Papers matching “spatial omics” in Single-cell and spatial transcriptomics 50
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Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data2021 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Attila Gábor, Ricardo Ramirez Flores, Denis Schapiro, Julio Sáez-Rodríguez
10citations -
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 -
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 -
Peer Review Report For: Community-driven ELIXIR activities in single-cell omics [version 1; peer review: 2 approved with reservations]2023 peer-review 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
0citations -
Single‐cell omics: Overview, analysis, and application in biomedical science2021 Journal of Cellular Biochemistry article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Catarina M. Stein, Ralf Weiskirchen, Frédérik Damm, Paulina M. Strzelecka
43citations -
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering2026 Nature Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jieran Sun, Kirti Biharie, Peiying Cai, Niklas Müller‐Bötticher, Paul Kießling, Meghan A. Turner, +48 more
4citations -
Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies2020 Frontiers in Oncology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 2 patents
Natasja L. De Vries, Ahmed Essam Mahfouz, Frits Koning, Noel F.C.C. de Miranda
60citations -
AtlasOT - The Fused Unbalanced Gromov-Wasserstein for Multimodal Integration of Disease Atlases2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kai Peng, Mayra L. Ruiz Tejada Segura, Barthélémy Caron, Christoph Kuppe, James Shiniti Nagai, Ivan G. Costa
0citations -
Semi-automated background removal limits loss of data and normalises the images for downstream analysis of imaging mass cytometry data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Marieke E. Ijsselsteijn, Antonios Somarakis, Boudewijn P. F. Lelieveldt, Thomas Höllt, Noel F.C.C. de Miranda
2citations -
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ping‐Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien‐Yu Chen, +3 more
0citations -
LifeTime and improving European healthcare through cell-based interceptive medicine2020 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Nikolaus Rajewsky, Geneviève Almouzni, Stanislaw A. Gorski, Stein Aerts, Ido Amit, Michela Giulia Bertero, +91 more
154citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Kirti Biharie, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
6citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
1citations -
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, +3 more
0citations -
Image-guided alignment of consecutive multi-modal tissue slides2026 Cell Reports Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Benedetta Manzato, Claudio Novella-Rausell, Gangqi Wang, Nina Ogrinc, Rosalie G. J. Rietjens, Marleen E Jacobs, +3 more
0citations -
Atlas-scale spatially aware clustering with support for 3D and multimodal data using SpatialLeiden2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Niklas Müller‐Bötticher, Alexander Malt, Paul Kießling, Roland Eils, Christoph Kuppe, Naveed Ishaque
0citations -
Best practices for single-cell analysis across modalities2023 Nature Reviews Genetics review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 7 patents
Lukas Heumos, Anna Christina Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia, +36 more
1,043citations -
human heart failure atlas2027 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tore Bleckwehl, David Schumacher, Charlotte Heymanns, Alexander Leunig, Thomas Rathner, Ziche Chen, +22 more
0citations -
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
0citations