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Search · four archives
21 papers · ranked by Valyu relevance
Cameron G. Williams, Hyun Jae Lee, Takahiro Asatsuma, Roser Vento-Tormo + 1 more
'Roser Vento-Tormo' 'Ashraful Haque'] Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over the past decade, particularly in developmental biology, cancer, immunology, and neuroscience. Most commercially available scRNA-seq protocols require cells to be recovered intact and viable…
Wenhao Li, Yuan Zhou, Andrés Moya
Title: Simple Summary Spatial transcriptomics allows researchers to measure gene expression while preserving the positions of cells and molecules within tissues. Imaging-based spatial transcriptomics methods do this by directly visualizing RNA molecules or amplified signals in tissue samples, often at single-cell or…
Yoonji Lee, Mingyu Lee, Yoojin Shin, Kyuri Kim + 2 more
'Elisa De Paolis'] Spatial omics integrates molecular profiling with spatial tissue context, enabling high-resolution analysis of gene expression, protein interactions, and epigenetic modifications. This approach provides critical insights into disease mechanisms and therapeutic responses, with applications in cancer…
Lizhi He, Bin Wang, Timothy Wiggin, Renchao Chen + 18 more
Spatial transcriptomics has emerged as a transformative approach for elucidating tissue architecture, cellular heterogeneity, and disease mechanisms by preserving the spatial context of gene expression in cells. Despite these advances, many spatial transcriptomic methods underperform in archival or clinically relevant…
Bowen Zheng, Lin Fang
A major feature of cancer is the heterogeneity, both intratumoral and intertumoral. Traditional single-cell techniques have given us a comprehensive understanding of the biological characteristics of individual tumor cells, but the lack of spatial context of the transcriptome has limited the study of cell-to-cell…
Weizheng Liang, Zhenpeng Zhu, Dandan Xu, Peng Wang + 7 more
The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome…
Zhiwei Fan, Tiangang Wang, Kexin Huang, Binwu Ying + 1 more
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping of cellular heterogeneity, tissue architecture, and dynamic biological…
Haoxiu Wang, Xinwang Yang, Siheng Wang, Zhe Yang + 23 more
Spatial omics technologys help overcome key limitations of conventional omics approaches that lack spatial information, by providing a panoramic perspective from the molecular level to the microenvironment scale for addressing spatially resolved biological questions in life sciences. With the rapid advancement of this…
Esra Busra Isik, Yusuf Hakan Usta, Haozhe Liu, Maryam Riazi + 4 more
Recent developments in spatial omics technologies have enabled the generation of high dimensional molecular data, such as transcriptomes, proteomes, and epigenomes, within their spatial tissue context, either through cocprofiling on the same slice or through serial tissue sections. These datasets, which are often…
Ebtesam A. Abdel-Shafy, Moussa Kassim, Alessia Vignoli, Farag Mamdouh + 17 more
Spatial transcriptomics provides researchers with a powerful tool to investigate gene expression patterns within their native positional context in tissues, revealing intricate cellular relationships. However, analyzing spatial transcriptomics data presents unique challenges due to their high dimensionality and…
Archibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn, Hailing Zong + 12 more
Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics…
José Camacho, Michael Armstrong, Luz García, Caridad Díaz + 1 more
'Carolina Gómez‐Llorente'] Over the past few years, technological advances have allowed for measurement of omics data at the cell level, creating a new type of data generally referred to as single-cell (sc) omics. On the other hand, the so-called spatial omics are a family of techniques that generate biological…
Brian Long, Jeremy A. Miller, The SpaceTx Consortium
| Name | Affiliation | ORCID | | --- | --- | --- | | Boudewijn Lelieveldt | | 0000-0001-8269- | | | Leiden University Medical Center; Delft University of Technology | 7603 | | | Massachusetts Institute of Technology; Broad Institute of MIT and | 0000-0003-4201- | | Charles Comiter | Harvard; Massachusetts General…
Ninghui Hao, Xinxing Yang, Boshen Yan, Dong Li + 6 more
Spatial omics (SO) technologies enable spatially resolved molecular profiling, while hematoxylin and eosin (H&E) imaging remains the gold standard for morphological assessment in clinical pathology. Recent computational advances increasingly place H&E images at the center of SO analysis, bridging morphology with…
Aditya Venkatramani, Didar Ciftci, Limor Cohen, Christopher Li + 2 more
Spatial omics has brought a fundamental change in the way that we study cell and tissue biology in health and disease. Among various spatial omics methods, genome-scale imaging allows transcriptomic, 3D-genomic, and epigenomic profiling of individual cells with high spatial (subcellular) resolution but often requires a…
Xun Ding, Kendall Hoff, Radha Swaminathan, Mikaela Koutrouli + 13 more
Spatial transcriptomics enables analysis of gene expression that is spatially resolved within a tissue section, making it possible to elucidate the relationship between individual cells within the context of the tissue. This transformative technology enables researchers to better understand gene function within the…
Yingying Lu, Qin Chen, Lingling An
The advent of spatial transcriptomics technology has allowed for the acquisition of gene expression profiles with multi-cellular resolution in a spatially resolved manner, presenting a new milestone in the field of genomics. However, the aggregate gene expression from heterogeneous cell types obtained by these…
Authors not listed
Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) is a powerful technique for molecular analysis of surfaces; however, its application of single cell studies has not been previously published. In the current work, a commercial DESI setup (DESI XS) coupled to a mass spectrometer was used to analyze…
Hang Hu, Jyothsna Padmakumar Bindu, Julia Laskin
Mass spectrometry imaging (MSI) is widely used for the label-free molecular mapping of biological samples. The identification of co-localized molecules in MSI data is crucial to the understanding of biochemical pathways. However, complex MSI data are too large for manual annotation but too small for training deep…
Authors not listed
A thorough understanding of drug pharmacokinetics and target interaction within complex biological environments is critical for successful drug discovery. Quantitative matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI; qMSI) presents a promising avenue for such investigations. While…
Wojciech Michno, Patrick Wehrli, Srinivas Koutarapu, Christian Marsching + 9 more
Understanding of Alzheimer’s disease (AD) pathophysiology, requires molecular assessment of how key pathological factors, specifically amyloid β (Aβ) plaques, influence the surrounding microenvironment. Here, neuronal lipids are particularly of interest as these are implicated in pathological- and neurodegenerative…