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Understanding how genome structure and gene content evolve within and among plant species requires analytical frameworks that capture the full spectrum of allelic and structural variation. Plant pangenomes have progressed from gene-focused and linear representations …
Read PDFBACKGROUND: Accurately identifying functionally distinct tumor cell subpopulations remains a critical challenge in cancer research. While single-cell epigenomics assays provide powerful insights into tumor heterogeneity beyond gene expression, computational limitations have hindered their application. METHODS: …
Read PDF<h4>Background</h4>Syndromic forms of obesity are uncommon, complicated illnesses that include early-onset obesity along with other clinical characteristics such as organ-specific abnormalities, dysmorphic symptoms, and intellectual incapacity. These syndromes frequently have a strong genetic foundation, involving …
Read PDF<b>Background:</b> Accurate identification of cancer driver genes is essential for understanding tumorigenesis and developing targeted therapies. Although graph neural networks (GNNs) have advanced multi-omics integration, existing methods often simply concatenate omics features and underutilize the …
Read PDF<h4>Summary</h4>The vast amount of publicly available genomic data requires analysis and visualization tools. Here, we present figeno, an application for generating publication-quality FIgures for GENOmics. Figeno particularly focuses on multi-region views across genomic breakpoints and …
Read PDF<h4>Background</h4>Lung cancer, particularly the non-small cell lung cancer (NSCLC) subtypes lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD), exhibits high heterogeneity and high mortality. This study aimed to explore their tumor microenvironment (TME) features, …
Read PDFChimeric antigen receptor T cell (CAR T) immunotherapies have transformed cancer treatment. These therapies typically involve lentiviral vector-mediated CAR gene integration, followed by reinfusion into patients, necessitating rigorous quality control. Critical parameters, including transduction efficiency …
Read PDFThe inflammation-intestinal metaplasia (IM)-carcinoma cascade has been proposed as a framework for gastric cancer (GC) development, yet the cell-level heterogeneity and microenvironmental remodeling underlying this progression remain poorly characterized. Here, we constructed a single-cell transcriptomic …
Read PDFMitochondria contain their own genome, mitochondrial DNA (mtDNA), which is under strict control by the cell nucleus. mtDNA occurs in many copies per cell and mutations often only affect a proportion of them, giving rise …
Read PDFAllele-specific expression (ASE) of somatic mutations can be caused by <i>cis</i>-activation of the mutant allele or silencing of the wild-type allele and has been investigated by examining the enrichment of mutant allele in RNA relative …
Read PDFDUX4 initiates the first wave of zygotic genome activation (ZGA) in the human embryo, and its misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). However, other factors that help regulate ZGA-like transcription in human …
Read PDFThe human genome is partitioned into functional compartments that replicate at specific times during S-phase. This temporal program, referred to as replication timing (RT), is coregulated with the 3D genome organization, is cell type-specific, and …
Read PDFStem lodging significantly reduces soybean yield stability, particularly under dense planting and intercropping systems. Stem breaking strength is a key component of lodging resistance, but its genetic basis remains incompletely understood. In this study, an …
Read PDFA complex structural variation on chicken chromosome 27 is the causal mutation for the muffs and beard (Mb) phenotype. The Mb variant region contains copy number variations in several genes important for nervous system development, …
Read PDFExposure to hypoxia is linked to increased cellular plasticity and enhanced metastasis, effects that are primarily attributed to the transcriptional activation of large gene programs downstream of hypoxia-inducible factors (HIFs). However, translational effects in hypoxia, …
Read PDFCancer molecular subtype classification is an essential component of precision oncology which provides insights into cancer prognosis and guides targeted therapy. Despite the growing applications of AI for cancer molecular subtype classification, challenges persist due …
Read PDFPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with limited therapeutic options. While genome profiling has benefitted clinical decision-making in many cancer types, PDAC remains among the most lethal solid cancers and has relatively …
Read PDFThe plant pathogen <i>Dickeya solani</i> causes soft rot and blackleg diseases in several crops including <i>Solanum tuberosum</i>. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato …
Read PDFThe subtribe Leptoboeinae (Gesneriaceae: Trichosporeae) comprises seven genera-<i>Rhynchotechum</i> Blume, <i>Boeica</i> C.B.Clarke, <i>Beccarinda</i> Kuntze, <i>Leptoboea</i> Benth., <i>Platystemma</i> Wall., <i>Crassicaulis</i> Lei Cai & Mich.Moller, and <i>Championia</i> Gardner. It is highly valuable in horticulture and medicine. However, long-standing …
Read PDFUnderstanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. <i>Quercus</i> is a keystone genus in Northern Hemisphere forests, and its wide …
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