23 papers · ranked by Valyu relevance
Haoyu Wang, Brittany Cody, Manuel Saavedra, Lanuza A P Faccioli + 3 more
Spatial transcriptomics (ST) technologies provide genome-wide transcriptomic profiles in tissue context but lack direct protein-level measurements, which are critical for interpreting cellular function and microenvironmental organization. We present DGAT (Dual-Graph Attention Network), a deep learning framework that…
Peilei Deng, Jiaruo Huang, Wencan He, Zhiyuan Li + 6 more
Spatiotemporal heterogeneity is recognized as a key driver of functional diversity in tissues. Spatial transcriptomics, which integrates high-throughput transcriptomics with high-resolution tissue imaging, enables the precise mapping of gene expression patterns at the tissue section level. This technology overcomes the…
Mohammad Faiz Iqbal Faiz, Elliot Jokl, Rachel Jennings, Karen Piper Hanley + 3 more
Spatial transcriptomics is rapidly advancing toward single cell level resolution, revealing complex tissue architectures organized across continuous anatomical gradients. However, accurate identification of spatial domains remains a central computational challenge, as many existing clustering approaches blur anatomical…
Aishwarya Budhkar, Juhyung Ha, Qianqian Song, Jing Su + 1 more
Integrating transcriptome-wide single-cell gene expression data with spatial context significantly enhances our understanding of tissue biology, cellular interactions, and disease progression. Although single-cell RNA sequencing (scRNA-seq) provides high-resolution gene expression data, it lacks crucial spatial…
Lixia Chen Wu, Xinyu Hu, Fengwei Zhan, Chuhanwen Sun + 6 more
Sequencing-based spatial transcriptomics technologies, including Visium HD and Stereo-seq, now enable transcriptome-wide profiling at subcellular resolution. However, these platforms generate measurements over spatially barcoded units rather than biologically segmented cells, creating a fundamental bottleneck for…
Sean Chang, Christelle El Haj, Jan Mulder, Lipin Loo + 1 more
Over the past century, studying the human brain has been one of the most complex and enduring biological challenges. Initial approaches, ranging from gross neural anatomy to cellular subtype organization, have significantly advanced our understanding of the intricate structure of the human brain. Recent innovations in…
Xianghao Zhan, Jingyu Xu, Yuanning Zheng, Zinaida Good + 1 more
Spatial transcriptomics enables spatial gene expression profiling, motivating computational models that capture spatially conditioned regulatory relationships. We introduce SAGE-FM, a lightweight spatial transcriptomics foundation model based on graph convolutional networks (GCN) trained with a masked-central-spot…
Hyun Cheol Koo, Aaron J. Molstad
Popular technologies for generating spatially resolved transcriptomic data measure gene expression at the resolution of a "spot", i.e., a small tissue region 55 microns in diameter. Each spot can contain many cells of different types. In typical analyses, researchers are interested in using these data to identify and…
Fahim Hafiz, Riasat Azim, Swakkhar Shatabda
Recent advancements in spatially resolved transcriptomics (SRT) have enabled near single-cell resolution, providing rich spatial context crucial for uncovering biological insights. However, high-resolution SRT datasets remain sparse and prone to dropout events that may impede accurate interpretation. Computational…
Hanwen Ni, Feng Liang, Huanhuan Huo, Xuechao Feng + 1 more
Introduction Pressure overload-induced myocardial hypertrophy is associated with complex spatial and temporal remodeling of cardiac cell populations. However, the spatial organization of these changes and their dynamic transcriptional programs remain incompletely understood. Integrating spatial transcriptomics with…
Maliha Mashkoor, Shihua Zhang, Allan Stensballe, Ioannis Kanakis + 1 more
Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by complex immune cell associations and continuous joint damage. Personalized clinical assessment and treatment options for RA remain hindered by a precision gap due to an inability to precisely match current global treatment strategies to…
Yijun Li, Stefan Stanojevic, Bing He, Zheng Jing + 4 more
Spatial omics technologies are one of the breakthroughs in science in the last several years (, , , ). Such technologies are able to systematically measure transcriptome information in the tissue space, thereby preserving the spatial context of gene expression. The addition of spatial information allows researchers to…
Yiyang Zhang, Bokai Zhao, Xiaoru Zhang, Zongchang Du + 2 more
Single-cell-resolution spatial transcriptomics profiles gene expression at cellular locations in native tissues, yet accurate cell-type annotation remains challenging: imaging-based platforms are constrained by targeted gene panels, whereas sequencing-based platforms often suffer from sparse molecular capture and…
Christina Huan Shi, Juan C. Piña-Crespo, Kevin Y. Yip, Timothy Y. Huang
Alzheimer’s disease (AD) is a complex neurodegenerative disorder that is associated with cognitive decline in the elderly. While β-amyloid (Aβ) plaques and neurofibrillary tau tangles have been used to define and stage AD onset in human brain, how these pathologies can affect various cell types nearby remains a subject…
Lorenzo Testa, Jing Lei, Kathryn Roeder
Spatial transcriptomics is increasingly extended by computational reconstruction of unmeasured genes from matched single-cell RNA-sequencing references, enabling transcriptome-wide analyses from targeted or sparse assays. Yet downstream analyses typically treat reconstructed expression as experimentally observed…
Macrina Lobo, Ziqi Zhang, Xiuwei Zhang
Spot-based spatial transcriptomics (ST) captures aggregated transcriptomic profiles at spatial locations (spots) in tissue slices. Cell type deconvolution methods decode each spot and estimate the proportion of every cell type in the spot, necessary for uncovering spatial cell type distributions for further downstream…
Hongyu Dong, Sheng Mao, Yukuan Liu, Tian Tian + 8 more
Recent advances in spatial omics technologies have enabled the simultaneous analysis of multiple molecular patterns in tissue sections, offering unprecedented insights into cellular microenvironments. However, the high cost of measurements and the sparsity of data restrict the availability of paired spatial multi-omics…
Yuhang Yang, Yonggan Bu, Shengyuan Zhou, Yiming Luo + 1 more
Spatial Transcriptomics (ST) measures gene expression while preserving spatial context, but its high cost and low throughput leave public datasets small. Inferring expression directly from widely available Hematoxylin and Eosin (H&E) stained histology offers a cost-effective alternative. However, existing approaches…
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…
Joseph Boyd, Matthew Lyon, Martino Mansoldo, Christian Hurry + 1 more
Spatial transcriptomics (ST) is a powerful tool for exploring biological properties dependent on structure, proximity, and interaction in tissue. The methods underpinning ST are developing rapidly but are limited in their ability to profile many thousands of genes at a subcellular scale. Although dissociated from…
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Understanding how plants respond to dynamic and spatially variable stimuli is a key goal in plant sciences. Traditional imaging methods often involve a trade-off between environmental control and spatial resolution, limiting their ability to capture real-time responses in high resolution. Microfluidic technology…
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Genetically encoded covalent warheads at the protein-protein interface, enable the locking of interaction from the transient complex into a stable covalent adduct, which could improve the binding affinity, selectivity, and kinetics between a protein binder and its target. Given the diverse chemical microenvironments…
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Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…