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FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets

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Differentiating Microplastics from Natural Particles in Aqueous Suspensions Using Flow Cytometry with Machine Learning

Wang, X., Li, Y., Kroll, A., & Mitrano, D. M. (2024) · Environmental Science & Technology · doi:10.1021/acs.est.4c00304 · Cited by 22

PD-1 endocytosis unleashes the cytolytic potential of checkpoint blockade in tumor immunity

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IKAROS levels are associated with antigen escape in CD19- and CD22-targeted therapies for B-cell malignancies

Domizi, P., Sarno, J., Jager, A., Merchant, M. J., Pacheco, K. Z., Yamada‐Hunter, S. A., Rotiroti, M. C., Liu, Y., Baskar, R., Reynolds, W. D., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58868-2 · Cited by 21

Induced Treg‐Derived Extracellular Vesicles Suppress CD4 + T‐Cell‐Mediated Inflammation and Ameliorate Bone Loss During Periodontitis Partly Through CD73/Adenosine‐Dependent Immunomodulatory Mechanisms

Rojas, C., García, M., González, L., Campos‐Mora, M., de León, E. P., Sierra‐Cristancho, A., Terraza‐Aguirre, C., Cortéz, C., Sansores‐España, L. D., Carvajal, P., et al. (2025) · Journal of Extracellular Vesicles · doi:10.1002/jev2.70118 · Cited by 21

Can we incorporate MRD assessment into clinical practice in AML?

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Individual liver plasmacytoid dendritic cells are capable of producing IFNα and multiple additional cytokines during chronic HCV infection

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Cancer systems immunology

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Bacterial and Fungal Toll-Like Receptor Activation Elicits Type I IFN Responses in Mast Cells

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Age-Dependent Reduction in Asthmatic Pathology through Reprogramming of Postviral Inflammatory Responses

Hazan, G., Eubanks, A., Gierasch, C. M., Atkinson, J. J., Fox, C., Hernandez-Leyva, A. J., Rosen, A. L., Kau, A. L., Agapov, E. V., Alexander‐Brett, J. M., et al. (2022) · The Journal of Immunology · doi:10.4049/jimmunol.2101094 · Cited by 22

Development of an HIV reporter virus that identifies latently infected CD4+ T cells

Kim, E. H., Manganaro, L., Schotsaert, M., Brown, B. D., Mulder, L. C. F., & Simon, V. R. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2022.100238 · Cited by 21

Deep immune profiling of patients with renal impairment unveils distinct immunotypes associated with disease severity

Wu, I., Wu, Y., Yang, H., Hsu, C.-K., Chang, L., Twu, Y., Chang, Y., Chung, W., Yang, C.-W., Hsieh, W., et al. (2022) · Clinical Kidney Journal · doi:10.1093/ckj/sfac196 · Cited by 21

Evolving polarisation of infiltrating and alveolar macrophages in the lung during metastatic progression of melanoma suggests CCR1 as a therapeutic target

Tapmeier, T. T., Howell, J. H., Zhao, L., Papież, B. W., Schnabel, J. A., Muschel, R. J., & Gal, A. (2022) · Oncogene · doi:10.1038/s41388-022-02488-3 · Cited by 22

Geometry Regularized Autoencoders

Duque, A. F., Morin, S., Wolf, G., & Moon, K. R. (2022) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2022.3222104 · Cited by 30

From data to diagnosis: how machine learning is revolutionizing biomarker discovery in idiopathic inflammatory myopathies

McLeish, E., Slater, N., Mastaglia, F. L., Needham, M., & Coudert, J. D. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad514 · Cited by 21

Clonal GZMK+CD8+ T cells are identified as a hallmark of the pathogenesis of cGVHD-induced bronchiolitis obliterans syndrome after allogeneic hematopoietic stem cell transplantation

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Applications for single cell trajectory analysis in inner ear development and regeneration

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Role of Immune Aging in Susceptibility to West Nile Virus

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Multiparameter Single Cell Profiling of Airway Inflammatory Cells

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Tumor-Resident Dendritic Cells and Macrophages Modulate the Accumulation of TCR-Engineered T Cells in Melanoma

Hotblack, A., Holler, A., Piapi, A., Ward, S., Stauss, H. J., & Bennett, C. L. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2018.03.011 · Cited by 21

Generating Quantitative Cell Identity Labels with Marker Enrichment Modeling (MEM)

Diggins, K. E., Gandelman, J. S., Roe, C. E., & Irish, J. M. (2018) · Current Protocols in Cytometry · doi:10.1002/cpcy.34 · Cited by 21

Sox7 Regulates Lineage Decisions in Cardiovascular Progenitor Cells

Doyle, M. J., Magli, A., Estharabadi, N., Amundsen, D. B., Mills, L. J., & Martin, C. M. (2019) · Stem Cells and Development · doi:10.1089/scd.2019.0040 · Cited by 21

Highly Sensitive and Multiplexed Protein Imaging With Cleavable Fluorescent Tyramide Reveals Human Neuronal Heterogeneity

Liao, R., Mondal, M., Nazaroff, C. D., Mastroeni, D., Coleman, P. D., LaBaer, J., & Guo, J. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.614624 · Cited by 22

Mass Cytometry, Imaging Mass Cytometry, and Multiplexed Ion Beam Imaging Use in a Clinical Setting

Devine, R. D., & Behbehani, G. K. (2021) · Clinics in Laboratory Medicine · doi:10.1016/j.cll.2021.03.008 · Cited by 22

Imaging mass cytometry for high-dimensional tissue profiling in the eye

Schlecht, A., Boneva, S., Salié, H., Killmer, S., Wolf, J., Hajdú, R. I., Auw‐Haedrich, C., Agostini, H. T., Reinhard, T., Schlunck, G., et al. (2021) · BMC Ophthalmology · doi:10.1186/s12886-021-02099-8 · Cited by 21

Clustering Single-Cell Expression Data Using Random Forest Graphs

Pouyan, M. B., & Nourani, M. (2016) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2016.2565561 · Cited by 21

Application of artificial intelligence in laboratory hematology: Advances, challenges, and prospects

Liao, H., Zhang, F., Chen, F., Li, Y., Sun, Y., Sloboda, D. D., Zheng, Q., Ying, B., & Hu, Y. (2025) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2025.05.036 · Cited by 26

Cobalt protoporphyrin IX increases endogenous G‐CSF and mobilizes HSC and granulocytes to the blood

Szade, A., Szade, K., Nowak, W. N., Bukowska-Straková, K., Lucie Muchova, A., Gońka, M., Żukowska, M., Cieśla, M., Kachamakova‐Trojanowska, N., Rams‐Baron, M., et al. (2019) · EMBO Molecular Medicine · doi:10.15252/emmm.201809571 · Cited by 20

Visualizing high-dimensional data

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viSNE and Wanderlust, two algorithms for the visualization and analysis of high-dimensional single-cell data

Amir, E.-A. D. (2014) · doi:10.7916/d8sb43vk · Cited by 1

A multidimensional overview

McCarthy, N. J. (2013) · Nature reviews. Cancer · doi:10.1038/nrc3549 · Cited by 4

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types

van Unen, V., Höllt, T., Pezzotti, N., Li, N., Reinders, M. J. T., Eisemann, E., Koning, F., Vilanova, A., & Lelieveldt, B. P. F. (2017) · Nature Communications · doi:10.1038/s41467-017-01689-9 · Cited by 229

Using Visualization of t-Distributed Stochastic Neighbor Embedding To Identify Immune Cell Subsets in Mouse Tumors

Acuff, N. V., & Linden, J. M. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1602077 · Cited by 23