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Eleven grand challenges in single-cell data science2020 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 2 patents
David Laehnemann, Johannes Köster, Ewa Szczurek, Davis James McCarthy, Stephanie C. Hicks, Mark D. Robinson, +45 more
1,504citations -
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data2022 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 1 patent
Daniel Dimitrov, Dénes Türei, Martín Garrido‐Rodríguez, Paul L Burmedi, James Shiniti Nagai, Charlotte Boys, +7 more
670citations -
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 RNA sequencing analysis of the human fetal epicardium results in novel epicardial-specific markers and reveals a role for CRIP1 in epicardial EMT2023 European Heart Journal article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Anke M. Smits, T J Streef, Els Groeneveld, Tessa van Herwaarden, Marie‐José Goumans
0citations -
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 -
NS-Forest: A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencing2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, +3 more
12citations -
Cell-type-specific damage scores reveal kidney and liver disease trajectories in single-cell and spatial transcriptomics2026 Cell Genomics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tsimafei Padvitski, Paula Unger Avila, He Chen, Cem Özel, Fabian Braun, Marie-Kristin Kroll, +16 more
1citations -
Post-transcriptional regulatory mechanisms in human islets inferred from cell type-specific eQTLs detected by single-cell RNA-seq2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Twan J. J. de Winter, Miha Sovrovic, Han Sun, James D. Johnson, Patrick Edward MacDonald, Anna L. Gloyn, +3 more
0citations -
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 -
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data2020 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan G. Gleixner, Manu P. Kumar, Elisabetta Mereu, +6 more
367citations -
SIRV: spatial inference of RNA velocity at the single-cell resolution2024 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
33citations -
Single-cell, whole-embryo phenotyping of mammalian developmental disorders2023 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Oana Veronica Amarie, +35 more
41citations -
Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis2020 Cell Metabolism article Biochemistry, Genetics and Molecular Biology Angiogenesis and VEGF in Cancer Open access
Kateřina Rohlenová, Jermaine Goveia, Melissa García‐Caballero, Abhishek Subramanian, Joanna Maria Kalucka, Lucas Treps, +33 more
307citations -
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 -
scDecorr: feature decorrelation based representation learning enables self-supervised alignment of multiple single-cell experiments2026 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ritabrata Sanyal, Yang Xu, Hyojin Kim, Rafael Kramann, Sikander Hayat
0citations -
SIRV: Spatial inference of RNA velocity at the single-cell resolution2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens M. Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
12citations