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Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context2022 Cell Metabolism article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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A Comprehensive Workflow for Applying Single-Cell Clustering and Pseudotime Analysis to Flow Cytometry Data2020 The Journal of Immunology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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56citations -
Inferring spatially transient gene expression pattern from spatial transcriptomic studies2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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A guide to the BRAIN Initiative Cell Census Network data ecosystem2023 PLoS Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging2023 Nature Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Semi‐automated background removal limits data loss and normalizes imaging mass cytometry data2021 Cytometry Part A article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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A 34-Marker Panel for Imaging Mass Cytometric Analysis of Human Snap-Frozen Tissue2020 Frontiers in Immunology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Single‐cell omics: Overview, analysis, and application in biomedical science2021 Journal of Cellular Biochemistry article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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43citations -
Single-cell reference mapping to construct and extend cell-type hierarchies2023 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Single-cell, whole-embryo phenotyping of mammalian developmental disorders2023 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing2020 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 1 patent
Patrick S. Stumpf, Haruka Imanishi, Yuya Kunisaki, Yuichiro Semba, Timothy J. Noble, Rosanna C. G. Smith, +8 more
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A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery2023 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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An integrated single‐cell RNA ‐seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptomic and functional types2024 Journal of Neuroendocrinology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)2023 Molecular Systems Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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Computational Stem Cell Biology: Open Questions and Guiding Principles2021 Cell stem cell article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Patrick Cahan, Davide Cacchiarelli, Sara-Jane Dunn, Martin Hemberg, Susana M. Chuva de Sousa Lopes, Samantha A. Morris, +3 more
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Revealing the spatio-phenotypic patterning of cells in healthy and tumor tissues with mLSR-3D and STAPL-3D2021 Nature Biotechnology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ravian L. van Ineveld, Michiel Kleinnijenhuis, María Alieva, Sam de Blank, Mario Barrera Román, Esmée J. van Vliet, +9 more
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Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer2026 Cancer Cell article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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33citations -
SIRV: spatial inference of RNA velocity at the single-cell resolution2024 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
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A community-based transcriptomics classification and nomenclature of neocortical cell types2020 Nature Neuroscience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Rafael Yuste, Michael Hawrylycz, Nadia Aalling, Argel Aguilar‐Valles, Detlev Arendt, Rubén Armañanzas, +59 more
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Differential analysis of binarized single-cell RNA sequencing data captures biological variation2021 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
29citations -
Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Ricardo O. Ramirez Flores, Attila Gábor, Denis Schapiro, Julio Sáez-Rodríguez
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