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Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mina Shaigan, Deepika Puri, Giulia Fornero, René Krüger, Mara Steiger, Hannes Klump, +4 more
0citations -
Federated single-cell QTL meta-analysis reveals novel disease mechanisms2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Dan Kaptijn, Lieke Michielsen, Drew R. Neavin, Aida Ripoll-Cladellas, José Alquicira-Hernández, Maryna Korshevniuk, +52 more
1citations -
Differential dropout analysis captures biological variation in single-cell RNA sequencing data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
3citations -
Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Jeroen Eggermont, Thomas Höllt, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Boudewijn P. F. Lelieveldt
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
0citations -
High-Dimensional Single-Cell Analysis of Natural Killer Cell Heterogeneity in Human Blood2024 Research Square preprint Immunology and Microbiology Immune Cell Function and Interaction Open access
Eric D. Vivier, Lucas Rebuffet, Janine E. Melsen, Daniela Basurto-Lozada, Avinash Bhandoola, Niklas K. Björkström, +21 more
3citations -
PHLOWER - Single cell trajectory analysis using Hodge Decomposition2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingbo Cheng, Jitske Jansen, Katharina C. Reimer, James Shiniti Nagai, Zhijian Li, Paul Kießling, +5 more
0citations -
PILOT-GM-VAE: Patient-Level Analysis of single cell Disease Atlas with Optimal Transport of Gaussian Mixture Variational Autoencoders2025 bioRxiv (Cold Spring Harbor Laboratory) preprint 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 -
Single Cell Analysis of Regions of Interest (SCARI) using a novel photoswitchable tag2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Anne M. van der Leun, Mirjam E. Hoekstra, Luuk Reinalda, Colinda L. G. J. Scheele, Mireille Toebes, Michel J. van de Graaff, +10 more
1citations -
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Daniel Osorio, Anna Capasso, S. Gail Eckhardt, Uma P. Giri, Alexander J. Somma, Todd M. Pitts, +8 more
2citations -
scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
0citations -
Fast model-free standardization and integration of single-cell transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
0citations -
On the benchmarking of clustering algorithms and hyperparameter influence for cell type detection in single-cell RNA sequencing data2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Aleksandra Szmigiel, Ivan G. Costa, Ricardo J. G. B. Campello
2citations -
Single cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Chaido Ori, Meshal Ansari, Ilias Angelidis, Fabian Joachim Theis, Herbert B. Schiller, Micha Drukker
2citations -
Single cell RNA sequence analysis of human bone marrow samples reveals new targets for isolation of skeletal stem cells using DNA-coated gold nanoparticles2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Mesenchymal stem cell research Open access
Elloise Matthews, Stuart Lanham, Maria Eleni Kyriazi, Konstantina Alexaki, Afaf Helmy El-Sagheer, Tom Brown, +5 more
3citations -
Characterization of the human fetal rete region by single cell transcriptional analysis of gonads and mesonephros/epididymis2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Sperm and Testicular Function Open access
Jasin Taelman, Sylwia M. Czukiewska, Ioannis Moustakas, Yolanda W. Chang, Sanne Hillenius, Talia van der Helm, +3 more
8citations -
WALDO: community-Wide Annotation of γδ Lymphocytes in single-cell Data, Openly benchmarked2026 Zenodo (CERN European Organization for Nuclear Research) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Farid Keramati, Moosa Rezwani, Likai Tan, David Hamilton, Zheng Song, Tao Yang, +10 more
0citations -
Single Cell Raman and Mass Spectrometry Analysis to Probe Cellular Heterogeneity in Tamoxifen Uptake, Metabolism and Effect2025 SSRN Electronic Journal preprint 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
0citations -
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ping‐Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien‐Yu Chen, +3 more
0citations -
Integrative learning of disentangled representations from single-cell RNA-sequencing datasets2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Dorien J.M. Peters, Ahmed Essam Mahfouz
0citations -
Single Cell Analysis of Regions of Interest (SCARI) using a Novel Photoswitchable Tag2020 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Anne M. van der Leun, Mirjam E. Hoekstra, Luuk Reinalda, Colinda L. G. J. Scheele, Mireille Toebes, Michel J. van de Graaff, +10 more
0citations -
scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments0citations