key":"10293_CR166","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1038\/s41592-019-0535-3","volume":"16","author":"HA Pliner","year":"2019","unstructured":"Pliner, H. A., Shendure, J., & Trapnell, C. (2019). Supervised classification enables rapid annotation of cell atlases. Nature Methods, 16, 983\u2013986. https:\/\/doi.org\/10.1038\/s41592-019-0535-3","journal-title":"Nature Methods"},{"key":"10293_CR167","doi-asserted-by":"publisher","first-page":"1818","DOI":"10.1038\/s41467-020-15523-2","volume":"11","author":"C Li","year":"2020","unstructured":"Li, C., Liu, B., Kang, B., Liu, Z., Liu, Y., Chen, C., Ren, X., & Zhang, Z. (2020). SciBet as a portable and fast single cell type identifier. Nature Communications, 11, 1818. https:\/\/doi.org\/10.1038\/s41467-020-15523-2","journal-title":"Nature Communications"},{"key":"10293_CR168","doi-asserted-by":"publisher","first-page":"gkaf018","DOI":"10.1093\/nar\/gkaf018","volume":"53","author":"Y Chen","year":"2025","unstructured":"Chen, Y., Chen, L., Lun, A. T. L., Baldoni, P. L., & Smyth, G. K. (2025). edgeR v4: Powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Research, 53, gkaf018. https:\/\/doi.org\/10.1093\/nar\/gkaf018","journal-title":"Nucleic Acids Research"},{"key":"10293_CR169","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1093\/nar\/gkw377","volume":"44","author":"MV Kuleshov","year":"2016","unstructured":"Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., McDermott, M. G., Monteiro, C. D., Gundersen, G. W., & Ma\u2019ayan, A. (2016). Enrichr: A comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research, 44, 90\u201397. https:\/\/doi.org\/10.1093\/nar\/gkw377","journal-title":"Nucleic Acids Research"},{"key":"10293_CR170","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. https:\/\/doi.org\/10.1186\/s13059-014-0550-8","journal-title":"Genome Biology"},{"key":"10293_CR171","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1186\/1471-2105-9-559","volume":"9","author":"P Langfelder","year":"2008","unstructured":"Langfelder, P., & Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559. https:\/\/doi.org\/10.1186\/1471-2105-9-559","journal-title":"BMC Bioinformatics"},{"key":"10293_CR172","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1038\/nmeth.3734","volume":"13","author":"J Fan","year":"2016","unstructured":"Fan, J., Salathia, N., Liu, R., Kaeser, G. E., Yung, Y. C., Herman, J. L., Kaper, F., Fan, J.-B., Zhang, K., Chun, J., & Kharchenko, P. V. (2016). Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nature Methods, 13, 241\u2013244. https:\/\/doi.org\/10.1038\/nmeth.3734","journal-title":"Nature Methods"},{"key":"10293_CR173","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1038\/nmeth.2967","volume":"11","author":"PV Kharchenko","year":"2014","unstructured":"Kharchenko, P. V., Silberstein, L., & Scadden, D. T. (2014). Bayesian approach to single-cell differential expression analysis. Nature Methods, 11, 740\u2013742. https:\/\/doi.org\/10.1038\/nmeth.2967","journal-title":"Nature Methods"},{"key":"10293_CR174","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","volume":"10","author":"Y Zhou","year":"2019","unstructured":"Zhou, Y., Zhou, B., Pache, L., Chang, M., Khodabakhshi, A. H., Tanaseichuk, O., Benner, C., & Chanda, S. K. (2019). Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nature Communications, 10, 1523. https:\/\/doi.org\/10.1038\/s41467-019-09234-6","journal-title":"Nature Communications"},{"key":"10293_CR175","doi-asserted-by":"publisher","unstructured":"Korotkevich, G., Sukhov, V., Budin, N., Shpak, B., Artyomov, M. (2016) A. Sergushichev, Fast gene set enrichment analysi. https:\/\/doi.org\/10.1101\/060012.","DOI":"10.1101\/060012"},{"key":"10293_CR176","doi-asserted-by":"publisher","first-page":"W741","DOI":"10.1093\/nar\/gki475","volume":"33","author":"B Zhang","year":"2005","unstructured":"Zhang, B., Kirov, S., & Snoddy, J. (2005). WebGestalt: An integrated system for exploring gene sets in various biological contexts. Nucleic Acids Research, 33, W741-748. https:\/\/doi.org\/10.1093\/nar\/gki475","journal-title":"Nucleic Acids Research"},{"key":"10293_CR177","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv873","volume":"44","author":"Z Ji","year":"2016","unstructured":"Ji, Z., Vokes, S. A., Dang, C. V., & Ji, H. (2016). Turning publicly available gene expression data into discoveries using gene set context analysis. Nucleic Acids Research, 44, Article e8. https:\/\/doi.org\/10.1093\/nar\/gkv873","journal-title":"Nucleic Acids Research"},{"issue":"W1","key":"10293_CR178","doi-asserted-by":"publisher","first-page":"W216","DOI":"10.1093\/nar\/gkac194","volume":"50","author":"BT Sherman","year":"2022","unstructured":"Sherman, B. T., Hao, M., Qiu, J., Jiao, X., Baseler, M. W., Lane, H. C., Imamichi, T., & Chang, W. (2022). DAVID: A web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Research, 50(W1), W216\u2013W221. https:\/\/doi.org\/10.1093\/nar\/gkac194","journal-title":"Nucleic Acids Research"},{"key":"10293_CR179","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae167","volume":"40","author":"A Jiang","year":"2024","unstructured":"Jiang, A., Snell, R. G., & Lehnert, K. (2024). ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells. Bioinformatics, 40, Article btae167. https:\/\/doi.org\/10.1093\/bioinformatics\/btae167","journal-title":"Bioinformatics"},{"key":"10293_CR180","doi-asserted-by":"publisher","DOI":"10.1093\/neuonc\/noac054","author":"V Law","year":"2022","unstructured":"Law, V., Chen, Z., Vena, F., Smalley, I., Macaulay, R., Evernden, B. R., Tran, N., Pina, Y., Puskas, J., Caceres, G., Bayle, S., Johnson, J., Liu, J. K. C., Etame, A., Vogelbaum, M., Rodriguez, P., Duckett, D., Czerniecki, B., Chen, A., \u2026 Forsyth, P. A. (2022). A preclinical model of patient-derived cerebrospinal fluid circulating tumor cells for experimental therapeutics in leptomeningeal disease from melanoma. Neuro-Oncology. https:\/\/doi.org\/10.1093\/neuonc\/noac054","journal-title":"Neuro-Oncology"},{"key":"10293_CR181","doi-asserted-by":"publisher","first-page":"803","DOI":"10.21037\/tau-21-1140","volume":"11","author":"Z Yang","year":"2022","unstructured":"Yang, Z., Bai, H., Wu, Q., Hu, L., Li, G., Kong, D., Zhang, Q., Wan, D., Gu, Z., Zhao, C., Zhang, K., Zhang, W., & Shou, J. (2022). Telomerase positive CTCs with PSMA high expression associated with prostate cancer metastasis. Translational Andrology and Urology, 11, 803\u2013813. https:\/\/doi.org\/10.21037\/tau-21-1140","journal-title":"Translational Andrology and Urology"},{"key":"10293_CR182","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1097\/HEP.0000000000000934","volume":"81","author":"Y Sun","year":"2025","unstructured":"Sun, Y., Li, T., Ding, L., Wang, J., Chen, C., Liu, T., Liu, Y., Li, Q., Wang, C., Huo, R., Wang, H., Tian, T., Zhang, C., Pan, B., Zhou, J., Fan, J., Yang, X., Yang, W., Wang, B., & Guo, W. (2025). Platelet-mediated circulating tumor cell evasion from