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Identification of Kidney Cell Types in Single-Cell RNA Sequencing and Single-Nucleus RNA Sequencing Data Using Machine-Learning Algorithms2024 Journal of the American Society of Nephrology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Siddharth Madapoosi, Adam Tisch, Jan Rosa, Sean F. Eddy, Abhijit S. Naik, Christine P. Limonte, +8 more
0citations -
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 -
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 -
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 -
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 -
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 -
MASI enables fast model-free standardization and integration of single-cell transcriptomics data2023 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
4citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Kirti Biharie, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
6citations -
Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data2022 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tommaso Andreani, Linda M. Slot, Samuel Gabillard, Carsten Strübing, Yaligara Veeranagouda, Aleida M. Bakker, +5 more
14citations -
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 -
Differential analysis of binarized single-cell RNA sequencing data captures biological variation2021 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
29citations -
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories2025 Nature Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingbo Cheng, Jitske Jansen, Katharina C. Reimer, Vincent P. Grande, James Shiniti Nagai, Zhijian Li, +6 more
9citations -
Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Sidrah Maryam, Martin Manolov, Rafael Kramann, Sikander Hayat
0citations -
Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen2021 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Zhijian Li, Christoph Kuppe, Susanne Maria Ziegler, Mingbo Cheng, Nazanin Kabgani, Sylvia Menzel, +3 more
141citations -
Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling2022 PLoS Computational Biology article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Niklas Kolbe, Lorenz Hexemer, Lukas-Malte Bammert, Alexander Loewer, Mária Lukáčová-Medviďová, Stefan Legewie
9citations -
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