Tumour heterogeneity and metastasis at single-cell resolution

Signatures of mutational processes in human cancer

Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660

Microenvironmental regulation of tumor progression and metastasis

Quail, D. F., & Joyce, J. A. (2013) · Nature Medicine · doi:10.1038/nm.3394 · Cited by 7,994

Cancer Genome Landscapes

Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A., & Kinzler, K. W. (2013) · Science · doi:10.1126/science.1235122 · Cited by 7,863

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1113205 · Cited by 7,774

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

Verhaak, R. G. W., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2009.12.020 · Cited by 7,575

Massively parallel digital transcriptional profiling of single cells

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., et al. (2017) · Nature Communications · doi:10.1038/ncomms14049 · Cited by 7,353

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science · doi:10.1126/science.1254257 · Cited by 5,063

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944

Full-length RNA-seq from single cells using Smart-seq2

Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137

Molecular principles of metastasis: a hallmark of cancer revisited

Fares, J., Fares, M. Y., Khachfe, H. H., Salhab, H. A., & Fares, Y. (2020) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-020-0134-x · Cited by 2,536

Exploring tissue architecture using spatial transcriptomics

Rao, A., Barkley, D., França, G. S., & Yanai, I. (2021) · Nature · doi:10.1038/s41586-021-03634-9 · Cited by 1,700

Eleven grand challenges in single-cell data science

Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-1926-6 · Cited by 1,327

A compendium of mutational cancer driver genes

Martínez-Jiménez, F., Muiños, F., Sentís, I., Deu-Pons, J., Reyes-Salazar, I., Arnedo-Pac, C., Mularoni, L., Pich, O., Bonet, J., Kranas, H., et al. (2020) · Nature reviews. Cancer · doi:10.1038/s41568-020-0290-x · Cited by 1,340

Macrophage diversity in cancer revisited in the era of single-cell omics

Ma, R., Black, A., & Qian, B. (2022) · Trends in Immunology · doi:10.1016/j.it.2022.04.008 · Cited by 732

Defining the Hallmarks of Metastasis

Welch, D. R., & Hurst, D. R. (2019) · Cancer Research · doi:10.1158/0008-5472.can-19-0458 · Cited by 722

Breast cancer as an example of tumour heterogeneity and tumour cell plasticity during malignant progression

Lüönd, F., Tiede, S., & Christofori, G. (2021) · British Journal of Cancer · doi:10.1038/s41416-021-01328-7 · Cited by 463

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

Marjanovic, N. D., Hofree, M., Chan, J. E., Canner, D. A., Wu, K., Trakala, M., Hartmann, G. G., Smith, O. C. G., Kim, J. Y., Evans, K. V., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.06.012 · Cited by 407

Comprehensive analysis of spatial architecture in primary liver cancer

Wu, R. T., Guo, W., Qiu, X., Wang, S., Sui, C., Lian, Q., Wu, J., Shan, Y., Zhao, Y., Yang, S., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg3750 · Cited by 383

Role of m6A RNA methylation in cardiovascular disease (Review)

Qin, Y., Li, L., Luo, E., Hou, J., Yan, G., Wang, D., Qiao, Y., & Tang, C. (2020) · International Journal of Molecular Medicine · doi:10.3892/ijmm.2020.4746 · Cited by 328

Advances in PET imaging of cancer

Schwenck, J., Sonanini, D., Cotton, J. M., Rammensee, H., la Fougère, C., Zender, L., & Pichler, B. J. (2023) · Nature reviews. Cancer · doi:10.1038/s41568-023-00576-4 · Cited by 343

The single-cell sequencing: new developments and medical applications

Tang, X., Huang, Y., Lei, J., Luo, H., & Zhu, X. M. (2019) · Cell & Bioscience · doi:10.1186/s13578-019-0314-y · Cited by 313

Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing

Davis, R. T., Blake, K., Ma, D., Gabra, M. B. I., Hernandez, G. A., Phung, A. T., Yang, Y., Maurer, D., Lefebvre, A. E. Y. T., Alshetaiwi, H. S., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0477-0 · Cited by 301

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

The CRUK IMAXT Grand Challenge Team, O’Flanagan, C. H., Campbell, K. R., Zhang, A. W., Kabeer, F., Lim, J. L., Biele, J., Eirew, P. D., Lai, D., McPherson, A., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1830-0 · Cited by 265

