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The Cell Ontology in the age of single-cell omics2026 Scientific Data data-paper Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian D. Aevermann, Alida Avola, +28 more
0citations -
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 -
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and function types2024 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jari B. Berkhout, Delaram Poormoghadam, Chun‐Xia Yi, Andries Kalsbeek, Onno Cornelis Meijer, Ahmed Essam Mahfouz
0citations -
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and function types2024 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jari B. Berkhout, Delaram Poormoghadam, Chun‐Xia Yi, Andries Kalsbeek, Onno Cornelis Meijer, Ahmed Essam Mahfouz
0citations -
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and function types2023 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jari B. Berkhout, Delaram Poormoghadam, Chun‐Xia Yi, Andries Kalsbeek, Onno Cornelis Meijer, Ahmed Essam Mahfouz
0citations -
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 -
From Mythology to Methodology: Untargeted Single-Cell Metabolomics in R with MeDUSA2026 Journal of the American Society for Mass Spectrometry article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies
Laura Ann Castaneda, Eric Hetzel, Fercan Gül, Thomas Hankemeier
0citations -
Community-driven ELIXIR activities in single-cell omics2022 F1000Research article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Paulo Czarnewski, Ahmed Essam Mahfouz, Raffaele Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez‐Uriarte, +21 more
11citations -
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 -
Single-cell reference mapping to construct and extend cell-type hierarchies2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Lieke Michielsen, Mohammad Lotfollahi, Daniel C. Strobl, Lisa Sikkema, Marcel J. T. Reinders, Fabian Joachim Theis, +1 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 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 -
Optimized summary-statistic-based single-cell eQTL meta-analysis2025 Scientific Reports article Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Maryna Korshevniuk, Harm-Jan Westra, Roy Oelen, Monique G.P. van der Wijst, Lude Franke, Marc Jan Bonder, +31 more
3citations -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
3citations