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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 -
Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications2025 Nucleic Acids Research article Biochemistry, Genetics and Molecular Biology RNA modifications and cancer Open access
Charlotte Hewel, Anna Wierczeiko, Johannes Miedema, Johannes H. Friedrich, Stephan Weißbach, Laura Holthöfer, +15 more
21citations -
Long non-coding RNA expression profiling by RNA-sequencing in osteoarthritis cartilage2020 Osteoarthritis and Cartilage article Medicine Osteoarthritis Treatment and Mechanisms Open access
Marcella van Hoolwerff, P.M. Metselaar, M. Teurlings, H. Eka D. Suchiman, Rob G. H. H. Nelissen, Y.F. Ramos, +2 more
0citations -
Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA–minus RNA sequencing data2021 GigaScience article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Youri Hoogstrate, Malgorzata A. Komor, René Böttcher, Job van Riet, Harmen J.G. van de Werken, Stef van Lieshout, +22 more
13citations -
HiFi long-read RNA sequencing enhances clinical diagnostics in rare disorders2026 European Journal of Human Genetics article Biochemistry, Genetics and Molecular Biology Genomics and Rare Diseases Open access
Carolina Jaramillo Oquendo, Federico Ferraro, Htoo A. Wai, Heather Ferrao, Herma van der Linde, Evita Karelioti, +11 more
5citations -
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 -
Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing2022 Journal of Visualized Experiments article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Yang Ge, Lieke van Roon, H. Sophia Chen, Ruben Methorst, Marco C. DeRuiter, Szymon M. Kiełbasa, +1 more
3citations -
Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing2022 Journal of Visualized Experiments article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Yang Ge, Lieke van Roon, H. Sophia Chen, Ruben Methorst, Marco C. DeRuiter, Szymon M. Kiełbasa, +1 more
2citations -
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 -
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 -
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-Nucleus RNA Sequencing Reveals Sex-Specific Renoprotective Mechanisms in Diabetic Kidney Disease2024 Journal of the American Society of Nephrology article Medicine Chronic Kidney Disease and Diabetes
Shuya Liu, Tianran Zhang, Shun Yan Lu, Martin Strauch, Michaël Goedertier, Ivan G. Costa, +3 more
0citations -
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 -
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data2023 Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Ping‐Han Hsieh, Camila M. Lopes‐Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer
10citations -
Platelet RNA sequencing for cancer screening in patients with unprovoked venous thromboembolism: a prospective cohort study2023 Journal of Thrombosis and Haemostasis article Medicine Venous Thromboembolism Diagnosis and Management Open access
Frits I. Mulder, Noémie Kraaijpoel, Marc Carrier, Noori A.M. Guman, Luis Jara‐Palomares, Marcello Di Nisio, +20 more
13citations -
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
69citations -
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 -
Identifying differential gene expression induced by mechanical stress in cartilage of human explants using RNA-sequencing2021 Osteoarthritis and Cartilage article Medicine Osteoarthritis Treatment and Mechanisms Open access
Evelyn Houtman, Margo Tuerlings, Janne Riechelman, H. Eka D. Suchiman, Rob G. H. H. Nelissen, Y.F. Ramos, +2 more
0citations -
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