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Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single‐cell metabolomics2023 Electrophoresis article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Dirk Wevers, Rawi Ramautar, Charles Clark, Thomas Hankemeier, Ahmed Ali
13citations -
Endothelial Recovery in Bare Metal Stents and Drug-Eluting Stents on a Single-Cell Level2021 Arteriosclerosis Thrombosis and Vascular Biology article Medicine Coronary Interventions and Diagnostics Open access
Anne Cornelissen, Liang Guo, Raquel Fernandez, Michael C. Kelly, Christine Janifer, Salome H. Kuntz, +9 more
20citations -
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 -
A single-cell atlas of mouse central nervous system immune cells reveals unique infection-stage immune signatures during the progression of meningitis caused by Streptococcus suis2025 Communications Biology article Immunology and Microbiology Bacterial Infections and Vaccines Open access
Xuan Jade Jiang, Jikun Mei, Junhui Zhu, Yanyan Tian, Ziheng Li, Zengshuai Wu, +4 more
7citations -
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
4citations -
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
1citations -
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 -
Tracking One-in-a-Million: Large-Scale Benchmark for Microbial Single-Cell Tracking with Experiment-Aware Robustness Metrics2025 RWTH Publications (RWTH Aachen) book-chapter Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Johannes Seiffarth, Luisa Blöbaum, Richard Dominik Paul, Nils Friederich, Angelo Jovin Yamachui Sitcheu, Ralf Mikut, +2 more
0citations -
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)2023 Molecular Systems Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, Roman David Bülow, Christoph Kuppe, David Laurin Hölscher, Mingbo Cheng, +10 more
36citations -
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, Roman David Bülow, Christoph Kuppe, David Laurin Hölscher, Mingbo Cheng, +9 more
8citations -
Single-cell T cell receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T cells2023 Nature Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Marie A.C. Depuydt, Frank H. Schaftenaar, Koen H.M. Prange, Arjan Boltjes, Esmeralda Hemme, Lucie Delfos, +14 more
96citations -
SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Ping Zhu, Rafael Kramann, Sikander Hayat, +1 more
1citations -
3074 – SINGLE CELL TRANSCRIPTOMIC ANALYSIS COMBINED WITH MACHINE LEARNING IDENTIFIES HSC-LIKE CELLS DIFFERENTIATED IN VITRO FROM HUMAN IPSCS.2020 Experimental Hematology article Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Patrick S. Stumpf, Prakash Ramachandran, Sara Tamagno, Ann C. Babtie, Alexander Medvinsky, Katrin Ottersbach, +2 more
0citations -
Unraveling Divergent Transcriptomic Profiles: A Comparative Single-Cell RNA Sequencing Study of Epithelium, Gingiva, and Periodontal Ligament Tissues12citations
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SciViewer- An interactive browser for visualizing single cell datasets2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Dhawal S. Jain, Sikander Hayat, Joydeep Charkaborty, Pooja Srinivasa, Michael H. Cho, Edwin K. Silverman, +2 more
1citations -
Cytosplore EvoViewer: Visual Analytics of Conserved Evolutionary Patterns in multi-species single-cell sequencing data2025 IEEE Pacific Visualization Conference (PacificVis) conference-paper Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Soumyadeep Basu, Morgan E. Wirthlin, Jeroen Eggermont, Thomas Kroes, Boudewijn P. F. Lelieveldt, Ed S. Lein, +2 more
1citations