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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 -
Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis2021 European Heart Journal Open article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Lennart P. L. Landsmeer, Kai Cui, Marie A.C. Depuydt, Maarten C. Verwer, Joost M. Mekke, +17 more
77citations -
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 -
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 -
Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis2021 medRxiv preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Lennart P. L. Landsmeer, Kai Cui, Marie A.C. Depuydt, Maarten C. Verwer, Joost M. Mekke, +17 more
4citations -
The Cell Ontology in the age of single-cell omics2026 eScholarship (California Digital Library) article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian D. Aevermann, Alida Avola, +29 more
7citations -
Best practices for single-cell analysis across modalities2023 Nature Reviews Genetics review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 7 patents
Lukas Heumos, Anna Christina Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia, +36 more
1,043citations -
Single-cell Raman and mass spectrometry analysis to probe cellular heterogeneity in tamoxifen uptake and metabolism2025 Analytical and Bioanalytical Chemistry article Biochemistry, Genetics and Molecular Biology Spectroscopy Techniques in Biomedical and Chemical Research Open access
Congrou Zhang, Yasmine Abouleila, Sylvia E. Le Dévédec, Thomas Hankemeier, Arno Germond
1citations -
scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access cited by 1 patent
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
41citations -
scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
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 -
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and functional types2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jari B. Berkhout, Delaram Poormoghadam, Chun‐Xia Yi, Andries Kalsbeek, Onno Cornelis Meijer, Ahmed Essam Mahfouz
0citations