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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 -
A Comprehensive Workflow for Applying Single-Cell Clustering and Pseudotime Analysis to Flow Cytometry Data2020 The Journal of Immunology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Janine E. Melsen, Monique M. van Ostaijen-ten Dam, Arjan C. Lankester, Marco W. Schilham, Erik B. van den Akker
56citations -
Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mina Shaigan, Deepika Puri, Giulia Fornero, René Krüger, Mara Steiger, Hannes Klump, +4 more
0citations -
PILOT-GM-VAE: patient-level analysis of single-cell disease atlas with optimal transport of Gaussian mixture variational autoencoders2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa
0citations -
Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis2023 Frontiers in Microbiology article Engineering Microfluidic and Capillary Electrophoresis Applications Open access
Keitaro Kasahara, Markus Leygeber, Johannes Seiffarth, Karina Ruzaeva, Thomas Drepper, Katharina Nöh, +1 more
16citations -
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 -
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data2020 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan G. Gleixner, Manu P. Kumar, Elisabetta Mereu, +6 more
367citations -
Optimized summary-statistic-based single-cell eQTL meta-analysis2025 Scientific Reports review Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Maryna Korshevniuk, Harm-Jan Westra, Roy Oelen, Monique G.P. van der Wijst, Lude Franke, Marc Jan Bonder, +31 more
3citations -
Federated single-cell QTL meta-analysis reveals novel disease mechanisms2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Dan Kaptijn, Lieke Michielsen, Drew R. Neavin, Aida Ripoll-Cladellas, José Alquicira-Hernández, Maryna Korshevniuk, +52 more
1citations -
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 -
Differential dropout analysis captures biological variation in single-cell RNA sequencing data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
3citations -
Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Jeroen Eggermont, Thomas Höllt, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Boudewijn P. F. Lelieveldt
2citations -
MeDUSA: Taming your metabolic data sets using an R-package for data processing of Direct Infusion Untargeted Single-Cell Analysis0citations
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MeDUSA: Taming your metabolic data sets using an R-package for data processing of Direct Infusion Untargeted Single-Cell Analysis0citations
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Single-cell analysis of innate immune cell mechanics: an application to cancer immunology2024 Materials Advances article Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Tom M. J. Evers, Antoinette van Weverwijk, Karin E. de Visser, Alireza Mashaghi
8citations -
Unveiling the Impact of Microglial Cells in Alzheimer's Disease Pathogenesis: Insights from Single-Cell RNA-seq Analysis and In Vivo Validation2024 Research Square preprint Neuroscience Neuroinflammation and Neurodegeneration Mechanisms Open access
Nima Sanadgol, Adib Miraki Feriz, Laya Ravanjoo, Mohammad Haddadi, Cordian Beyer, Adib Zendedel, +1 more
0citations -
Single-cell analysis reveals chemokine-mediated differential regulation of monocyte mechanics2021 iScience article Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access cited by 1 patent
Tom M. J. Evers, Vahid Sheikhhassani, Mariëlle C. Haks, Cornelis Storm, Tom H. M. Ottenhoff, Alireza Mashaghi
30citations -
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
0citations