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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 -
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 -
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 -
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 -
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 -
High-dimensional single-cell analysis of human natural killer cell heterogeneity2024 Nature Immunology article Immunology and Microbiology Immune Cell Function and Interaction Open access
Lucas Rebuffet, Janine E. Melsen, Bertrand Escalière, Daniela Basurto-Lozada, Avinash Bhandoola, Niklas K. Björkström, +21 more
278citations -
Single-cell analysis of regions of interest (SCARI) using a photosensitive tag2021 Nature Chemical Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 1 patent
Anne M. van der Leun, Mirjam E. Hoekstra, Luuk Reinalda, Colinda L. G. J. Scheele, Mireille Toebes, Michel J. van de Graaff, +11 more
18citations -
Single-cell analysis of human fetal epicardium reveals its cellular composition and identifies CRIP1 as a modulator of EMT2023 Stem Cell Reports article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Thomas J. Streef, Esmee J. Groeneveld, Tessa van Herwaarden, Jesper Hjortnaes, Marie‐José Goumans, Anke M. Smits
16citations -
Single‐cell omics: Overview, analysis, and application in biomedical science2021 Journal of Cellular Biochemistry article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Catarina M. Stein, Ralf Weiskirchen, Frédérik Damm, Paulina M. Strzelecka
43citations -
scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access cited by 1 patent
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
41citations -
Single-cell RNA sequencing analysis of the human fetal epicardium results in novel epicardial-specific markers and reveals a role for CRIP1 in epicardial EMT2023 European Heart Journal 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 -
Single-Cell Transcriptomics Analysis of Human Small Antral Follicles2021 International Journal of Molecular Sciences article Medicine Reproductive Biology and Fertility Open access
Xueying Fan, Ioannis Moustakas, Monika Bialecka, Julieta S. del Valle, Arend W. Overeem, Leoni A. Louwé, +4 more
35citations -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
12citations