Papers matching “cell trajectory inference” 22
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Untangling biological factors influencing trajectory inference from single cell data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mohammed Charrout, Marcel J. T. Reinders, Ahmed Essam Mahfouz
2citations -
Untangling biological factors influencing trajectory inference from single cell data2020 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mohammed Charrout, Marcel J. T. Reinders, Ahmed Essam Mahfouz
12citations -
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 -
scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access cited by 1 patent
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
41citations -
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 -
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 -
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 -
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 -
Tviblindi algorithm identifies branching developmental trajectories of human B cell development2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology T-cell and B-cell Immunology Open access
Marina Bakardjieva, Jan Stuchlý, Ondřej Pelák, Marjolein W. J. Wentink, Hana Glier, David Novák, +6 more
1citations -
Tviblindi algorithm identifies branching developmental trajectories of human B‐cell development and describes abnormalities in RAG‐1 and WAS patients2024 European Journal of Immunology article Immunology and Microbiology T-cell and B-cell Immunology Open access
Marina Bakardjieva, Ondřej Pelák, Marjolein W. J. Wentink, Hana Glier, David Novák, Jitka Stančíková, +7 more
5citations -
PILOT-GM-VAE: patient-level analysis of single-cell disease atlas with optimal transport of Gaussian mixture variational autoencoders2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa
0citations -
PILOT-GM-VAE: Patient-Level Analysis of single cell Disease Atlas with Optimal Transport of Gaussian Mixture Variational Autoencoders2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa
0citations -
Single-cell transcriptional diversity is a hallmark of developmental potential2020 Science article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 4 patents
Gunsagar Singh Gulati, Shaheen S. Sikandar, Daniel J. Wesche, Anoop Manjunath, Anjan Bharadwaj, Mark J. Berger, +12 more
1,715citations -
SpatialCOC: an integrative framework for spatial continuous mapping and cross-omics correction in spatial multi-omics data2026 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingxuan Li, Peisen Sun, Yisi Luo, Guancheng Zhou, Xiaofei Yang, Deyu Meng, +1 more
1citations -
Platelet-Instructed SPP1 Macrophages Drive Myofibroblast Activation in Fibrosis in a CXCL4-Dependent Manner2022 Journal of the American Society of Nephrology conference-abstract Medicine Cardiac Fibrosis and Remodeling Open access
Konrad Hoeft, Gideon J L Schaefer, David Schumacher, Hyoijn Kim, Barbara M. Klinkhammer, Christoph Kuppe, +3 more
0citations
22 results