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An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and function types2023 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jari B. Berkhout, Delaram Poormoghadam, Chun‐Xia Yi, Andries Kalsbeek, Onno Cornelis Meijer, Ahmed Essam Mahfouz
0citations -
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and function types2024 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jari B. Berkhout, Delaram Poormoghadam, Chun‐Xia Yi, Andries Kalsbeek, Onno Cornelis Meijer, Ahmed Essam Mahfouz
0citations -
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 -
scTopoGAN: unsupervised manifold alignment of single-cell data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
1citations -
Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics2020 Circulation Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Marie A.C. Depuydt, Koen H.M. Prange, Lotte Slenders, Tiit Örd, D. Elbersen, Arjan Boltjes, +17 more
619citations -
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 -
OP0243 SINGLE-CELL RNA SEQUENCING OF ACPA-ENRICHED B CELLS REVEALED A CD11c+ ATYPICAL B CELL GENE SIGNATURE IN RHEUMATOID ARTHRITIS2025 Annals of the Rheumatic Diseases conference-abstract Medicine Rheumatoid Arthritis Research and Therapies Open access
Yasuo Nagafuchi, Linda M. Slot, Deimantė Šimaitė, Aleida M. Bakker, Erik B. van den Akker, Tom W. J. Huizinga, +3 more
0citations -
De-novoreconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters2023 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Mhaned Oubounyt, Maria L. Elkjaer, Tanja Laske, Alexander G. B. Grønning, Marcus Johannes Moeller, Jan Baumbach
8citations -
Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access
Daniel Osorio, Parastoo Shahrouzi, Xavier Tekpli, Vessela Nedelcheva Kristensen, Marieke L. Kuijjer
4citations -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
3citations -
Single-cell RNA sequencing of human fetal epicardium reveals novel markers and regulators of EMT2020 European Heart Journal article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
T J Streef, Tessa van Herwaarden, Anke M. Smits, Marie‐José Goumans
0citations -
A single-cell atlas of mouse central nervous system immune cells reveals unique infection-stage immune signatures during the progression of meningitis caused by Streptococcus suis2025 Communications Biology article Immunology and Microbiology Bacterial Infections and Vaccines Open access
Xuan Jade Jiang, Jikun Mei, Junhui Zhu, Yanyan Tian, Ziheng Li, Zengshuai Wu, +4 more
5citations -
Identification of endothelial-to-mesenchymal transition gene signatures in single-cell transcriptomics of human atherosclerotic tissue2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Marian Wesseling, Arjan Boltjes, Daniek Kapteijn, Marie A.C. Depuydt, Koen H.M. Prange, +8 more
6citations -
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Cornelis A.M. van Bergen, Ewa Szczurek
1citations -
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Cornelis A.M. van Bergen, Ewa Szczurek
0citations -
Unraveling Divergent Transcriptomic Profiles: A Comparative Single-Cell RNA Sequencing Study of Epithelium, Gingiva, and Periodontal Ligament Tissues12citations