Single‐Cell Analysis Using Droplet Microfluidics

Matuła, K., Rivello, F., & Huck, W. T. S. (2019) · Advanced Biosystems · doi:10.1002/adbi.201900188 · Cited by 284

Open-ST: High-resolution spatial transcriptomics in 3D

Schott, M., León-Periñán, D., Splendiani, E., Strenger, L., Licha, J. R., Pentimalli, T. M., Schallenberg, S., Alles, J., Tagliaferro, S. S., Boltengagen, A., et al. (2024) · Cell · doi:10.1016/j.cell.2024.05.055 · Cited by 253

Intratumoral Heterogeneity: More Than Just Mutations

Hinohara, K., & Polyák, K. (2019) · Trends in Cell Biology · doi:10.1016/j.tcb.2019.03.003 · Cited by 241

Metabolic Reprogramming of Cancer Cells during Tumor Progression and Metastasis

Ohshima, K., & Morii, E. (2021) · Metabolites · doi:10.3390/metabo11010028 · Cited by 236

Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma

LaFave, L. M., Kartha, V. K., Ma, S., Meli, K., Priore, I. S. D., Lareau, C. A., Naranjo, S., Westcott, P. M. K., Duarte, F. M., Sankar, V., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.06.006 · Cited by 216

Glial and myeloid heterogeneity in the brain tumour microenvironment

Andersen, B. M., Akl, C. F., Wheeler, M. A., Chiocca, E. A., Reardon, D. A., & Quintana, F. J. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00397-3 · Cited by 216

Multiomic Analysis of Lung Tumors Defines Pathways Activated in Neuroendocrine Transformation

Quintanal-Villalonga, A., Taniguchi, H., Zhan, Y. A., Hasan, M., Chavan, S. S., Meng, F., Uddin, F., Manoj, P., Donoghue, M. T. A., Won, H. H., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-1863 · Cited by 197

Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis

Bonnay, F., Veloso, A., Steinmann, V., Köcher, T., Abdusselamoglu, M. D., Bajaj, S., Rivelles, E., Landskron, L., Esterbauer, H., Zinzen, R. P., et al. (2020) · Cell · doi:10.1016/j.cell.2020.07.039 · Cited by 191

Metal-free bioorthogonal click chemistry in cancer theranostics

Wu, D., Yang, K., Zhang, Z., Feng, Y., Rao, L., Chen, X. S., & Yu, G. (2022) · Chemical Society Reviews · doi:10.1039/d1cs00451d · Cited by 179

Cancer Stem Cells and Epithelial-to-Mesenchymal Transition in Cancer Metastasis

Celià-Terrassa, T., & Jolly, M. K. (2020) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a036905 · Cited by 163

Combined Single‐Cell and Spatial Transcriptomics Reveal the Metabolic Evolvement of Breast Cancer during Early Dissemination

Liu, Y., Ge, J., Chen, Y., Liu, T., Chen, L., Liu, C., Ma, D., Chen, Y., Cai, Y., Xu, Y., et al. (2023) · Advanced Science · doi:10.1002/advs.202205395 · Cited by 167

Clinical application and mechanism of traditional Chinese medicine in treatment of lung cancer

Su, X., Wang, J., Che, H., Wang, C., Jiang, H., Lei, X., Zhao, W., Kuang, H., & Wang, Q. (2020) · Chinese Medical Journal · doi:10.1097/cm9.0000000000001141 · Cited by 155

Fast and precise single-cell data analysis using a hierarchical autoencoder

Tran, D., Nguyen, H., Tran, B., La Vecchia, C., Luu, H. N., & Nguyen, T. (2021) · Nature Communications · doi:10.1038/s41467-021-21312-2 · Cited by 145

Cell and Nucleus Shape as an Indicator of Tissue Fluidity in Carcinoma

Grosser, S., Lippoldt, J., Oswald, L., Merkel, M., Sussman, D. M., Renner, F., Gottheil, P., Morawetz, E. W., Fuhs, T., Xie, X., et al. (2021) · Physical Review X · doi:10.1103/physrevx.11.011033 · Cited by 140

