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Reference-based cell type matching of spatial transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
5citations -
Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors2022 Clinical Cancer Research article Medicine Musculoskeletal synovial abnormalities and treatments Open access
David G.P. van IJzendoorn, Magdalena Matusiak, Gregory W. Charville, Geert Spierenburg, Sushama Varma, Deana R.C. Colburg, +10 more
35citations -
OX40 agonism enhances efficacy of PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access
Guillaume Beyrend, Tetje Cornelia van der Sluis, Esmé T.I. van der Gracht, Tamim Abdelaal, Simon P. Jochems, Robert A. Belderbos, +16 more
0citations -
Sex-dependent gene regulation of human atherosclerotic plaques by DNA methylation and transcriptome integration points to smooth muscle cell involvement in women2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Epigenetics and DNA Methylation Open access
Robin J. G. Hartman, Marten A. Siemelink, Saskia Haitjema, Koen F. Dekkers, Lotte Slenders, Arjan Boltjes, +8 more
3citations -
Additional file 8 of Human cortical spheroids with a high diversity of innately developing brain cell types2023 Figshare dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kim M. A. De Kleijn, Wieteke Ameliek Zuure, Kirsten R. Straasheijm, M. Cristina Avramut, Roman I. Koning, Gerard J.M. Martens
0citations -
Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs2024 Nature Biomedical Engineering article Biochemistry, Genetics and Molecular Biology CRISPR and Genetic Engineering Open access
Yufeng Li, Minkang Tan, Almira Akkari-Henić, L.S. Zhang, Maarten Kip, Jorian J. Sepers, +9 more
19citations -
Human umbilical cord mesenchymal stem cell-derived treatment of severe pulmonary arterial hypertension2022 Nature Cardiovascular Research article Medicine Mesenchymal stem cell research Open access cited by 3 patents
Georg Hansmann, Philippe Chouvarine, Franziska Diekmann, Martin A. Giera, Markus Ralser, Michael Mülleder, +4 more
23citations -
Identification of CD8+ T cell PRDM1 in high-risk human plaques and its regulatory role in murine lesion development2022 Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Han Young Jin, Chang Wei Lu, Jan Nagenborg, Marco Manca, Joël Karel, Rachel Cavill, +7 more
0citations -
Identification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms2024 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Adam Tisch, Siddharth Madapoosi, Jan Rosa, Sean F. Eddy, Laura H. Mariani, Abhijit S. Naik, +8 more
2citations -
Recent Advances in Practical Methods for Liver Cell Biology: A Short Overview2020 International Journal of Molecular Sciences article Medicine Liver physiology and pathology Open access
Sandra Torres, Zeinab Abdullah, Maximilian Joseph Brol, Claus Hellerbrand, Mercedes Fernández, Romina Fiorotto, +11 more
16citations -
scAGG: Sample-level embedding and classification of Alzheimer's disease from single-nucleus data2025 Computational and Structural Biotechnology Journal article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Timo Verlaan, Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
2citations -
Tissue microenvironment dictates the state of human induced pluripotent stem cell-derived endothelial cells of distinct developmental origin in 3D cardiac microtissues2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Xu Cao, Maria Mircea, Francijna E. van den Hil, Hailiang Mei, Katrin Neumann, Konstantinos Anastassiadis, +3 more
1citations -
Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions2025 Briefings in Bioinformatics review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Giulia Cesaro, James Shiniti Nagai, Gnoato Nicolò, Alice Chiodi, Gaia Tussardi, Vanessa Klöker, +6 more
44citations -
Cell type matching across species using protein embeddings and transfer learning2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kirti Biharie, Lieke Michielsen, Marcel J. T. Reinders, Ahmed Essam Mahfouz
0citations -
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Magda Grudniewska, Dorien J.M. Peters, Ahmed Essam Mahfouz
5citations -
Predicting cell population-specific gene expression from genomic sequence2022 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Lieke Michielsen, Marcel J. T. Reinders, Ahmed Essam Mahfouz
0citations