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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 -
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 -
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 -
Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets2026 Computational and Structural Biotechnology Journal article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Dorien J.M. Peters, Ahmed Essam Mahfouz
1citations -
Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development2020 Journal of the American Society of Nephrology article Biochemistry, Genetics and Molecular Biology RNA Research and Splicing Open access
Yishay Wineberg, Tali Hana Bar-Lev, Anna Futorian, Nissim Ben-Haim, Leah Armon, Debby Ickowicz, +9 more
24citations -
Single-cell T-cell receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T-cells2023 Atherosclerosis article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Marie A.C. Depuydt, Frank H. Schaftenaar, Koen H.M. Prange, Arjan Boltjes, E. Hemme, L. Delfos, +12 more
6citations -
Single-cell RNA sequencing of human fetal epicardium reveals novel markers and regulators of EMT2020 European Heart Journal article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
T J Streef, Tessa van Herwaarden, Anke M. Smits, Marie‐José Goumans
0citations -
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing2022 Bioinformatics article Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access cited by 1 patent
Hana Rozhoňová, Daniel Danciu, Stefan G. Stark, Gunnar Rätsch, André Kahles, Kjong-Van Lehmann
9citations -
Single-cell RNA sequencing analysis of the human fetal epicardium reveals several new genes involved in regulation of epicardial activation2024 Cardiovascular Research article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Anke M. Smits, T J Streef, Els Groeneveld, Tessa van Herwaarden, Marie‐José Goumans
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Unraveling Divergent Transcriptomic Profiles: A Comparative Single-Cell RNA Sequencing Study of Epithelium, Gingiva, and Periodontal Ligament Tissues12citations
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Single-cell T cell receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T cells2023 Nature Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Marie A.C. Depuydt, Frank H. Schaftenaar, Koen H.M. Prange, Arjan Boltjes, Esmeralda Hemme, Lucie Delfos, +14 more
96citations -
Cross-species single-cell RNA sequencing reveals divergent phenotypes and activation states of adaptive immunity in human carotid and experimental murine atherosclerosis2024 Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Hauke Horstmann, Nathaly Anto Michel, Sophie Hansen, Alexandra Lindau, Katharina Pfeil, Marbely C. Fernández, +27 more
36citations -
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 -
Human and murine single-cell RNA-sequencing reveal fibroblast heterogeneity in healthy and diseased vasculature and differential regulation by ageing and serum cholesterol2023 Atherosclerosis article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Kim van Kuijk, Ian R McCracken, Renée J. H. A. Tillie, S. Asselberghs, Dlzar Ali Kheder, Stan Muitjens, +21 more
0citations -
Single-Cell Analysis of Refractory Celiac Disease Demonstrates Inter- and Intra-Patient Aberrant Cell Heterogeneity2022 Cellular and Molecular Gastroenterology and Hepatology article Medicine Celiac Disease Research and Management Open access
Tessa Dieckman, Mette Schreurs, Ahmed Essam Mahfouz, Yvonne Kooy–Winkelaar, Andra Neefjes‐Borst, Gerd Bouma, +1 more
18citations -
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 -
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 -
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