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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 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 -
Single‐Cell Mechanical Characterization of Human Macrophages2022 Advanced NanoBiomed Research article Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Tom M. J. Evers, Vahid Sheikhhassani, Huaqi Tang, Mariëlle C. Haks, Tom H. M. Ottenhoff, Alireza Mashaghi
18citations -
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Magda Grudniewska, Dorien J.M. Peters, Ahmed Essam Mahfouz
5citations -
Multi-omic analyses in immune cell development with lessons learned from T cell development2023 Frontiers in Cell and Developmental Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Martijn Cordes, Karin Pike‐Overzet, Erik B. van den Akker, Frank J. T. Staal, Kirsten Canté-Barrett
9citations -
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery2023 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Magda Grudniewska, Dorien J.M. Peters, Ahmed Essam Mahfouz
38citations -
Donor-specific, but not sex-specific, signatures dominate cell-type classification in lung scRNA-seq data2026 Biochemistry and Biophysics Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Nora Ghenciulescu, Marcel J. T. Reinders, Ahmed Essam Mahfouz
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 -
User-friendly high-content imaging analysis on a single desktop: R package H5CellProfiler2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Steven Wink, Gerhard A. Burger, Sylvia E. Le Dévédec, Joost B. Beltman, Bob van de Water
3citations -
GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data2025 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
scACCorDiON: a clustering approach for explainable patient level cell–cell communication graph analysis2025 Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
James Shiniti Nagai, Tiago Maié, Michael T. Schaub, Ivan G. Costa
3citations -
Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions2025 Briefings in Bioinformatics review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Giulia Cesaro, James Shiniti Nagai, Gnoato Nicolò, Alice Chiodi, Gaia Tussardi, Vanessa Klöker, +6 more
44citations -
FAIR GraphRAG: A Retrieval-Augmented Generation Approach for Semantic Data Analysis2025 IEEE International Conference on Knowledge Graph (ICKG) conference-paper Computer Science Research Data Management Practices Open access
Marlena Flüh, Soo-Yon Kim, Carolin Victoria Schneider, Sandra Geisler
1citations -
LifeTime and improving European healthcare through cell-based interceptive medicine2020 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Nikolaus Rajewsky, Geneviève Almouzni, Stanislaw A. Gorski, Stein Aerts, Ido Amit, Michela Giulia Bertero, +91 more
154citations