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Single-cell immune profiling reveals thymus-seeding populations, T cell commitment, and multilineage development in the human thymus2022 Science Immunology article Immunology and Microbiology T-cell and B-cell Immunology Open access
Martijn Cordes, Kirsten Canté-Barrett, Erik B. van den Akker, Federico A. Moretti, Szymon M. Kiełbasa, Sandra A. Vloemans, +6 more
69citations -
Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer2026 Cancer Cell article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Valentin Marteau, Niloofar Nemati, Kristina Handler, Deeksha Raju, Alexander Kirchmair, Dietmar Rieder, +40 more
34citations -
Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling2024 Nature Methods article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Joana B. Nunes, Marieke E. Ijsselsteijn, Tamim Abdelaal, Rick Ursem, Manon van der Ploeg, Martin A. Giera, +4 more
92citations -
Single-Cell Multiomic Profiling of Peripheral Blood Mononuclear Cells Reveals Immune Heterogeneity and Therapeutic Target Expression in IgAN2025 Journal of the American Society of Nephrology article Medicine Renal Diseases and Glomerulopathies
Turgay Saritas, Felix Schreibing, Vivien Goepp, Teresa Maria Schreibing, Sikander Hayat, Rafael Kramann
0citations -
Single-cell profiling reveals age-associated immunity in atherosclerosis2023 Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Virginia Smit, Jill de Mol, Frank H. Schaftenaar, Marie A.C. Depuydt, Rimke J. Postel, Diede Smeets, +19 more
70citations -
Comment to: Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemia2021 Cellular and Molecular Immunology article Immunology and Microbiology Immune Cell Function and Interaction Open access
Janine E. Melsen, Gertjan Lugthart, Monique M. van Ostaijen-ten Dam, Marco W. Schilham
6citations -
Multimodal single-cell profiling reveals crosstalk between macrophages and stromal cells in poor prognostic cholangiocarcinoma patients2026 npj Precision Oncology article Medicine Cholangiocarcinoma and Gallbladder Cancer Studies Open access
Lara Rosaline Heij, Sikander Hayat, Konrad Reichel, Sidrah Maryam, Colm J. O’Rourke, Xiuxiang Tan, +27 more
3citations -
Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets2022 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 4 patents
Lukas Mathur, Bence Szalai, N. H. Du, Ramesh Utharala, Martine Ballinger, Jonathan J. M. Landry, +4 more
27citations -
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 -
Single-cell profiling reveals age-associated immune cells in atherosclerosis2023 Atherosclerosis article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Virginia Smit, J. De Mol, Frank H. Schaftenaar, Marie A.C. Depuydt, R. Postel, Diede Smeets, +13 more
2citations -
Imaging‐Guided Live Single‐Cell Lipid Profiling of Leader and Follower Cells During Collective Migration of Triple‐Negative Breast Cancer Cells2026 Advanced Science article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Xiaoyue Huang, Judit González Riera, Mai Nguyen, Jeremy Broekhuis, Sylvia E. Le Dévédec, Thomas Hankemeier
0citations -
The Cell Ontology in the age of single-cell omics2026 eScholarship (California Digital Library) article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian D. Aevermann, Alida Avola, +29 more
6citations -
Single-cell, whole-embryo phenotyping of mammalian developmental disorders2023 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Oana Veronica Amarie, +35 more
41citations -
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 -
scTopoGAN: unsupervised manifold alignment of single-cell data2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Kirti Biharie, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
6citations