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Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data2024 Nature Computational Science article 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
19citations -
Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequenc-ing data analysis2020 Zenodo (CERN European Organization for Nuclear Research) dataset 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
0citations -
Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequenc-ing data analysis2020 Zenodo (CERN European Organization for Nuclear Research) dataset 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
0citations -
Cytosplore EvoViewer: Visual Analytics of Conserved Evolutionary Patterns in multi-species single-cell sequencing data2025 IEEE Pacific Visualization Conference (PacificVis) conference-paper Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Soumyadeep Basu, Morgan E. Wirthlin, Jeroen Eggermont, Thomas Kroes, Boudewijn P. F. Lelieveldt, Ed S. Lein, +2 more
0citations -
Differential analysis of binarized single-cell RNA sequencing data captures biological variation2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
0citations -
Differential analysis of binarized single-cell RNA sequencing data captures biological variation2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
0citations -
SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Fu Zhu, Rafael Kramann, Sikander Hayat, +1 more
1citations -
SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Ping Zhu, Rafael Kramann, Sikander Hayat, +1 more
1citations -
Combining Knowledge About Metabolic Networks and Single-Cell Data with Maximum Entropy2025 conference-paper Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Carola Sophia Heinzel, Johann F. Jadebeck, Elisabeth Zelle, Johannes Seiffarth, Katharina Nöh
0citations -
GraphComm predicts cell cell communication using a graph based deep learning method in single cell RNA sequencing data2025 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Emily So, Sikander Hayat, Sisira Kadambat Nair, Bo Wang, Benjamin Haibe‐Kains
6citations -
Visual cohort comparison for spatial single-cell omics-data2020 IEEE Transactions on Visualization and Computer Graphics article Computer Science Data Visualization and Analytics Open access
Antonios Somarakis, Marieke E. Ijsselsteijn, Sietse J. Luk, Boyd Kenkhuis, Noel F.C.C. de Miranda, Boudewijn P. F. Lelieveldt, +1 more
20citations -
MACA: Marker-based automatic cell-type annotation for single cell expression data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Simon J. Baumgart, Christian M. Stegmann, Sikander Hayat
2citations