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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 -
Tracking one-in-a-million: Large-scale benchmark for microbial single-cell tracking with experiment-aware robustness metrics2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Johannes Seiffarth, Luisa Blöbaum, Angelo Jovin Yamachui Sitcheu, Ralf Mikut, Hanno Scharr, Alexander Grünberger, +1 more
0citations -
Enabling high-sensitivity live single-cell mass spectrometry using an integrated electrical lysis and nano electrospray ionization interface2024 Analytica Chimica Acta article Chemistry Mass Spectrometry Techniques and Applications Open access
Kanchana Pandian, Luís Daniel de Aguiar Homem e Almeida de Matos, Laura Ann Hetzel, Raphaël Zwier, Charelle Schubert, Jayaprakash Karuppusamy, +3 more
7citations -
SIngle cell level Genotyping Using scRna Data (SIGURD)2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Martin Graßhoff, Milena Kalmer, Nicolas Chatain, Kim Kricheldorf, Angela Maurer, Ralf Weiskirchen, +2 more
0citations -
Single-cell immune multi-omics and repertoire analyses in pancreatic ductal adenocarcinoma reveal differential immunosuppressive mechanisms within different tumour microenvironments2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Pancreatic and Hepatic Oncology Research Open access
Shivan Sivakumar, Ashwin Jainarayanan, Edward H. Arbe-Barnes, Piyush Kumar Sharma, Máire Ní Leathlobhair, Sakina Amin, +25 more
4citations -
SIngle cell level Genotyping Using scRna Data (SIGURD)2024 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Martin Graßhoff, Milena Kalmer, Nicolas Chatain, Kim Kricheldorf, Angela Maurer, Ralf Weiskirchen, +2 more
2citations -
QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations2023 Cell Reports article Biochemistry, Genetics and Molecular Biology Amino Acid Enzymes and Metabolism Open access
Leonard R. Pelgrom, Gavin M. Davis, Simon O’Shaughnessy, Sander I. van Kasteren, David K. Finlay, Linda V. Sinclair
34citations -
Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Alexandra de la Porte, Julia Schröder, Moritz Thomas, Johanna Geuder, Michael Sterr, Leslie E. Sanderson, +5 more
1citations -
Single-Cell Roadmap of Early Hemato-Endothelial Development: Functions of Atf3, Zfp711 and Bcl6b2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Hematopoietic Stem Cell Transplantation Open access
Rıdvan Çeti̇n, Giulia Picco, Jente van Staalduinen, Eric M. Bindels, Remco Michiel Hoogenboezem, Gregory van Beek, +7 more
0citations -
DART: A design-aware microfluidic chip paradigm for real-time live-cell image analysis2026 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Johannes Seiffarth, Matthias Pesch, Lukas Scholtes, Dietrich Kohlheyer, Hanno Scharr, Katharina Nöh
0citations -
Human and murine fibroblast single-cell transcriptomics reveals fibroblast clusters are differentially affected by ageing and serum cholesterol2023 Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Kim van Kuijk, Ian R McCracken, Renée J. H. A. Tillie, S. Asselberghs, Dlzar Ali Kheder, Stan Muitjens, +22 more
48citations -
Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes2020 BMC Bioinformatics article Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Lu Cao, Andries D. van der Meer, Fons J. Verbeek, Robert C. J. J. Passier
14citations -
PILOT-GM-VAE: Patient-Level Analysis of Single Cell Disease Atlas with Optimal Transport of Gaussian Mixtures Variational Autoencoders0citations
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EAP4EMSIG - Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cells Analysis2024 conference-paper Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Nils Friederich, Angelo Jovin Yamachui Sitcheu, Annika Nassal, Matthias Pesch, Erenus Yildiz, Maximilian Beichter, +9 more
1citations -
User-friendly high-content imaging analysis on a single desktop: R package H5CellProfiler2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Steven Wink, Gerhard A. Burger, Sylvia E. Le Dévédec, Joost B. Beltman, Bob van de Water
3citations -
Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis2021 Journal of Proteome Research article Chemistry Advanced Proteomics Techniques and Applications Open access
Sara Kassem, Kyra van der Pan, Anniek L. de Jager, Brigitta A. E. Naber, Inge F. de Laat, Alesha Louis, +3 more
37citations