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Articles by Weize Xu
Loss-of-function variants in ODAD1 disrupt ODA docking and induce actin cytoskeletal remodeling in primary ciliary dyskinesia
Abstract Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder characterized by defective mucociliary clearance due to impaired motile cilia function. Outer dynein arm docking complex subunit 1 (ODAD1) encodes a structural component of the outer dynein arm docking complex (ODA-DC), which is crucial for effective ciliary beating. However, the full spectrum of ODAD1-associated pathogenesis remains incompletely defined.
PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery
Abstract The convergence of large language model-powered autonomous agent systems and single-cell biology promises a paradigm shift in biomedical discovery. However, existing biological agent systems, building upon single-agent architectures, are narrowly specialized or overly general, limiting applications to routine analyses. We introduce PantheonOS (https://PantheonOS.stanford.edu), an evolvable, privacy-preserving multi-agent framework designed to reconcile generality with domain specificity.
A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application
1 Introduction The spatial organization of molecular and cellular components underlies the functional architecture of biological systems [1]. Although conventional omics technologies provide comprehensive molecular inventories, they lack spatial context. This limitation has motivated the rapid development of spatial omics, which maps molecular information directly within intact tissues [2].
Disruption of zinc homeostasis reduces histone acetylation levels in normal and tumor cells - Scientific Reports
Abstract Zinc homeostasis plays a critical role in cellular function, yet its dysregulation may lead to cytotoxicity. Based on the unexpected finding that excessive zinc downregulates the transcription of cardiac-related factors in mouse cardiomyocytes, this study reveals a mechanistic pathway wherein cytoplasmic zinc overload reduces histone acetyltransferase activity, subsequently lowering histone acetylation and ultimately decreasing the transcriptional levels of target genes.
Ambient Ozone Exposure and Global Child Health: A Systematic Review of Epidemiological Studies
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Excessive zinc reduces histone acetylation in mouse cardiomyocytes by downregulating acetyltransferases
Abstract Zinc plays a critical role in cellular functions, but its excess may lead to detrimental effects, including cardiac abnormalities. The impact of zinc overload on cardiomyocytes is investigated in this study. For the first time, we report the regulatory relationship between zinc and histone acetylation. Excessive zinc downregulates the transcription of Bmp4 in HL-1 cell line and primary cardiomyocytes.
U-FISH: a universal deep learning approach for accurate FISH spot detection across diverse datasets
Abstract In the rapidly advancing landscape of fluorescence in situ hybridization (FISH) technologies, there is a critical need for sophisticated yet adaptable methods for spot detection. This study introduces U-FISH, a deep learning approach that significantly improves accuracy and generalization capabilities.
Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics
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The Detection of 5-Hydroxymethylcytosine in Neural Stem Cells and Brains of Mice
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Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture
Chromosome conformation capture (3C) technologies can be used to investigate 3D genomic structures. However, high background noise, high costs, and a lack of straightforward noise evaluation in current methods impede the advancement of 3D genomic research. Here we developed a simple digestion-ligation-only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation, without the need for biotin labeling and pulldown.
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