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Identifying commonalities between cell lines and tumors at the single cell level using Sobolev Alignment of deep generative models2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Soufiane M. C. Mourragui, Joseph C. Siefert, Marcel J. T. Reinders, Marco Loog, Lodewyk F.A. Wessels
2citations -
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 -
Human pluripotent stem cell-derived cardiomyocytes align under cyclic strain when guided by cardiac fibroblasts2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Dylan Mostert, Bart G. W. Groenen, Leda Klouda, Robert C. J. J. Passier, Marie‐José Goumans, Nicholas A. Kurniawan, +1 more
1citations -
scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments0citations
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How cells align to structured collagen fibrils: A hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions1citations
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Cell type matching across species using protein embeddings and transfer learning2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kirti Biharie, Lieke Michielsen, Marcel J. T. Reinders, Ahmed Essam Mahfouz
0citations -
Effects of MRI on an Injectable Hydrogel with Magnetically Alignable Microstructures for Oriented Cell Growth2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Hydrogels: synthesis, properties, applications Open access
Yas Oloumi Yazdi, Tanya J. Bennet, Andrew C. Yung, Kirsten Bale, Alex Pieters, Iryna Liubchak, +5 more
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Molecular, hierarchical and acoustical cues promote mesenchymal stromal cell differentiation toward tympanic membrane regeneration2024 Research Square preprint Materials Science Electrospun Nanofibers in Biomedical Applications Open access
Shivesh Anand, Claudia Del Toro Runzer, Elizabeth Rosado Balmayor, Martijn van Griensven, Lorenzo Moroni
0citations -
A soft active matter models explains spiral epithelial cell migration on in-vivo corneas2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Kaja Kostanjevec, Rastko Sknepnek, Jon Martin Collinson, Silke Henkes
0citations -
scRIPT: a rapid, high-coverage single-cell lineage-tracing method applied to the hematoendothelial differentiation of embryonic stem cells2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Rıdvan Çeti̇n, Eric M. Bindels, Jente van Staalduinen, Lucas Kuijpers, Giulia Picco, Mathijs Arnoud Sanders, +6 more
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Human coronavirus 229E infection inactivates pyroptosis executioner gasdermin D but ultimately leads to lytic cell death partly mediated by gasdermin E2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Inflammasome and immune disorders Open access
Xavier Martiáñez–Vendrell, Jonna Bloeme, Roy Hutchinson, Coralie Guy, Andrew G. Bowie, Marjolein Kikkert
2citations -
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
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YAP1 Contributes to The Development of Contractile Force and Sarcomere Maturation in Human Pluripotent Stem Cell-Derived Cardiomyocytes2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Vladimír Vinarský, Stefania Pagliari, Cristina Mazzotti, Katerina Jirakova, Zuzana Garlíková, Enrico Di Iuri, +9 more
1citations -
Local synchronization of cilia and tissue-scale cilia alignment are sufficient for global metachronal waves2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic and Kidney Cyst Diseases Open access
Christa Ringers, Stephan Bialonski, A. S. Solov’ev, Jan N. Hansen, Mert Ege, Benjamin M. Friedrich, +1 more
2citations -
Morphoelectric Diversity and Specialization of Neuronal Cell Types in the Primate Striatum2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Xiao-Ping Liu, Rachel A. Dalley, Nelson Johansen, Agata Budzillo, Julian Thijssen, Jeremy A. Miller, +84 more
0citations -
Structural guidance in 3D microgel-in-hydrogel systems to improve chondrogenesis2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Hydrogels: synthesis, properties, applications Open access
Julia van de Kamp, Alisa C. Suturin, Claudia A. Garrido, Xiaole Tong, Jietao Xu, Nicole Kops, +6 more
0citations -
Mitotic adaptations shape acquired resistance and vulnerabilities to KIF18A inhibition in cancer2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microtubule and mitosis dynamics Open access
Sjoerd J. Klaasen, Kruno Vukušić, Michael M.R. van Gerven, Haico van Attikum, Iva M. Tolić, Martijn S. Luijsterburg
0citations -
Cross-species analyses reveal RORγt-expressing dendritic cells are a lineage of antigen presenting cells conserved across tissues2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Immunotherapy and Immune Responses Open access cited by 3 patents
Hamsa Narasimhan, Maria Lucia Richter, Ramin Shakiba, Nikos E. Papaioannou, Christina Stehle, Isabel Ulmert, +12 more
5citations -
Fabrication of Short Polymeric µFibers as Building Blocks for Anisotropic High-Throughput Compatible 3D Tissue Models2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Engineering 3D Printing in Biomedical Research Open access
Anna A. Meyer, Abdolrahman Omidinia‐Anarkoli, Michelle Harmeth, Joscha D Graeve, Karoline Rengel, Ramin Nasehi, +7 more
1citations