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Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq2026 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yiyi Cheng, Toby Kettlewell, Ross F Laidlaw, Olympia M Hardy, A. McCluskey, Thomas D. Otto, +1 more
0citations -
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells2021 Genome Medicine article Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, +5 more
10citations -
Kidney Tubuloid Model to Study Aquaporin 2-Mediated Water Transport in the Collecting Duct2024 Journal of the American Society of Nephrology article Biochemistry, Genetics and Molecular Biology Ion Transport and Channel Regulation
Joost G.J. Hoenderop, Emre Dilmen, Charlotte J.A. Olde Hanhof, Femke Latta, Marianne Christina Verhaar, Jeroen H. F. de Baaij, +1 more
0citations -
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, +5 more
4citations -
A bypass flow model to study endothelial cell mechanotransduction across diverse flow environments2024 Materials Today Bio article Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Zhuotao Xiao, Rudmer J. Postma, Anton Jan van Zonneveld, Bernard M. van den Berg, Nicholas A. White, Huybert J. F. van de Stadt, +4 more
3citations -
Investigating T cell Recruitment in Atherosclerosis using a novel Human 3D Tissue-Culture Model reveals the role of CXCL12 in intraplaque neovessels2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Laura Parma, Nadja Sachs, Zhaolong Adrian Li, Nikola Sobczak, Bram Slütter, Lars Mäegdefessel, +3 more
1citations -
A Bypass Flow Model to Study Endothelial Cell Mechanotransduction across Diverse Flow Environments2024 Journal of the American Society of Nephrology article Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions
Zhuotao Xiao, Rudmer J. Postma, Anton Jan van Zonneveld, Bernard M. van den Berg, Nicholas A. White, Asad M. Mirza, +3 more
0citations -
A community-based transcriptomics classification and nomenclature of neocortical cell types2020 Nature Neuroscience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Rafael Yuste, Michael Hawrylycz, Nadia Aalling, Argel Aguilar‐Valles, Detlev Arendt, Rubén Armañanzas, +59 more
30citations -
A gastruloid model of the interaction between embryonic and extra-embryonic cell types2022 Journal of Tissue Engineering article Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Noémie M. L. P. Bérenger-Currias, Maria Mircea, Esmée Adegeest, Patrick R. van den Berg, Marleen Feliksik, Mazène Hochane, +3 more
26citations -
Analyzing Cell Type-Specific Dynamics of Metabolism in Kidney Repair2022 Journal of the American Society of Nephrology article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies
Ton J. Rabelink, Gangqi Wang, Bram Heijs, Sarantos Kostidis, Ahmed Essam Mahfouz, Rosalie G. J. Rietjens, +8 more
4citations -
Single cell guided deconvolution of bulk transcriptomics recapitulates differentiation stages of acute myeloid leukemia and predicts drug response2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Acute Myeloid Leukemia Research Open access
Emin Onur Karakaslar, Jeppe F. Severens, Elena Sánchez‐López, Peter A. van Veelen, Mihaela Zlei, Jacques J. M. van Dongen, +7 more
1citations -
NuclearIDTracker resolves intestinal cell identity and lineage dynamics through nuclear phenotypic signatures2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Nguyen BT Nguyen, Rutger N.U. Kok, Sira Gevers, Max A. Betjes, Lukas Ritter, Danny Feijtel, +5 more
0citations -
Privacy-Preserving Detection of Rare Disease-Associated Cell Subsets via Secure Multi-Party Computation2026 arXiv (Cornell University) preprint Computer Science Privacy-Preserving Technologies in Data Open access
Şeyma Selcan Mağara, Esther Havemann, Debora Jutz, Ali Burak Ünal, Mete Akgün
0citations -
Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes2020 BMC Bioinformatics article Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Lu Cao, Andries D. van der Meer, Fons J. Verbeek, Robert C. J. J. Passier
14citations -
Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors2023 iScience article Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Chaido Ori, Meshal Ansari, Ilias Angelidis, Ruth Olmer, Ulrich Martin, Fabian Joachim Theis, +2 more
4citations -
Tissue microenvironment dictates the state of human induced pluripotent stem cell-derived endothelial cells of distinct developmental origin in 3D cardiac microtissues2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Xu Cao, Maria Mircea, Francijna E. van den Hil, Hailiang Mei, Katrin Neumann, Konstantinos Anastassiadis, +3 more
1citations -
Identification of CD8+ T cell PRDM1 in high-risk human plaques and its regulatory role in murine lesion development2022 Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Han Young Jin, Chang Wei Lu, Jan Nagenborg, Marco Manca, Joël Karel, Rachel Cavill, +7 more
0citations