26 papers · ranked by Valyu relevance
Dario Bressan, Giorgia Battistoni, Gregory J. Hannon
Spatial omics has been widely heralded as the new frontier in life sciences. This term encompasses a wide range of techniques that promise to transform many areas of biology and eventually revolutionize pathology by measuring physical tissue structure and molecular characteristics at the same time. Although the field…
Yingbo Cui, Yong Zhao, Canqun Yang, Tao Tang + 5 more
Recent breakthroughs in spatially resolved multi-omics have unlocked the ability to simultaneously profile multiple molecular layers within tissues, offering unprecedented insights into their coordinated roles in development and disease. Despite these advancements, integrative analysis of multi-omics data remains a…
Jinxia Wang, Yuying Huo, Rui Zhao, Yan Pan + 2 more
Recent advances in spatial multi-omics technologies have opened new avenues for characterizing tissue architecture and function in situ, by simultaneously providing multimodal and complementary information—such as spatially resolved transcriptomic, epigenomic, and proteomic features. Current computational approaches…
Yang Liu, Kexin Ma, Haoran Xu, Ke Xu + 8 more
Spatial multi-omics technologies have revolutionized our understanding of biological systems by providing spatially resolved molecular profiles from multiple perspectives. Existing spatial multi-omics integration methods often assume that data from different modalities share a common underlying distribution, aiming to…
Wenhao Cai, Weizhong Li
Recent advances in spatial multi-omics technologies provide unprecedented opportunities to integrate and interpret molecular features within the tissue microenvironment. Here we present SpatialFuser, the first unified deep learning framework for detailed molecular profiling within individual tissue sections and…
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…
Yannick Mahlich, Harkirat Sohi, Paul Piehowski, Jason E McDermott + 1 more
Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance…
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…
Yannick Mahlich, Harkirat Sohi, Marija Velickovic, Paul Piehowski + 2 more
Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance…
Paul Kiessling, Christoph Kuppe
Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in…
Esra Busra Isik, Yusuf Hakan Usta, Maryam Riazi, Haozhe Liu + 5 more
Title: Summary Recent developments in spatial omics technologies have enabled the generation of high-dimensional molecular data, including transcriptomics, proteomics, and epigenomics, within their spatial tissue context, either through co-profiling on the same slice or through profiling across serial tissue sections.…
Xiaofeng Wu, Weize Xu, Da Lin, Leqiang Sun + 2 more
Biological macromolecules assemble into sophisticated spatial architectures to orchestrate fundamental cellular processes. Understanding this architecture is therefore essential for deciphering the mechanisms of life. Driven by advances in high-throughput sequencing and single-molecule imaging, spatial omics…
Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, Isaac Virshup + 10 more
Spatially resolved omics technologies are transforming our understanding of biological tissues. However, handling uni- and multi-modal spatial omics datasets remains a challenge owing to large volumes of data, heterogeneous data types and the lack of unified spatially-aware data structures. Here, we introduce…
Theodore Alexandrov, Julio Saez‐Rodriguez, Sinem K Saka
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly…
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…
Lambda Moses, Aurelie Herault, Lauriane Cabon, Bianca Dumitrascu
Spatial biology spans multiple length scales, from intracellular organization to tissue-level architecture. Spatial transcriptomics captures this structure, yet most analyses operate at a single spatial resolution, implicitly assuming that biological organization is scale-consistent. In practice, spatial…
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…
Martin Emons, Samuel Gunz, Helena L. Crowell, Izaskun Mallona + 2 more
'Reinhard Furrer' 'Mark D. Robinson'] Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencingbased, can give rise to very different data modalities. The characteristics of the two data…
Jonatan A. González, Julia Wrobel, Simon Vandekar, Paula Moraga
This tutorial reviews methods and procedures relating to spatial point patterns for complex data analysis. We consider tissue cells as a realisation of a spatial point process for each patient. We focus on proper functional descriptors for each observation and techniques that allow us to obtain information about…
Tianyu Liu, Yuge Wang, Rex Ying, Hongyu Zhao
Discovering genes with similar functions across diverse biomedical contexts poses a significant challenge in gene representation learning due to data heterogeneity. In this study, we resolve this problem by introducing a novel model called Multimodal Similarity Learning Graph Neural Network, which combines Multimodal…
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Mass spectrometry (MS) is a cornerstone technology in modern molecular biology, powering diverse applications across proteomics, metabolomics, lipidomics, glycomics, and beyond. As the field continues to evolve, rapid advancements in instrumentation, acquisition strategies, machine learning, and scalable computing have…
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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…
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Untargeted metabolomics is a powerful approach for exploring the chemical diversity and dynamics of biological systems. However, the types of questions that can be addressed depend not only on experimental design but also on the data processing and analysis workflows employed, many of which require advanced…
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Herein, we introduce MAYA (Multiple Activity Analyzer), a tool designed to automatically construct a chemical multiverse, generating multiple visualizations of chemical spaces of a compound data set described by structural descriptors of different nature such as Molecular ACCess Systems (MACCS) keys, extended…
José L. Medina-Franco, Ana L. Chávez-Hernández, Edgar López-López, Fernanda I. Saldívar-González
Technological advances and practical applications of the chemical space concept in drug discovery, natural product research, and other research areas have attracted the scientific community´s attention. The large- and ultra-large chemical spaces are associated not only with the significant increase in the number of…
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One Health seeks to integrate and balance the health of humans, animals, and environmental systems. These three spheres are intricately interconnected through microbiomes, which are universally present and exchange microbes and genes, influencing not only human and animal health but also key environmental…