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Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Sidrah Maryam, Martin Manolov, Rafael Kramann, Sikander Hayat
0citations -
Reference-based cell type matching of spatial transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. F. Lelieveldt, Brian Long, Tamim Abdelaal, +12 more
5citations -
SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Tamim Abdelaal, Thomas Höllt, Boudewijn P. F. Lelieveldt
2citations -
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain2023 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. F. Lelieveldt, Brian Long, Tamim Abdelaal, +12 more
20citations -
SpaceWalker enables interactive gradient exploration for spatial transcriptomics data2023 Cell Reports Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Mitchell M. de Boer, Tamim Abdelaal, Thomas Höllt, +1 more
4citations -
Cell-type-specific damage scores reveal kidney and liver disease trajectories in single-cell and spatial transcriptomics2026 Cell Genomics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tsimafei Padvitski, Paula Unger Avila, He Chen, Cem Özel, Fabian Braun, Marie-Kristin Kroll, +16 more
1citations -
A community-based transcriptomics classification and nomenclature of neocortical cell types2020 Nature Neuroscience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Rafael Yuste, Michael Hawrylycz, Nadia Aalling, Argel Aguilar‐Valles, Detlev Arendt, Rubén Armañanzas, +59 more
30citations -
MASI enables fast model-free standardization and integration of single-cell transcriptomics data2023 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
4citations -
GRIDGENE: Guided Region Identification based on Density of GENEs – a transcript density-based approach to characterize tissues by spatial transcriptomics2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ana Marta Sequeira, Marieke E. Ijsselsteijn, Miguel Rocha, Jessica P Roelands, Noel F.C.C. de Miranda
3citations -
Fast model-free standardization and integration of single-cell transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
0citations -
GRIDGENE: Guided Region Identification based on Density of GENEs—a transcript density-based approach to characterize tissues by spatial transcriptomics2026 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ana Marta Sequeira, Marieke E. Ijsselsteijn, M Rocha, Jessica P Roelands, Noel F.C.C. de Miranda
0citations -
Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics2020 Circulation Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Marie A.C. Depuydt, Koen H.M. Prange, Lotte Slenders, Tiit Örd, D. Elbersen, Arjan Boltjes, +17 more
619citations -
Single-cell spatial transcriptomics unravels cell states and ecosystems associated with clinical response to immunotherapy2025 Journal for ImmunoTherapy of Cancer article Medicine Cancer Immunotherapy and Biomarkers Open access
Ziena Abdulrahman, Roderick C. Slieker, Daniel McGuire, Marij J.P. Welters, Mariëtte I.E. van Poelgeest, Sjoerd H. van der Burg
23citations -
962 Single-cell spatial in situ transcriptomics unravels vulvar HSIL composition associated with complete response to therapeutic vaccination2023 Regular and Young Investigator Award Abstracts conference-abstract Medicine Cervical Cancer and HPV Research Open access
Ziena Abdulrahman, Mariëtte I.E. van Poelgeest, Marij J.P. Welters, Sjoerd van der Burg
0citations -
Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis2021 European Heart Journal Open article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Lennart P. L. Landsmeer, Kai Cui, Marie A.C. Depuydt, Maarten C. Verwer, Joost M. Mekke, +17 more
77citations -
Identification of endothelial-to-mesenchymal transition gene signatures in single-cell transcriptomics of human atherosclerotic tissue2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Marian Wesseling, Arjan Boltjes, Daniek Kapteijn, Marie A.C. Depuydt, Koen H.M. Prange, +8 more
6citations -
Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis2021 medRxiv preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Lennart P. L. Landsmeer, Kai Cui, Marie A.C. Depuydt, Maarten C. Verwer, Joost M. Mekke, +17 more
4citations -
161 Single-cell spatial in situ transcriptomics unravels vulvar HSIL composition associated with complete response to therapeutic vaccination2022 Regular and Young Investigator Award Abstracts conference-abstract Medicine Cervical Cancer and HPV Research Open access
Ziena Abdulrahman, Mariette I. van Poelgeest, Marij JP Welters, Sjoerd H. van der Burg
0citations -
Spatial transcriptomics defines the mechanisms of hiPSC-derived stem cell-mediated repair in human articular cartilage2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Osteoarthritis Treatment and Mechanisms Open access
Y.F. Ramos, Sayedeh Sana Sayedipour, Georgina Shaw, Margo Tuerlings, Timo Schomann, H. Eka D. Suchiman, +7 more
0citations