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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 -
SCHNEL: scalable clustering of high dimensional single-cell data2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Paul de Raadt, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
9citations -
SCHNEL: Scalable clustering of high dimensional single-cell data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Paul de Raadt, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
2citations -
GraphHDBSCAN*: Graph-based Hierarchical Clustering on High Dimensional Single-cell RNA Sequencing Data2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Seyed Ardalan Ghoreishi, Aleksandra Szmigiel, James Shiniti Nagai, Ivan G. Costa, Arthur Zimek, Ricardo J. G. B. Campello
1citations -
A Comprehensive Workflow for Applying Single-Cell Clustering and Pseudotime Analysis to Flow Cytometry Data2020 The Journal of Immunology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Janine E. Melsen, Monique M. van Ostaijen-ten Dam, Arjan C. Lankester, Marco W. Schilham, Erik B. van den Akker
56citations -
An m/z- and intensity-based HRMS clustering algorithm targeted toward single-cell metabolomics2026 Leiden Repository (Leiden University) article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
L.D. Wevers, Laura Koldenhof, L. Castaneda, A. van der Zeeuw, H. Fass, Thomas Hankemeier, +2 more
0citations -
An m / z - and Intensity-Based HRMS Clustering Algorithm Targeted toward Single-Cell Metabolomics2026 Journal of the American Society for Mass Spectrometry article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Dirk Wevers, Laura Koldenhof, Laura Ann Hetzel, Anouschka van der Zeeuw, Hellen Fass, Thomas Hankemeier, +1 more
0citations -
scE(match): Privacy-Preserving Cluster Matching of Single-Cell Data2024 IEEE International Conference on Trust, Security and Privacy in Computing and Communications (TrustCom) conference-paper Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Johannes Lohmöller, Jannis Scheiber, Rafael Kramann, Klaus Wehrle, Sikander Hayat, Jan Pennekamp
2citations -
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data2020 Life Science Alliance article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Thin Nguyen, Buu Minh Thanh Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, +32 more
25citations -
Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations2022 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Maria Mircea, Mazène Hochane, Xueying Fan, Susana M. Chuva de Sousa Lopes, Diego Garlaschelli, Stefan Semrau
19citations -
A clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Maria Mircea, Mazène Hochane, Xueying Fan, Susana M. Chuva de Sousa Lopes, Diego Garlaschelli, Stefan Semrau
0citations -
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing2022 Bioinformatics article Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access cited by 1 patent
Hana Rozhoňová, Daniel Danciu, Stefan G. Stark, Gunnar Rätsch, André Kahles, Kjong-Van Lehmann
9citations -
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access
Hana Rozhoňová, Daniel Danciu, Stefan G. Stark, Gunnar Rätsch, André Kahles, Kjong-Van Lehmann
1citations -
Single-cell spatial transcriptomics unravels cell states and ecosystems associated with clinical response to immunotherapy2025 Journal for ImmunoTherapy of Cancer article Medicine Cancer Immunotherapy and Biomarkers Open access
Ziena Abdulrahman, Roderick C. Slieker, Daniel McGuire, Marij J.P. Welters, Mariëtte I.E. van Poelgeest, Sjoerd H. van der Burg
23citations -
Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis2021 medRxiv preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Lennart P. L. Landsmeer, Kai Cui, Marie A.C. Depuydt, Maarten C. Verwer, Joost M. Mekke, +17 more
4citations