Papers matching “spatial transcriptomics” 146
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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 -
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 -
Evaluating exon-skipping therapies targeting the central nervous system in Duchenne muscular dystrophy using high-resolution spatial transcriptomics2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Sharon I. de Vries, Laura G.M. Heezen, Ophélie Vacca, Mathilde Doisy, Annemieke M Aartsma-Rus, Maaike van Putten, +3 more
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 -
Single-cell and spatial transcriptomics resolve airway obliteration in bronchiolitis obliterans syndrome2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Transplantation: Methods and Outcomes Open access
Jannik Ruwisch, Hande Yilmaz, Leonard Christian, Lavinia Neubert, Lena Maureen Leiber, Annalea Brüggemann, +29 more
0citations -
Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Laura G.M. Heezen, Tamim Abdelaal, Maaike van Putten, Annemieke M Aartsma-Rus, Ahmed Essam Mahfouz, Pietro Spitali
5citations -
GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
spacedeconv: deconvolution of tissue architecture from spatial transcriptomics2024 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Constantin Zackl, Maria Zopoglou, Reto Stauffer, Markus Außerhofer, Marieke E. Ijsselsteijn, Gregor Sturm, +2 more
4citations -
Same-section spatial metabolo-transcriptomics using Stereo-meta-seq reveals DHA-driven kidney maturation2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Roan H van Scheppingen, Baihua Wu, Yumeng Zhang, Sytske Schep, Ulli Winter, Yilong Zou, +9 more
0citations -
A multicenter spatial transcriptomics atlas of human tuberculosis and non-tuberculous mycobacterial disease2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Tuberculosis Research and Epidemiology Open access
Xun Jiang, Leonard Christian, Liang Zhou, Xiaoyi Zheng, Nienke van Unen, Lavinia Neubert, +14 more
1citations -
Spatial transcriptomics uncovers hybrid, pro-inflammatory and pro-fibrotic cellular niches in pulmonary granuloma of patients with chronic sarcoidosis2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Sarcoidosis and Beryllium Toxicity Research Open access
Leonard Christian, Hande Yilmaz, Jannik Ruwisch, Leon Giercke, Benjamin Seeliger, Jan C. Kamp, +16 more
3citations -
Inferring spatially transient gene expression pattern from spatial transcriptomic studies2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jan Kueckelhaus, Jasmin von Ehr, Vidhya Madapusi Ravi, Paulina Will, Kevin Joseph, Jürgen Beck, +4 more
53citations -
Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
28citations -
SIRV: Spatial inference of RNA velocity at the single-cell resolution2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens M. Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
12citations -
A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Madeleine N. Hewitt, Meghan A. Turner, Nelson Johansen, Delissa McMillen, Shu Dan, Mike DeBerardine, +46 more
8citations -
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 -
Spatial patterning of transcriptional and regulatory programs in the primate subcortex2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shu Dan, Meghan A. Turner, Michael DeBerardine, Lakme Caceres, Victor E. Nieto-Caballero, Jessica Schembri, +27 more
2citations -
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 Transcriptomic Characterization of Novel Pathologic Niches in IPF2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis Open access
Christoph H. Mayr, Diana Santacruz, Sebastian Jarosch, Charlotte Lempp, Lavinia Neubert, Berenice Rath, +7 more
1citations