natural killer cell killing through immune checkpoint CD155-TIGIT. Hepatology, 81, 791\u2013807. https:\/\/doi.org\/10.1097\/HEP.0000000000000934","journal-title":"Hepatology"},{"key":"10293_CR183","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1038\/s41388-024-03212-z","volume":"44","author":"MJ Schmidt","year":"2025","unstructured":"Schmidt, M. J., Naghdloo, A., Prabakar, R. K., Kamal, M., Cadaneanu, R., Garraway, I. P., Lewis, M., Aparicio, A., Zurita-Saavedra, A., Corn, P., Kuhn, P., Pienta, K. J., Amend, S. R., & Hicks, J. (2025). Polyploid cancer cells reveal signatures of chemotherapy resistance. Oncogene, 44, 439\u2013449. https:\/\/doi.org\/10.1038\/s41388-024-03212-z","journal-title":"Oncogene"},{"key":"10293_CR184","doi-asserted-by":"publisher","DOI":"10.3390\/ijms26041435","volume":"26","author":"J-P Arnault","year":"2025","unstructured":"Arnault, J.-P., Chemmama, K., Ferroudj, K., Demagny, J., Panicot-Dubois, L., Galmiche, A., & Saidak, Z. (2025). The dynamic landscape of the coagulome of metastatic malignant melanoma. International Journal of Molecular Sciences, 26, Article 1435. https:\/\/doi.org\/10.3390\/ijms26041435","journal-title":"International Journal of Molecular Sciences"},{"key":"10293_CR185","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2024.114512","author":"H Yang","year":"2024","unstructured":"Yang, H., Wang, H., He, Y., Yang, Y., Thompson, E. W., Xia, D., Burke, L. J., Cao, L., Hooper, J. D., Roberts, M. S., Crawford, D. H. G., & Liang, X. (2024). Identification and characterization of TM4SF1+ tumor self-seeded cells. Cell Reports. https:\/\/doi.org\/10.1016\/j.celrep.2024.114512","journal-title":"Cell Reports"},{"key":"10293_CR186","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1007\/s11684-024-1081-7","volume":"18","author":"Z Nian","year":"2024","unstructured":"Nian, Z., Wang, D., Wang, H., Liu, W., Ma, Z., Yan, J., Cao, Y., Li, J., Zhao, Q., & Liu, Z. (2024). Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in neuroblastoma. Frontiers in Medicine, 18, 690\u2013707. https:\/\/doi.org\/10.1007\/s11684-024-1081-7","journal-title":"Frontiers in Medicine"},{"key":"10293_CR187","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-022-01553-5","volume":"21","author":"KN Suvilesh","year":"2022","unstructured":"Suvilesh, K. N., Nussbaum, Y. I., Radhakrishnan, V., Manjunath, Y., Avella, D. M., Staveley-O\u2019Carroll, K. F., Kimchi, E. T., Chaudhuri, A. A., Shyu, C.-R., Li, G., Pantel, K., Warren, W. C., Mitchem, J. B., & Kaifi, J. T. (2022). Tumorigenic circulating tumor cells from xenograft mouse models of non-metastatic NSCLC patients reveal distinct single cell heterogeneity and drug responses. Molecular Cancer, 21, Article 73. https:\/\/doi.org\/10.1186\/s12943-022-01553-5","journal-title":"Molecular Cancer"},{"key":"10293_CR188","doi-asserted-by":"publisher","first-page":"36425","DOI":"10.1021\/acsami.2c09085","volume":"14","author":"W-J Zheng","year":"2022","unstructured":"Zheng, W.-J., Wang, P.-X., Sun, Y.-F., Cheng, J.-W., Zhong, Y.-C., Xu, Y., Guo, W., Hu, B., Zhou, J., Fan, J., Chen, X., & Yang, X.