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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 -
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 -
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 -
Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease2022 Nature Genetics article Biochemistry, Genetics and Molecular Biology Genetic and Kidney Cyst Diseases Open access cited by 1 patent
Yaoxian Xu, Christoph Kuppe, Javier Perales-Patón, Sikander Hayat, Jennifer Kranz, Ali Taleb Abdallah, +33 more
67citations -
NKG2A is a late immune checkpoint on CD8 T cells and marks repeated stimulation and cell division2021 International Journal of Cancer article Immunology and Microbiology Immune Cell Function and Interaction Open access cited by 2 patents
Linda Borst, Marjolein Sluijter, Gregor Sturm, Pornpimol Charoentong, Saskia J A M Santegoets, Mandy van Gulijk, +8 more
58citations -
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 -
Metabolic profiling of material-limited cell samples by dimethylaminophenacyl bromide derivatization with UPLC-MS/MS analysis2020 Microchemical Journal article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Cornelius C.W. Willacey, Naama Karu, Amy C. Harms, Thomas Hankemeier
13citations -
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Darvish Shafighi, Szymon M. Kiełbasa, Hugo W van Kessel, Ruben A. L. de Groen, +6 more
1citations -
Microbial Invasion and Immunosuppression Drives Adenoma Progression in Early Colorectal Cancer Development2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gut microbiota and health Open access
Wei Liang, Lisa Falk, Daniele Lucarelli, Philipp Putze, Amira Metwaly, Yiran Zheng, +13 more
0citations -
Mapping the Molecular Atlas of Podocyte Response to Glucocorticoids Using Multi-Omics Analyses2023 Journal of the American Society of Nephrology conference-abstract Medicine Renal Diseases and Glomerulopathies
Martijn van den Broek, Bartholomeus T. van den Berge, Michiel F. Schreuder, Bart Smeets, Jitske Jansen
0citations -
What makes the human brain special: from cellular function to clinical translation2025 Journal of Neurophysiology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Karen M. J. van Loo, Aniella Bak, Rebecca D. Hodge, Francesco Bedogni, Julian S.B. Ramirez, Steve Emerson, +5 more
4citations -
Long-term human organotypic brain slice cultures: a detailed protocol to provide a comprehensive framework for single-neuron and neuronal network investigations2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Neuroscience and Neuropharmacology Research Open access
Aniella Bak, Henner Koch, Karen M. J. van Loo, Katharina Schmied, Birgit Gittel, Yvonne G. Weber, +4 more
1citations -
Donor-specific, but not sex-specific, signatures dominate cell-type classification in lung scRNA-seq data2026 Biochemistry and Biophysics Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Nora Ghenciulescu, Marcel J. T. Reinders, Ahmed Essam Mahfouz
0citations -
Serum proteomics of adults with acute liver failure provides mechanistic insights and attractive prognostic biomarkers2025 JHEP Reports article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Katharina Remih, Franziska-Maria Hufnagel, Anna Sophie Karl, Valerie L. Durkalski‐Mauldin, William M. Lee, Constantine Jason Karvellas, +14 more
4citations -
Exploring Parameter and Hyper-Parameter Spaces of Neuroscience Models on High Performance Computers With Learning to Learn2022 Frontiers in Computational Neuroscience article Neuroscience Neural dynamics and brain function Open access
Alper Yegenoglu, Anand Subramoney, Thorsten Hater, Cristian Jimenez-Romero, Wouter Klijn, Aarón Pérez Martín, +4 more
9citations