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<h4>Background</h4>Virus mutants are commonly used for studying the role of individual viral proteins in infections and are increasingly investigated with functional genomics experiments of infected cells that use sequencing-based assays such as RNA-seq or ATAC-seq. …
Read PDFBACKGROUND: Sanghuangporus species are white-rot basidiomycetes of notable ecological and economic importance, playing critical roles in wood decomposition and medicinal applications. However, comprehensive genus-level mitochondrial genome analyses for Sanghuangporus remain limited, which constrains understanding of …
Read PDF<h4>Background/aim</h4>T-cell large granular lymphocyte leukemia (T-LGLL) is a rare, indolent lymphoproliferative disorder of cytotoxic T cells in the peripheral blood, bone marrow, and spleen. This analysis was conducted to characterize genomic alterations and highlight potential …
Read PDF<i>Calanthe aristulifera</i> is a critically endangered orchid species of profound horticultural and ecological significance. However, establishing its species integrity is complicated by frequent natural introgression with sympatric relatives, such as <i>C. sieboldii</i> and <i>C. discolor</i>. …
Read PDFCotton improvement remains a major challenge in plant biotechnology because stable yield, fiber quality, and stress resilience must be delivered from complex allopolyploid genomes under variable environmental conditions. Genetic mapping has progressively transformed this challenge …
Read PDFBACKGROUND: A highly complex karyotype (high-CK) is a key biomarker of poor prognosis in chronic lymphocytic leukemia (CLL). While conventional methods lack the resolution to fully characterize complex structural variants (SVs), emerging technologies such as …
Read PDFImproving crop productivity is essential to ensure global food security in the context of climate change and an increasing global population. Over the past few decades, sequencing has significantly expanded our ability to explore complex …
Read PDFLarge-scale genomic rearrangements are prevalent in cancer genomes and can profoundly rewire three-dimensional (3D) genome architecture, leading to aberrant oncogene activation through enhancer hijacking. The rewired 3D organization generates unique chromatin contact signatures, which can …
Read PDF<b>Background</b>: Comprehensive genomic profiling (CGP) is increasingly used in precision oncology to identify actionable genomic alterations and guide targeted therapies in solid tumors. However, the clinical implementation of CGP assays requires rigorous analytical validation to …
Read PDFCopy number variants (CNVs) have been shown to play a significant role in the pathogenesis of various human diseases. Although several tools have been developed for detecting CNVs based on whole-exome sequencing (WES) data, their …
Read PDF<h4>Motivation</h4>Tumor viruses account for ∼10% of cancer diagnoses. Virally induced tumorigenesis is understood as direct signaling through oncogenes such as E6 and E7 genes in the case of human papillomavirus. Furthermore, pathogen characteristics such as …
Read PDFLung adenocarcinoma (LUAD), the most common subtype of nonsmall cell lung cancer, exhibits substantial molecular heterogeneity, complicating subtype classification, progression assessment, and treatment decision-making. Advances in high-throughput sequencing enable multi-omics analysis to reveal cancer mechanisms …
Read PDF<h4>Motivation</h4>Copy-number variants (CNVs) are a form of genetic structural variation with increasing importance in complex human disorders. Both DNA sequencing and microarray data can be used to detect CNVs, which can be used in genetic …
Read PDFNonsyndromic orofacial clefts (NSOC) are common congenital craniofacial developmental defects. Current evidence suggests that genetic factors, environmental exposures, and their interactions jointly contribute to the development of the disease. Owing to the high heritability of …
Read PDF<h4>Aims & methods</h4>DNA methylation and genomic instability are critical drivers of cancer initiation and malignant progression. However, the roles of methylation aberrations and genomic instability in malignant progression have not been thoroughly investigated in intrahepatic …
Read PDFStructural variations (SVs ≥ 50 bp) are a critical but underexplored source of genetic diversity in cattle, shaping traits vital for productivity, adaptability, and health. Advances in long-read sequencing, pangenome graph construction, and near-complete genome …
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