Cancer cell cycle heterogeneity as a critical determinant of therapeutic resistance

Maleki, E. H., Bahrami, A. R., & Matin, M. M. (2023) · Genes & Diseases · doi:10.1016/j.gendis.2022.11.025 · Cited by 138

Stem cells in cancer initiation and progression

Bajaj, J., Diaz, E., & Reya, T. (2019) · The Journal of Cell Biology · doi:10.1083/jcb.201911053 · Cited by 132

Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients

Liu, T., Liu, C., Yan, M., Zhang, L., Zhang, J., Xiao, M., Li, Z., Wei, X., & Zhang, H. (2022) · Nature Communications · doi:10.1038/s41467-022-34581-2 · Cited by 123

Single-Cell Analyses Reveal Mechanisms of Cancer Stem Cell Maintenance and Epithelial–Mesenchymal Transition in Recurrent Bladder Cancer

Wang, H., Mei, Y., Luo, C., Huang, Q., Wang, Z., Lu, G.-M., Qin, L., Sun, Z., Huang, C.-W., Yang, Z.-W., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-4796 · Cited by 116

Dynamic single-cell phenotyping of immune cells using the microfluidic platform DropMap

Bounab, Y., Eyer, K., Dixneuf, S., Rybczynska, M., Chauvel, C., Mistretta, M., Tran, T., Aymerich, N., Chenon, G., Llitjos, J., et al. (2020) · Nature Protocols · doi:10.1038/s41596-020-0354-0 · Cited by 111

Circulating Tumor Cells as a Tool for Assessing Tumor Heterogeneity

Tellez-Gabriel, M., Heymann, M., & Heymann, D. (2019) · Theranostics · doi:10.7150/thno.34337 · Cited by 112

Subpopulation targeting of pyruvate dehydrogenase and GLUT1 decouples metabolic heterogeneity during collective cancer cell invasion

Commander, R., Wei, C., Sharma, A., Mouw, J. K., Burton, L. J., Summerbell, E. R., Mahboubi, D., Peterson, R. J., Konen, J. M., Zhou, W., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15219-7 · Cited by 117

Single-cell resolved imaging reveals intra-tumor heterogeneity in glycolysis, transitions between metabolic states, and their regulatory mechanisms

Kondo, H., Ratcliffe, C. D. H., Hooper, S., Ellis, J., MacRae, J. I., Hennequart, M., Dunsby, C. W., Anderson, K. I., & Sahai, E. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108750 · Cited by 109

Maximizing transcription of nucleic acids with efficient T7 promoters

Conrad, T., Plumbom, I., Alcobendas, M., Vidal, R. O., & Sauer, S. (2020) · Communications Biology · doi:10.1038/s42003-020-01167-x · Cited by 109

Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum

Chakraborty, P., George, J. T., Tripathi, S., Levine, H., & Jolly, M. K. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00220 · Cited by 105

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

Sun, H., Cao, S., Mashl, R. J., Mo, C.-K., Zaccaria, S., Wendl, M. C., Davies, S. R., Bailey, M. H., Primeau, T. M., Hoog, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25177-3 · Cited by 104

Moving pan-cancer studies from basic research toward the clinic

Chen, F., Wendl, M. C., Wyczalkowski, M. A., Bailey, M. H., Li, Y., & Ding, L. (2021) · Nature Cancer · doi:10.1038/s43018-021-00250-4 · Cited by 108

Quantification of tumor heterogeneity: from data acquisition to metric generation

Kashyap, A., Rapsomaniki, M., Barros, V., Khartchenko, A. F., Martinelli, A. L., Foncubierta–Rodríguez, A., Gabrani, M., Rosen‐Zvi, M., & Kaigala, G. V. (2021) · Trends in biotechnology · doi:10.1016/j.tibtech.2021.11.006 · Cited by 110

Emerging Roles of the Endoplasmic Reticulum Associated Unfolded Protein Response in Cancer Cell Migration and Invasion

Limia, C. M., Sauzay, C., Urra, H., Hetz, C. A., Chevet, É., & Avril, T. (2019) · Cancers · doi:10.3390/cancers11050631 · Cited by 103

