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Multimodal single-cell profiling reveals cancer crosstalk between macrophages and stromal cells in poor prognostic cholangiocarcinoma patients2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cholangiocarcinoma and Gallbladder Cancer Studies Open access
Lara Rosaline Heij, Sikander Hayat, Konrad Reichel, Sidrah Maryam, Colm J. O’Rourke, Xiuxiang Tan, +22 more
0citations -
Single-Cell Analysis of Refractory Celiac Disease Demonstrates Inter- and Intra-Patient Aberrant Cell Heterogeneity2022 Cellular and Molecular Gastroenterology and Hepatology article Medicine Celiac Disease Research and Management Open access
Tessa Dieckman, Mette Schreurs, Ahmed Essam Mahfouz, Yvonne Kooy–Winkelaar, Andra Neefjes‐Borst, Gerd Bouma, +1 more
18citations -
Single-cell profiling reveals age-associated immune cells in atherosclerosis2023 Atherosclerosis article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Virginia Smit, J. De Mol, Frank H. Schaftenaar, Marie A.C. Depuydt, R. Postel, Diede Smeets, +13 more
2citations -
Faculty Opinions recommendation of Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation.0citations
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Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mina Shaigan, Deepika Puri, Giulia Fornero, René Krüger, Mara Steiger, Hannes Klump, +4 more
0citations -
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing2021 Genome Research preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Mohamed Keshk, Trygve E. Bakken, Jeremy A. Miller, +4 more
96citations -
Imaging‐Guided Live Single‐Cell Lipid Profiling of Leader and Follower Cells During Collective Migration of Triple‐Negative Breast Cancer Cells2026 Advanced Science article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Xiaoyue Huang, Judit González Riera, Mai Nguyen, Jeremy Broekhuis, Sylvia E. Le Dévédec, Thomas Hankemeier
0citations -
The Cell Ontology in the age of single-cell omics2026 eScholarship (California Digital Library) article 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, +29 more
7citations -
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
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WALDO: community-Wide Annotation of γδ Lymphocytes in single-cell Data, Openly benchmarked2026 Zenodo (CERN European Organization for Nuclear Research) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Farid Keramati, Moosa Rezwani, Likai Tan, David Hamilton, Zheng Song, Tao Yang, +10 more
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scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
0citations -
Integration of Mass Cytometry and Mass Spectrometry Imaging for Spatially Resolved Single Cell Metabolic Profiling2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Joana B. Nunes, Marieke E. Ijsselsteijn, Tamim Abdelaal, Rick Ursem, Manon van der Ploeg, Bart Everts, +3 more
3citations -
Single-cell, whole-embryo phenotyping of mammalian developmental disorders2023 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Oana Veronica Amarie, +35 more
41citations -
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and functional types2023 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
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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