-R. (2022). Uncovering the heterogeneity and clinical relevance of circulating tumor-initiating cells in hepatocellular carcinoma using an integrated immunomagnetic-microfluidic platform. ACS Applied Materials & Interfaces, 14, 36425\u201336437. https:\/\/doi.org\/10.1021\/acsami.2c09085","journal-title":"ACS Applied Materials & Interfaces"},{"key":"10293_CR189","doi-asserted-by":"publisher","DOI":"10.3390\/cancers13112763","volume":"13","author":"TCY Pang","year":"2021","unstructured":"Pang, T. C. Y., Xu, Z., Mekapogu, A. R., Pothula, S., Becker, T., Corley, S., Wilkins, M. R., Goldstein, D., Pirola, R., Wilson, J., & Apte, M. (2021). HGF\/c-Met inhibition as adjuvant therapy improves outcomes in an orthotopic mouse model of pancreatic cancer. Cancers, 13, Article 2763. https:\/\/doi.org\/10.3390\/cancers13112763","journal-title":"Cancers"},{"key":"10293_CR190","doi-asserted-by":"publisher","DOI":"10.3390\/cancers14163871","volume":"14","author":"TL Sutton","year":"2022","unstructured":"Sutton, T. L., Patel, R. K., Anderson, A. N., Bowden, S. G., Whalen, R., Giske, N. R., & Wong, M. H. (2022). Circulating cells with macrophage-like characteristics in cancer: The importance of circulating neoplastic-immune hybrid cells in cancer. Cancers, 14, Article 3871. https:\/\/doi.org\/10.3390\/cancers14163871","journal-title":"Cancers"},{"key":"10293_CR191","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/s40364-024-00609-6","volume":"12","author":"AN Anderson","year":"2024","unstructured":"Anderson, A. N., Conley, P., Klocke, C. D., Sengupta, S. K., Pang, A., Farley, H. C., Gillingham, A. R., Dawson, A. D., Fan, Y., Jones, J. A., Gibbs, S. L., Skalet, A. H., Wu, G., & Wong, M. H. (2024). Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma. Biomarker Research, 12, 67. https:\/\/doi.org\/10.1186\/s40364-024-00609-6","journal-title":"Biomarker Research"},{"key":"10293_CR192","doi-asserted-by":"publisher","DOI":"10.3390\/cancers16071444","volume":"16","author":"AM Ali","year":"2024","unstructured":"Ali, A. M., & Raza, A. (2024). Scrnaseq and high-throughput spatial analysis of tumor and normal microenvironment in solid tumors reveal a possible origin of circulating tumor hybrid cells. Cancers, 16, Article 1444. https:\/\/doi.org\/10.3390\/cancers16071444","journal-title":"Cancers"},{"key":"10293_CR193","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s13045-023-01442-4","volume":"16","author":"X Ye","year":"2023","unstructured":"Ye, X., Huang, X., Fu, X., Zhang, X., Lin, R., Zhang, W., Zhang, J., & Lu, Y. (2023). Myeloid-like tumor hybrid cells in bone marrow promote progression of prostate cancer bone metastasis. Journal of Hematology & Oncology, 16, 46. https:\/\/doi.org\/10.1186\/s13045-023-01442-4","journal-title":"Journal of Hematology & Oncology"},{"key":"10293_CR194","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1002\/path.6083","volume":"260","author":"T Minowa","year":"2023","unstructured":"Minowa, T., Hirohashi, Y., Murata, K., Sasaki, K., Handa, T., Nakatsugawa, M., Mizue, Y., Murai, A., Kubo, T., Kanaseki, T., Tsukahara, T., Iwabuchi, S., Hashimoto, S., Ishida-Yamamoto, A., Uhara, H., & Torigoe, T. (2023). Fusion with type 2 macrophages induces melanoma cell heterogeneity that potentiates immunological escape from cytotoxic T lymphocytes. The Journal of Pathology, 260, 304\u2013316. https:\/\/doi.org\/10.1002\/path.6083","journal-title":"The Journal of Pathology"},{"key":"10293_CR195","doi-asserted-by":"publisher","DOI":"10.1002\/adbi.202200206","volume":"7","author":"ME Menyailo","year":"2023","unstructured":"Menyailo, M. E., Zainullina, V. R., Khozyainova, A. A., Tashireva, L. A., Zolotareva, SYu. ., Gerashchenko, T. S., Alifanov, V. V., Savelieva, O. E., Grigoryeva, E. S., Tarabanovskaya, N. A., Popova, N. O., Choinzonov, E. L., Cherdyntseva, N. V., Perelmuter, V. M., & Denisov, E. V. (2023). Heterogeneity of circulating epithelial cells in breast cancer at single-cell resolution: Identifying tumor and hybrid cells. Advanced Biology, 7, Article 2200206. https:\/\/doi.org\/10.1002\/adbi.202200206","journal-title":"Advanced Biology"},{"key":"10293_CR196","doi-asserted-by":"publisher","first-page":"E9989","DOI":"10.1073\/pnas.1710964114","volume":"114","author":"L Chen","year":"2017","unstructured":"Chen, L., Lee, J. W., Chou, C.