Hypoxia-driven intratumor heterogeneity and immune evasion

Terry, S., Engelsen, A. S. T., Buart, S., El‐Sayed, W., Venkatesh, G. H., & Chouaı̈b, S. (2020) · Cancer Letters · doi:10.1016/j.canlet.2020.07.004 · Cited by 102

Radiological tumour classification across imaging modality and histology

Wu, J., Li, C., Gensheimer, M. F., Padda, S. K., Kato, F., Shirato, H., Wei, Y., Schönlieb, C., Price, S. J., Jaffray, D. A., et al. (2021) · Nature Machine Intelligence · doi:10.1038/s42256-021-00377-0 · Cited by 98

Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection

Vera, J. C., Sun, J., Lin, Y. T., Drnevich, J., Ke, R., & Brooke, C. B. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008671 · Cited by 89

Multiplex protein imaging in tumour biology

de Souza, N., Zhao, S., & Bodenmiller, B. (2024) · Nature reviews. Cancer · doi:10.1038/s41568-023-00657-4 · Cited by 95

Clinical Implications of Colorectal Cancer Stem Cells in the Age of Single-Cell Omics and Targeted Therapies

Frank, M. H., Wilson, B. J., Gold, J. S., & Frank, N. Y. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.12.080 · Cited by 102

Solid stress, competition for space and cancer: The opposing roles of mechanical cell competition in tumour initiation and growth

Levayer, R. (2019) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2019.05.004 · Cited by 102

In Situ Single Cell Proteomics Reveals Circulating Tumor Cell Heterogeneity during Treatment

Khondakar, K. R., Dey, S., Wuethrich, A., Wang, J., Behren, A., Antaw, F., Wang, Y., Sina, A. A. I., & Trau, M. (2021) · ACS Nano · doi:10.1021/acsnano.0c10008 · Cited by 94

The prognostic value and molecular properties of tertiary lymphoid structures in oesophageal squamous cell carcinoma

Ling, Y., Zhong, J., Weng, Z., Lin, G., Liu, C., Pan, C., Yang, H., Wei, X., Xie, X., Wei, X., et al. (2022) · Clinical and Translational Medicine · doi:10.1002/ctm2.1074 · Cited by 92

Organ-Specificity of Breast Cancer Metastasis

Ibragimova, M. K., Tsyganov, M. M., Kravtsova, E. A., Tsydenova, I. A., & Литвяков, Н. В. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242115625 · Cited by 95

Breast cancers, mammary stem cells, and cancer stem cells, characteristics, and hypotheses

Taurin, S., & Alkhalifa, H. (2020) · Neoplasia · doi:10.1016/j.neo.2020.09.009 · Cited by 96

Over a century of cancer research: Inconvenient truths and promising leads

Sonnenschein, C., & Soto, A. M. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000670 · Cited by 90

Single-cell mapping of DNA G-quadruplex structures in human cancer cells

Hui, W. W. I., Simeone, A., Zyner, K. G., Tannahill, D., & Balasubramanian, S. (2021) · Scientific Reports · doi:10.1038/s41598-021-02943-3 · Cited by 85

Breast Cancer Heterogeneity and Response to Novel Therapeutics

Baliu‐Piqué, M., Pandiella, A., & Ocaña, A. (2020) · Cancers · doi:10.3390/cancers12113271 · Cited by 88

Mechano‐Responsive Leapfrog Micelles Enable Interactive Apoptotic and Ferroptotic Cancer Therapy

Li, Y., Qin, Y., Shang, Y., Li, Y., Liu, F., Luo, J., Zhu, J., Guo, X., Wang, Z., & Zhao, Y. (2022) · Advanced Functional Materials · doi:10.1002/adfm.202112000 · Cited by 84

Intratumor heterogeneity: the hidden barrier to immunotherapy against MSI tumors from the perspective of IFN-γ signaling and tumor-infiltrating lymphocytes

Wu, W., Liu, Y., Zeng, S., Han, Y., & Shen, H. (2021) · Journal of Hematology & Oncology · doi:10.1186/s13045-021-01166-3 · Cited by 83

Comprehensive analysis of tumour initiation, spatial and temporal progression under multiple lines of treatmentPreprint

Leshchiner, I., Livitz, D. G., Gainor, J. F., Rosebrock, D., Spiro, O., Martinez, A. Z., Mroz, E. A., Lin, J. J., Stewart, C., Kim, J., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/508127 · Cited by 76

Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression

Cao, S., Wang, J. R., Ji, S., Peng, Y., Dai, Y., Guo, S., Montierth, M. D., Shen, J. P., Zhao, X. H., Chen, J., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01342-x · Cited by 81

Addressing Patient Specificity in the Engineering of Tumor Models

Bray, L. J., Hutmacher, D. W., & Bock, N. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00217 · Cited by 79

Tumor‐Activated Size‐Enlargeable Bioinspired Lipoproteins Access Cancer Cells in Tumor to Elicit Anti‐Tumor Immune Responses

Li, J., Wang, H., Wang, Y., Gong, X., Xu, X., Sha, X., Zhang, A., Zhang, Z., & Li, Y. (2020) · Advanced Materials · doi:10.1002/adma.202002380 · Cited by 72

GelMA, Click-Chemistry Gelatin and Bioprinted Polyethylene Glycol-Based Hydrogels as 3D Ex Vivo Drug Testing Platforms for Patient-Derived Breast Cancer Organoids

Bock, N., Forouz, F., Hipwood, L., Clegg, J., Jeffery, P. L., Gough, M., van Wyngaard, T., Pyke, C., Adams, M. N., Bray, L. J., et al. (2023) · Pharmaceutics · doi:10.3390/pharmaceutics15010261 · Cited by 73

Deep Profiling of Cellular Heterogeneity by Emerging Single‐Cell Proteomic Technologies

Yang, L., George, J., & Wang, J. (2019) · PROTEOMICS · doi:10.1002/pmic.201900226 · Cited by 72

Single-Cell RNA Sequencing: Technological Progress and Biomedical Application in Cancer Research

Xu, C., Zheng, Y., & Xu, K. (2023) · Molecular Biotechnology · doi:10.1007/s12033-023-00777-0 · Cited by 79

Targeting Altered Energy Metabolism in Colorectal Cancer: Oncogenic Reprogramming, the Central Role of the TCA Cycle and Therapeutic Opportunities

Neitzel, C., Demuth, P., Wittmann, S., & Fahrer, J. (2020) · Cancers · doi:10.3390/cancers12071731 · Cited by 70

Single cell metabolomics using mass spectrometry: Techniques and data analysis

Liu, R., & Yang, Z. (2020) · Analytica Chimica Acta · doi:10.1016/j.aca.2020.11.020 · Cited by 69

Heterogeneity of Circulating Tumor Cells in Breast Cancer: Identifying Metastatic Seeds

Menyailo, M. E., Tretyakova, M. S., & Denisov, E. V. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21051696 · Cited by 67

Erythrocyte Membrane-Camouflaged IR780 and DTX Coloading Polymeric Nanoparticles for Imaging-Guided Cancer Photo–Chemo Combination Therapy

Yang, Q., Xiao, Y., Yin, Y., Li, G., & Peng, J. (2019) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.9b00413 · Cited by 66

SPARSim single cell: a count data simulator for scRNA-seq data

Baruzzo, G., Patuzzi, I., & Camillo, B. D. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz752 · Cited by 63

Disordered chromatin packing regulates phenotypic plasticity

Virk, R. K. A., Wu, W., Almassalha, L. M., Bauer, G. M., Li, Y., VanDerway, D., Frederick, J., Zhang, D., Eshein, A., Roy, H. K., et al. (2020) · Science Advances · doi:10.1126/sciadv.aax6232 · Cited by 62

Long Non-Coding RNA: Dual Effects on Breast Cancer Metastasis and Clinical Applications

Huang, Q.-Y., Liu, G., Qian, X., Tang, L.-B., Huang, Q.-Y., & Xiong, L. (2019) · Cancers · doi:10.3390/cancers11111802 · Cited by 64

Targeting of cancer stem cells by differentiation therapy

Arima, Y., Nobusue, H., & Saya, H. (2020) · Cancer Science · doi:10.1111/cas.14504 · Cited by 67

A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer

Stashko, C., Hayward, M.-K., Northey, J. J., Pearson, N., Ironside, A. J., Lakins, J. N., Oria, R., Goyette, M.-A., Mayo, L. N., Russnes, H. G., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39085-1 · Cited by 65

