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| http://dx.doi.org/10.1371/journal.pgen.1005414 | DOI Listing |
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STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model.
Brief Bioinform
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Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China.
Spatial transcriptomics (ST) technologies enable dissecting the tissue architecture in spatial context. To perceive the global contextual information of gene expression patterns in tissue, the spatial dependence of cells must be fully considered by integrating both local and non-local features by means of spatial-context-aware. However, the current ST integration algorithm ignores for ST dropouts, which impedes the spatial-aware of ST features, resulting in challenges in the accuracy and robustness of microenvironmental heterogeneity detecting, spatial domain clustering, and batch-effects correction.
View Article and Find Full Text PDFCorrigendum to "Mapping taste and flavour traits to genetic markers in lettuce " [Food Chem.: Mol. Sci. 9 (2024) 100215].
Food Chem (Oxf)
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Department of Food and Nutritional Sciences, University of Reading, Harry Nursten Building, Whiteknights, Reading RG6 6DZ, UK.
[This corrects the article DOI: 10.1016/j.fochms.
View Article and Find Full Text PDFConnections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence.
View Article and Find Full Text PDFWhole-genome sequencing identifies novel loci for keratoconus and facilitates risk stratification in a Han Chinese population.
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January 2025
National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
Background: Keratoconus (KC) is a prevalent corneal condition with a modest genetic basis. Recent studies have reported significant genetic associations in multi-ethnic cohorts. However, the situation in the Chinese population remains unknown.
View Article and Find Full Text PDFDetection of Mycobacterium tuberculosis DNA in intraocular fluid of 11 suspected tuberculous uveitis patients by multiplex PCR.
BMC Ophthalmol
January 2025
Department of Tuberculosis, New District Branch of Northern Jiangsu People's Hospital of Jiangsu Province, Yangzhou, 225001, Jiangsu Province, China.
Background: This study aims to detect Mycobacterium tuberculosis complex (MTBC) DNA in intraocular fluid from clinically suspected tuberculous uveitis patients using multiplex polymerase chain reaction (PCR) and investigate the diagnostic utility of multiplex PCR for tuberculous uveitis.
Methods: Primers targeting three specific genes (MPB64, CYP141, and IS6110) within the MTBC genome were designed. Multiplex PCR was conducted using DNA from the H37Rv strain as well as DNA extracted from fluids of confirmed tuberculosis patients to assess primer specificity and method feasibility.
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