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A systematic dissection of the functional impacts of non-coding variations across diverse tissues and cell types is essential for deciphering the molecular architecture underlying complex traits. Given the significance of chickens as both a key …
Read PDFUnderstanding antigen reactivity is crucial for characterizing CD4<sup>+</sup> T helper (Th) cell fate, yet conventional peptide restimulation assays introduce phenotypic bias by activating cells <i>ex vivo</i>. By combining single-cell RNA and T cell receptor (TCR) …
Read PDFCancer functional genomics enables high-throughput target discovery and mechanistic investigation, yet its application has remained largely confined to mouse models and established human cancer cell lines. Direct functional interrogation of heterogeneous primary tumors offers a …
Read PDFFli1b is an ETS transcription factor, which has been previously implicated in zebrafish vascular and hematopoietic development. Here we present single cell RNA sequencing data from wild-type and maternal zygotic <i>fli1b</i> mutant zebrafish embryos at …
Read PDF<h4>Background</h4>CRISPR-based genetic screening has become a central methodology in functional genomics, enabling systematic interrogation of gene function, genetic interactions and context-dependent vulnerabilities at scale. However, the rapid expansion of screening modalities-including multi-condition designs, combinatorial perturbations, …
Read PDFCancer research has undergone a fundamental transformation in recent decades due to the integration of artificial intelligence (AI) models into the study of tumor biology. However, tumor evolution, driven by genetic and phenotypic alterations leading …
Read PDFRetinoblastoma (RB) is the most prevalent malignant tumor that originates within the eye in children, occurring at a frequency of around 1:20,000 to 1:15,000. RB typically occurs when both alleles of the retinoblastoma 1 (RB1) …
Read PDF<h4>Background</h4>Altered lipid metabolism is increasingly recognized as a driver of tumor progression, yet its specific role in thyroid cancer remains unclear.<h4>Methods</h4>We combined Mendelian randomization with transcriptomic and single-cell analyses to identify lipid-related factors that contribute …
Read PDF<h4>Background</h4>Pediatric cough-variant asthma is characterized by chronic airway inflammation and epithelial dysfunction driven by complex cellular interactions and molecular regulatory networks. Understanding the cellular heterogeneity and molecular mechanisms underlying pediatric asthma pathogenesis remains challenging. Single-cell …
Read PDFBone and skeletal muscle are essential components of musculoskeletal system, enabling movement, load-bearing, and systemic homeostasis. These tissues communicate through dynamic bone-muscle crosstalk mediated by cytokines, growth factors, and extracellular-matrix (ECM) proteins. The spatial organization …
Read PDFSingle-cell RNA sequencing (scRNA-Seq) enables analysis of gene expression at single-cell resolution. RNA velocity analysis infers the temporal dynamics of transcriptional states from the relative abundances of spliced/unspliced mRNA quantified via scRNA-Seq. Classical RNA velocity …
Read PDFThe polychaete Capitella teleta is a primary model for evolutionary developmental biology, comparative genomics, conservation, and ecotoxicology. Although it was the first polychaete genome sequenced, the original assembly is outdated by modern standards. Here, we …
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 PDFBACKGROUND: Tumor heterogeneity poses a major challenge to elucidating the mechanisms underlying tumor progression and metastasis. However, the cellular heterogeneity of triple-negative breast cancer (TNBC) remains incompletely understood. METHODS: We performed an integrated analysis of …
Read PDFMicroorganisms represent the Earth's most abundant biomass and a vast reservoir of genetic diversity. However, traditional agar plate methods fail to recover the vast majority of these species, leaving a "microbial dark matter" that holds …
Read PDF<h4>Background</h4>Prolificacy is a crucial economic trait in goat production, yet its underlying molecular mechanisms remain incompletely understood due to its polygenic nature. While previous studies have identified several candidate genes, a comprehensive understanding of the …
Read PDFNeural Ordinary Differential Equations (Neural ODEs) have emerged as a prominent framework for modeling complex dynamical systems. Their ability to describe a system's underlying dynamical law has attracted attention to applications in life sciences. Single-cell …
Read PDFBACKGROUND Acute lung injury (ALI) after liver transplantation (LT) is a critical complication negatively affecting transplant outcomes and patient survival. However, effective biomarkers for early diagnosis remain unidentified. This study aimed to identify hub biomarkers …
Read PDF<h4>Summary</h4>Whereas transcriptomic and spatial profiling offer static snapshots of tissue structure, mechanistic models use biological rules to predict how tissues evolve. We present the BioInformatics WalkThrough (BIWT) software to directly initialize spatial agent-based models from …
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