-L., Nair, A. V., Battistone, M. A., P\u0103unescu, T. G., Merkulova, M., Breton, S., Verlander, J. W., Wall, S. M., Brown, D., Burg, M. B., & Knepper, M. A. (2017). Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. Proceedings of the National Academy of Sciences of the United States of America, 114, E9989\u2013E9998. https:\/\/doi.org\/10.1073\/pnas.1710964114","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10293_CR197","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1126\/science.aad0501","volume":"352","author":"I Tirosh","year":"2016","unstructured":"Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., Fallahi-Sichani, M., Dutton-Regester, K., Lin, J.-R., Cohen, O., Shah, P., Lu, D., Genshaft, A. S., Hughes, T. K., Ziegler, C. G. K., \u2026 Garraway, L. A. (2016). Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-Seq. Science, 352, 189\u2013196. https:\/\/doi.org\/10.1126\/science.aad0501","journal-title":"Science"},{"key":"10293_CR198","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1038\/s41588-020-0636-z","volume":"52","author":"H-O Lee","year":"2020","unstructured":"Lee, H.-O., Hong, Y., Etlioglu, H. E., Cho, Y. B., Pomella, V., Van den Bosch, B., Vanhecke, J., Verbandt, S., Hong, H., Min, J.-W., Kim, N., Eum, H. H., Qian, J., Boeckx, B., Lambrechts, D., Tsantoulis, P., De Hertogh, G., Chung, W., Lee, T., \u2026 Park, W.-Y. (2020). Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nature Genetics, 52, 594\u2013603. https:\/\/doi.org\/10.1038\/s41588-020-0636-z","journal-title":"Nature Genetics"},{"key":"10293_CR199","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1016\/j.ccell.2019.08.007","volume":"36","author":"L Ma","year":"2019","unstructured":"Ma, L., Hernandez, M. O., Zhao, Y., Mehta, M., Tran, B., Kelly, M., Rae, Z., Hernandez, J. M., Davis, J. L., Martin, S. P., Kleiner, D. E., Hewitt, S. M., Ylaya, K., Wood, B. J., Greten, T. F., & Wang, X. W. (2019). Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer. Cancer Cell, 36, 418-430.e6. https:\/\/doi.org\/10.1016\/j.ccell.2019.08.007","journal-title":"Cancer Cell"},{"issue":"2","key":"10293_CR200","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/s41591-019-0750-6","volume":"26","author":"AM Laughney","year":"2020","unstructured":"Laughney, A. M., Hu, J., Campbell, N. R., Bakhoum, S. F., Setty, M., Lavall\u00e9e, V.-P., Xie, Y., Masilionis, I., Carr, A. J., Kottapalli, S., Allaj, V., Mattar, M., Rekhtman, N., Xavier, J. B., Mazutis, L., Poirier, J. T., Rudin, C. M., Pe\u2019er, D., & Massagu\u00e9, J. (2020). Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Nature Medicine, 26(2), 259\u2013269. https:\/\/doi.org\/10.1038\/s41591-019-0750-6","journal-title":"Nature Medicine"},{"key":"10293_CR201","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-14256-1","volume":"11","author":"MA Durante","year":"2020","unstructured":"Durante, M. A., Rodriguez, D. A., Kurtenbach, S., Kuznetsov, J. N., Sanchez, M. I., Decatur, C. L., Snyder, H., Feun, L. G., Livingstone, A. S., & Harbour, J. W. (2020). Single-cell analysis reveals new evolutionary complexity in uveal melanoma. Nature Communications, 11, Article 496. https:\/\/doi.org\/10.1038\/s41467-019-14256-1","journal-title":"Nature Communications"},{"key":"10293_CR202","first-page":"2210","volume":"34","author":"DN Hu","year":"1993","unstructured":"Hu, D. N., McCormick, S. A., Ritch, R., & Pelton-Henrion, K. (1993). Studies of human uveal melanocytes in vitro: Isolation, purification and cultivation of human uveal melanocytes. Investigative Ophthalmology & Visual Science, 34, 2210\u20132219.","journal-title":"Investigative Ophthalmology & Visual Science"},{"key":"10293_CR203","doi-asserted-by":"publisher","first-page":"4734","DOI":"10.1016\/j.cell.2021.08.003","volume":"184","author":"K Pelka","year":"2021","unstructured":"Pelka, K., Hofree, M., Chen, J. H., Sarkizova, S., Pirl, J. D., Jorgji, V., Bejnood, A., Dionne, D., Ge, W. H., Xu, K. H., Chao, S. X., Zollinger, D. R., Lieb, D. J., Reeves, J. W., Fuhrman, C. A., Hoang, M. L., Delorey, T., Nguyen, L. T., Waldman, J., \u2026 Hacohen, N. (2021). Spatially organized multicellular immune hubs in human colorectal cancer. Cell, 184, 4734-4752.e20. https:\/\/doi.org\/10.1016\/j.cell.2021.08.003","journal-title":"Cell"},{"key":"10293_CR204","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1038\/s41588-021-00911-1","volume":"53","author":"SZ Wu","year":"2021","unstructured":"Wu, S. Z., Al-Eryani, G., Roden, D., Junankar, S., Harvey, K., Andersson, A., Thennavan, A., Wang, C., Torpy, J., Bartonicek, N., Wang, T., Larsson, L., Kaczorowski, D., Weisenfeld, N. I., Uytingco, C. R., Chew, J. G., Bent, Z. W., Chan, C.-L., Gnanasambandapillai, V., \u2026 Swarbrick, A. (2021). A single-cell and spatially resolved atlas of human breast cancers. Nature Genetics, 53, 1334\u20131347. https:\/\/doi.org\/10.1038\/s41588-021-00911-1","journal-title":"Nature Genetics"},{"key":"10293_CR205","doi-asserted-by":"publisher","first-page":"1464","DOI":"10.1016\/j.ccell.2021.09.005","volume":"39","author":"Y Kfoury","year":"2021","unstructured":"Kfoury, Y., Baryawno, N., Severe, N., Mei, S., Gustafsson, K., Hirz, T., Brouse, T., Scadden, E. W., Igolkina, A. A., Kokkaliaris, K., Choi, B. D., Barkas, N., Randolph, M. A., Shin, J. H., Saylor, P. J., Scadden, D. T., Sykes, D. B., & Kharchenko, P. V. (2021). Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment. Cancer Cell, 39, 1464-1478.e8. https:\/\/doi.org\/10.1016\/j.ccell.2021.09.005","journal-title":"Cancer Cell"},{"key":"10293_CR206","doi-asserted-by":"publisher","DOI":"10.1155\/2021\/9919080","volume":"2021","author":"Y Wang","year":"2021","unstructured":"Wang, Y., Tian, X., & Ai, D. (2021). Cell heterogeneity analysis in single-cell RNA-seq data using mixture exponential graph and Markov random field model. BioMed Research International, 2021, Article 9919080. https:\/\/doi.org\/10.1155\/2021\/9919080","journal-title":"BioMed Research International"},{"key":"10293_CR207","doi-asserted-by":"publisher","first-page":"288","DOI":"10.3389\/fcell.2020.00288","volume":"8","author":"T Thong","year":"2020","unstructured":"Thong, T., Wang, Y., Brooks, M. D., Lee, C. T., Scott, C., Balzano, L., Wicha, M. S., & Colacino, J. A. (2020). Hybrid stem cell states: Insights into the relationship between mammary development and breast cancer using single-cell transcriptomics. Frontiers in Cell and Developmental Biology, 8, 288. https:\/\/doi.org\/10.3389\/fcell.2020.00288","journal-title":"Frontiers in Cell and Developmental