Papers matching “single-cell spatial transcriptomics” 161
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Single-cell spatial transcriptomics unravels cell states and ecosystems associated with clinical response to immunotherapy2025 Journal for ImmunoTherapy of Cancer article Medicine Cancer Immunotherapy and Biomarkers Open access
Ziena Abdulrahman, Roderick C. Slieker, Daniel McGuire, Marij J.P. Welters, Mariëtte I.E. van Poelgeest, Sjoerd H. van der Burg
23citations -
Cell-type-specific damage scores reveal kidney and liver disease trajectories in single-cell and spatial transcriptomics2026 Cell Genomics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tsimafei Padvitski, Paula Unger Avila, He Chen, Cem Özel, Fabian Braun, Marie-Kristin Kroll, +16 more
1citations -
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data2020 Life Science Alliance article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Thin Nguyen, Buu Minh Thanh Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, +32 more
25citations -
Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Sidrah Maryam, Martin Manolov, Rafael Kramann, Sikander Hayat
0citations -
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
33citations -
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
Valentin Marteau, Niloofar Nemati, Kristina Handler, Deeksha Raju, Alexander Kirchmair, Dietmar Rieder, +40 more
34citations -
MASI enables fast model-free standardization and integration of single-cell transcriptomics data2023 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
4citations -
Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations2022 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Maria Mircea, Mazène Hochane, Xueying Fan, Susana M. Chuva de Sousa Lopes, Diego Garlaschelli, Stefan Semrau
19citations -
Encompassing view of spatial and single-cell RNA sequencing renews the role of the microvasculature in human atherosclerosis2024 Nature Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Tore Bleckwehl, Anne Babler, Merel Tebbens, Sidrah Maryam, Michael Nyberg, Markus Høybye Bosteen, +12 more
67citations -
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain2023 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. F. Lelieveldt, Brian Long, Tamim Abdelaal, +12 more
20citations -
Experimental and computational technologies to dissect the kidney at the single-cell level2020 Nephrology Dialysis Transplantation article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Christoph Kuppe, Javier Perales-Patón, Julio Sáez-Rodríguez, Rafael Kramann
12citations -
Identification of Kidney Cell Types in Single-Cell RNA Sequencing and Single-Nucleus RNA Sequencing Data Using Machine-Learning Algorithms2024 Journal of the American Society of Nephrology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Siddharth Madapoosi, Adam Tisch, Jan Rosa, Sean F. Eddy, Abhijit S. Naik, Christine P. Limonte, +8 more
0citations -
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data2022 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 1 patent
Daniel Dimitrov, Dénes Türei, Martín Garrido‐Rodríguez, Paul L Burmedi, James Shiniti Nagai, Charlotte Boys, +7 more
670citations -
GraphComm predicts cell cell communication using a graph based deep learning method in single cell RNA sequencing data2025 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Emily So, Sikander Hayat, Sisira Kadambat Nair, Bo Wang, Benjamin Haibe‐Kains
6citations -
Defining the variety of cell types in developing and adult human kidneys by single-cell RNA sequencing2021 npj Regenerative Medicine article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Anika Schumacher, Maarten B. Rookmaaker, Jaap A. Joles, Rafael Kramann, Tri Quang Nguyen, Martijn van Griensven, +1 more
60citations -
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
38citations -
Eleven grand challenges in single-cell data science2020 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 2 patents
David Laehnemann, Johannes Köster, Ewa Szczurek, Davis James McCarthy, Stephanie C. Hicks, Mark D. Robinson, +45 more
1,504citations -
Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data2022 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tommaso Andreani, Linda M. Slot, Samuel Gabillard, Carsten Strübing, Yaligara Veeranagouda, Aleida M. Bakker, +5 more
14citations