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SpatialCOC: an integrative framework for spatial continuous mapping and cross-omics correction in spatial multi-omics data2026 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingxuan Li, Peisen Sun, Yisi Luo, Guancheng Zhou, Xiaofei Yang, Deyu Meng, +1 more
1citations -
Multi-omics single-cell spatial profiling of paediatric and adult acute myeloid leukaemia links spatial organization, molecular genetics and microenvironmental interactions
Merel van der Meulen, Joost B. Koedijk, Emma S. Pool, Eva M. Argiro, Marijn A. Scheijde-Vermeulen, Livius Penter, +12 more
0citations -
Spatial multi-omics in whole skeletal muscle reveals complex tissue architecture2024 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Clara Martínez Mir, Paola Pisterzi, Isabel de Poorter, Maria Rilou, Melissa van Kranenburg, Bram Heijs, +3 more
18citations -
Visual cohort comparison for spatial single-cell omics-data2020 IEEE Transactions on Visualization and Computer Graphics article Computer Science Data Visualization and Analytics Open access
Antonios Somarakis, Marieke E. Ijsselsteijn, Sietse J. Luk, Boyd Kenkhuis, Noel F.C.C. de Miranda, Boudewijn P. F. Lelieveldt, +1 more
20citations -
Spatial multi-omics reveals targetable immunosuppressive macrophage T-cell interactions in human AML bone marrow2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Acute Myeloid Leukemia Research Open access
Merel van der Meulen, Emma S. Pool, Alicia Perzolli, Joost B. Koedijk, Eva M. Argiro, Li‐Ting Chen, +18 more
0citations -
Spatial multi-omic map of human myocardial infarction2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Christoph Kuppe, Ricardo O. Ramirez Flores, Zhijian Li, Monica Toft Hannani, Jovan Tanevski, Maurice Halder, +13 more
78citations -
OmniPath: integrated knowledgebase for multi-omics analysis2025 Nucleic Acids Research article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Dénes Türei, Jonathan Schaul, Nicolàs Palacio‐Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, +26 more
21citations -
OmniPath: integrated knowledgebase for multi-omics analysis2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Dénes Türei, Jonathan Schaul, Nicolàs Palacio‐Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, +26 more
0citations -
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 -
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 -
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data2022 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Ricardo O. Ramirez Flores, Attila Gábor, Denis Schapiro, Julio Sáez-Rodríguez
291citations