Biology"},{"key":"10293_CR208","doi-asserted-by":"publisher","first-page":"7687","DOI":"10.1038\/s41467-022-35296-0","volume":"13","author":"X Guo","year":"2022","unstructured":"Guo, X., Lin, F., Yi, C., Song, J., Sun, D., Lin, L., Zhong, Z., Wu, Z., Wang, X., Zhang, Y., Li, J., Zhang, H., Liu, F., Yang, C., & Song, J. (2022). Deep transfer learning enables lesion tracing of circulating tumor cells. Nature Communications, 13, 7687. https:\/\/doi.org\/10.1038\/s41467-022-35296-0","journal-title":"Nature Communications"},{"issue":"9","key":"10293_CR209","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22094563","volume":"22","author":"M Del Giudice","year":"2021","unstructured":"Del Giudice, M., Peirone, S., Perrone, S., Priante, F., Varese, F., Tirtei, E., Fagioli, F., & Cereda, M. (2021). Artificial intelligence in bulk and single-cell RNA-sequencing data to foster precision oncology. International Journal of Molecular Sciences, 22(9), Article 4563. https:\/\/doi.org\/10.3390\/ijms22094563","journal-title":"International Journal of Molecular Sciences"},{"key":"10293_CR210","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06052-0","volume":"9","author":"M Karaayvaz","year":"2018","unstructured":"Karaayvaz, M., Cristea, S., Gillespie, S. M., Patel, A. P., Mylvaganam, R., Luo, C. C., Specht, M. C., Bernstein, B. E., Michor, F., & Ellisen, L. W. (2018). Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nature Communications, 9, Article 3588. https:\/\/doi.org\/10.1038\/s41467-018-06052-0","journal-title":"Nature Communications"},{"key":"10293_CR211","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1002\/cyto.a.23507","volume":"93","author":"Y Lee","year":"2018","unstructured":"Lee, Y., Guan, G., & Bhagat, A. A. (2018). ClearCell\u00ae FX, a label-free microfluidics technology for enrichment of viable circulating tumor cells. Cytometry Part A, 93, 1251\u20131254. https:\/\/doi.org\/10.1002\/cyto.a.23507","journal-title":"Cytometry Part A"}],"container-title":["Cancer and Metastasis Reviews"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10555-025-10293-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10555-025-10293-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10555-025-10293-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T17:25:25Z","timestamp":1759771525000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10555-025-10293-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,6]]},"references-count":211,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["10293"],"URL":"https:\/\/doi.org\/10.1007\/s10555-025-10293-z","relation":{},"ISSN":["1573-7233"],"issn-type":[{"value":"1573-7233","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,6]]},"assertion":[{"value":"21 June 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"During the preparation of this work, the authors used ChatGPT 4.0 (\n                      \n                      ) to proofread the final manuscript. After using this tool, the authors reviewed and edited the content as needed and take full responsibility for the content of the publication.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declaration of generative AI and AI-assisted technologies in the writing process"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval and consent to participate"}},{"value":"All authors have given consent for publication.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no conflict of interest.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"75"}}