Nanobody Conjugates for Targeted Cancer Therapy and Imaging

Kang, W., Ding, C., Zheng, D., Ma, X., Yi, L., Tong, X., Wu, C., Xue, C., Yu, Y., & Zhou, Q. (2021) · Technology in Cancer Research & Treatment · doi:10.1177/15330338211010117 · Cited by 64

Cellular heterogeneity in TNF/TNFR1 signalling: live cell imaging of cell fate decisions in single cells

Preedy, M. K., White, M., & Tergaonkar, V. (2024) · Cell Death and Disease · doi:10.1038/s41419-024-06559-z · Cited by 69

Spatiotemporal pH Heterogeneity as a Promoter of Cancer Progression and Therapeutic Resistance

Korenchan, D. E., & Flavell, R. R. (2019) · Cancers · doi:10.3390/cancers11071026 · Cited by 61

Monitoring glycolytic dynamics in single cells using a fluorescent biosensor for fructose 1,6-bisphosphate

Koberstein, J. N., Stewart, M. L., Smith, C. B., Tarasov, A. I., Ashcroft, F. M., Stork, P. A., & Goodman, R. H. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2204407119 · Cited by 55

Linking Tumor Microenvironment to Plasticity of Cancer Stem Cells: Mechanisms and Application in Cancer Therapy

Zheng, X., Yu, C., & Xu, M. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.678333 · Cited by 63

Phenotypic heterogeneity, stability and plasticity in tumor‐promoting carcinoma‐associated fibroblasts

Mezawa, Y., & Orimo, A. (2021) · FEBS Journal · doi:10.1111/febs.15851 · Cited by 59

Advancing Breast Cancer Heterogeneity Analysis: Insights from Genomics, Transcriptomics and Proteomics at Bulk and Single-Cell Levels

Zhu, Z., Jiang, L., & Ding, X. (2023) · Cancers · doi:10.3390/cancers15164164 · Cited by 60

A review of computational strategies for denoising and imputation of single-cell transcriptomic data

Patruno, L., Maspero, D., Craighero, F., Angaroni, F., Antoniotti, M., & Graudenzi, A. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa222 · Cited by 56

Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer

Nath, A., Cosgrove, P. A., Mirsafian, H., Christie, E. L., Pflieger, L. T., Copeland, B., Majumdar, S., Cristea, M. C., Han, E. S., Lee, S. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23171-3 · Cited by 59

Spatial proteomics for understanding the tissue microenvironment

Mao, Y., Wang, X., Huang, P., & Tian, R. (2021) · The Analyst · doi:10.1039/d1an00472g · Cited by 55

From Chaos to Opportunity: Decoding Cancer Heterogeneity for Enhanced Treatment Strategies

Ottaiano, A., Ianniello, M., Santorsola, M., Ruggiero, R., Sirica, R., Sabbatino, F., Perri, F., Cascella, M., Marzo, M. D., Berretta, M., et al. (2023) · Biology · doi:10.3390/biology12091183 · Cited by 60

Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients

Wu, H., Temko, D., Maliga, Z., Moreira, A. L., Sei, E., Minussi, D. C., Dean, J., Lee, C., Xu, Q., Hochart, G., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100165 · Cited by 53

Nanopore approaches for single-molecule temporal omics: promises and challenges

Li, M., Jiang, J., Li, J., Niu, H., Ying, Y., Tian, R., & Long, Y. (2024) · Nature Methods · doi:10.1038/s41592-024-02492-3 · Cited by 63

Single-Cell-Derived Tumor-Sphere Formation and Drug-Resistance Assay Using an Integrated Microfluidics

Pang, L., Ding, J., Ge, Y., Fan, J., & Fan, S. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b01084 · Cited by 53

CyTOF: An Emerging Technology for Single‐Cell Proteomics in the Mouse

Tracey, L. J., An, Y., & Justice, M. J. (2021) · Current Protocols · doi:10.1002/cpz1.118 · Cited by 58

Pitfalls in Cancer Biomarker Discovery and Validation with Emphasis on Circulating Tumor DNA

Ren, A. H., Fiala, C., Diamandis, E. P., & Kulasingam, V. (2020) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-20-0074 · Cited by 52

