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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 -
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 -
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 -
Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing2022 Journal of Visualized Experiments article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Yang Ge, Lieke van Roon, H. Sophia Chen, Ruben Methorst, Marco C. DeRuiter, Szymon M. Kiełbasa, +1 more
3citations -
Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing2022 Journal of Visualized Experiments article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Yang Ge, Lieke van Roon, H. Sophia Chen, Ruben Methorst, Marco C. DeRuiter, Szymon M. Kiełbasa, +1 more
2citations -
Identification of kidney cell types in scRNA-seq and snRNA-seq data using machine learning algorithms2024 Heliyon article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Adam Tisch, Siddharth Madapoosi, Stephen R. Blough, Jan Rosa, Sean F. Eddy, Laura H. Mariani, +9 more
3citations -
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 -
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 -
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells2021 Genome Medicine article Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, +5 more
10citations -
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, +5 more
4citations -
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Cornelis A.M. van Bergen, Ewa Szczurek
1citations -
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Cornelis A.M. van Bergen, Ewa Szczurek
0citations -
CellGOSSIP (Cell-specific Graph Operation Strategy on Signaling of Intracellular Pathways) datasets2026 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Giulia Cesaro, James S. Nagai, Giacomo Baruzzo, Barbara Di Camillo, Ivan G. Costa
0citations -
CellGOSSIP (Cell-specific Graph Operation Strategy on Signaling of Intracellular Pathways) datasets2026 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Giulia Cesaro, James S. Nagai, Giacomo Baruzzo, Barbara Di Camillo, Ivan G. Costa
0citations -
Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yiyi Cheng, Toby Kettlewell, Ross F Laidlaw, Olympia M Hardy, Andrew McCluskey, Thomas D. Otto, +1 more
0citations -
Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq2026 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yiyi Cheng, Toby Kettlewell, Ross F Laidlaw, Olympia M Hardy, A. McCluskey, Thomas D. Otto, +1 more
0citations -
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain2023 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. F. Lelieveldt, Brian Long, Tamim Abdelaal, +12 more
20citations