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Articles by Hani Vu
SpaMTP: integrative statistical analysis and visualization of spatial metabolomics and transcriptomics data
Abstract Spatially resolved multimodal data enable the exploration of transcriptional, proteomic and metabolic regulation, yet analytical tools to integrate these spatial omics modalities, particularly spatial metabolomics, remain limited. We developed SpaMTP, an end-to-end framework that implements functions within a common Seurat architecture.
Unraveling lncRNA diversity at a single cell resolution and in a spatial context across different cancer types
Abstract Long noncoding RNAs (lncRNAs) participate in gene regulation underlying development and disease. Overcoming inherent limitations of bulk sequencing lncRNA analysis, we leveraged single-cell and spatial transcriptomics (ST) data to analyze 219,442 potential lncRNAs identified by the TAR-scRNA-seq pipeline across 13 cancer types. The lncRNA functions were assessed by identifying their cell-type specificity and spatial distributions across different tissue regions.
Spatial analysis of HPV‐associated cervical intraepithelial neoplastic tissues demonstrate distinct immune signatures associated with cervical cancer progression
Introduction Despite significant advances in biomedical research and public health interventions, cervical cancer persists as a major global health concern, ranking as the fourth most prevalent cancer among women worldwide [1, 2]. Moreover, the incidence of human papillomavirus (HPV)-driven anogenital and oropharyngeal cancers is on the rise globally, affecting both men and women [3-5].
Spatial Transcriptomic Signature of Progressive Fibrosis in Human MASLD: Role of Senescence and Metabolic Reprogramming.
Abstract Granular detail about the location and nature of liver cell interactions and the metabolic, inflammatory and fibrogenic pathways driving progressive fibrosis in metabolic dysfunction-associated steatotic liver disease (MASLD) is needed to deliver novel therapeutic targets. Here we used spatial transcriptomic data from human MASLD liver biopsies to identify the major cell types and their potential interconnected activities within specific tissue regions across the spectrum of MASLD.
Spatial analysis of HPV associated cervical intraepithelial neoplastic tissues demonstrate distinct immune signatures associated with cervical cancer progression
Abstract Cervical cancer remains the fourth most common cancer affecting women worldwide, and incidences of other HPV-related cancers continue to rise. For the development of effective prevention strategies in high-risk patients, we aimed to better understand the roles of inflammatory pathways and the tumour microenvironment as the main driver of progression to malignancy in HPV-infected tissues.
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