Dissecting the single-cell transcriptome network in patients with esophageal squamous cell carcinoma receiving operative paclitaxel plus platinum chemotherapy

Chen, Z., Huang, Y., Hu, Z., Zhao, M., Bian, Y., Chen, Z., Zheng, Y., Bi, G., Pang, Y., Zhan, C., et al. (2021) · Oncogenesis · doi:10.1038/s41389-021-00359-2 · Cited by 52

Spatial Transcriptomics for Tumor Heterogeneity Analysis

Li, Q., Zhang, X., & Ke, R. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.906158 · Cited by 57

Interrogation of Phenotypic Plasticity between Epithelial and Mesenchymal States in Breast Cancer

Bhatia, S., Monkman, J. H., Blick, T., Pinto, C., Waltham, M. C., Nagaraj, S. H., & Thompson, E. W. (2019) · Journal of Clinical Medicine · doi:10.3390/jcm8060893 · Cited by 52

Nanobodies as non-invasive imaging tools

Rashidian, M., & Ploegh, H. L. (2020) · Immuno-Oncology Technology · doi:10.1016/j.iotech.2020.07.001 · Cited by 56

Scalable co-sequencing of RNA and DNA from individual nuclei

Olsen, T. R., Talla, P., Sagatelian, R., Furnari, J. L., Bruce, J. N., Canoll, P., Zha, S., & Sims, P. A. (2025) · Nature Methods · doi:10.1038/s41592-024-02579-x · Cited by 50

ZNF689 deficiency promotes intratumor heterogeneity and immunotherapy resistance in triple-negative breast cancer

Ge, L., Jin, X., Ma, D., Wang, Z.-Y., Liu, C., Zhou, C., Zhao, S., Yu, T., Liu, X., Di, G. H., et al. (2024) · Cell Research · doi:10.1038/s41422-023-00909-w · Cited by 51

Targeting Epigenetics in Lung CancerPreprint

Chao, Y. L., & Pecot, C. V. (2020) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a038000 · Cited by 49

Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics

Huang, P., Kong, Q., Gao, W., Chu, B., Li, H., Mao, Y., Cai, Z., Xu, R., & Tian, R. (2020) · Analytica Chimica Acta · doi:10.1016/j.aca.2020.06.049 · Cited by 46

Volumetric stimulated Raman scattering imaging of cleared tissues towards three-dimensional chemical histopathology

Li, J., Lin, P., Tan, Y., & Cheng, J. (2019) · Biomedical Optics Express · doi:10.1364/boe.10.004329 · Cited by 46

Tumor biology and multidisciplinary strategies of oligometastasis in gastrointestinal cancers

Zhao, Y., Li, J., Li, D., Wang, Z., Zhao, J., Wu, X., Sun, Q., Lin, P. P., Plum, P. S., Damanakis, A. I., et al. (2019) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2019.08.026 · Cited by 47

Connecting Metabolic Rewiring With Phenotype Switching in Melanoma

Falletta, P., Goding, C. R., & Vivas, Y. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.930250 · Cited by 46

Understanding tumor ecosystems by single-cell sequencing: promises and limitations

Ren, X., Kang, B., & Zhang, Z. (2018) · Genome biology · doi:10.1186/s13059-018-1593-z · Cited by 220

Dive into Single, Seek Out Multiple: Probing Cancer Metastases via Single-Cell Sequencing and Imaging Techniques

Su, S., & Li, X. (2021) · Cancers · doi:10.3390/cancers13051067 · Cited by 7

Tumour Heterogeneity: The Key Advantages of Single-Cell Analysis

Tellez-Gabriel, M., Ory, B., Lamoureux, F., Heymann, M., & Heymann, D. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17122142 · Cited by 203

Unmasking tumor heterogeneity and clonal evolution by single-cell analysis

Shi, X., Chakraborty, P., & Chaudhuri, A. (2018) · Journal of Cancer Metastasis and Treatment · doi:10.20517/2394-4722.2018.32 · Cited by 12

Using single‐cell multiple omics approaches to resolve tumor heterogeneity

Ortega, M. A., Poirion, O., Zhu, X., Huang, S., Wolfgruber, T. K., Sebra, R., & Garmire, L. X. (2017) · Clinical and Translational Medicine · doi:10.1186/s40169-017-0177-y · Cited by 81