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Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production
Over the past decade, poultry genomics has undergone a transformative shift from genome assembly to functional annotation, mechanistic discovery, and integrative applications that advance sustainable poultry production. This symposium highlights emerging tools and resources that …
Read PDFDNA Methylation and Its Role in Personalized Nutrition: Mechanisms, Clinical Insights, and Future Perspectives
DNA methylation is a central epigenetic mechanism that mediates the interaction between nutritional exposures and gene regulation. Emerging evidence demonstrates that diet, bioactive compounds, genetic background, and lifestyle factors collectively shape the human methylome, influencing …
Read PDFDefining three dimensional chromatin structures of pediatric and adolescent B cells using primary B cell and EBV-immortalized B cell reference genomes
<h4>Background/purpose</h4>Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture …
Read PDFMulti-omics dissection of tumor microenvironment-mediated drug resistance: mechanisms and therapeutic reprogramming
Tumor drug resistance represents a major challenge in contemporary cancer therapeutics, significantly compromising the clinical efficacy of chemotherapy, targeted therapy, and immunotherapy. While existing research has elucidated the critical role of tumor cell-intrinsic mechanisms in …
Read PDFStability Matters: Revealing Causal Roles of G-Quadruplexes (G4s) in Regulation of Chromatin and Transcription
<h4>Background</h4>G-quadruplexes (G4s) are non-canonical higher-order nucleic acid structures that form at guanine-rich motifs, with features spanning both secondary and tertiary structural levels. These dynamic structures play pivotal roles in diverse cellular processes. Endogenous G4s (eG4s) …
Read PDFEpigenetic mechanisms and steroid-resistant nephrotic syndrome: The future potential for SRNS diagnosis
Nephrotic syndrome (NS) is commonly managed with glucocorticoid (GC) therapy, yet about 10%-30% of children do not achieve remission after an adequate initial steroid course and are classified as steroid-resistant nephrotic syndrome (SRNS); in adults, …
Read PDFIntegrative SMR prioritizes oxidative stress-related regulatory genes for Alzheimer's disease with brain-tissue validation
Oxidative stress (OS) plays a critical role in the pathogenesis of Alzheimer's disease (AD), yet its genetic and epigenetic regulatory mechanisms remain unclear. In this study, we applied a three-step summary-based Mendelian randomization (SMR) framework …
Read PDFNutritional ketosis modulates the methylation of cancer-related genes in patients with obesity and in breast cancer cells
Scientific evidence demonstrates that a very low-calorie ketogenic diet (VLCKD) is effective and beneficial in the treatment of obesity, capable of reversing the methylome associated with obesity and has immunomodulatory capacity. This effect is in …
Read PDFDeciphering genetic susceptibility to clear cell renal cell carcinoma
Genome-wide association studies (GWAS) have identified over 60 autosomal risk loci associated with clear cell renal cell carcinoma (ccRCC), yet the functional mechanisms underlying these associations remain largely unclear. To establish connections between risk variants …
Read PDFAdvances in Epigenomic Sequencing and Their Applications in Cancer Diagnostics
Cancer, a globally prevalent and life-threatening disease, remains a major area of focus in biomedical research. However, its substantial heterogeneity and complex pathogenesis continue to pose significant challenges for accurate diagnosis and effective treatment. The …
Read PDFDecoding sex differences in human immunity through systems immunology
Immune function varies widely across humans. Biological sex is a key factor underlying human immune variability, with men presenting with more severe infections and increased cancer rates, while women exhibit higher vaccine responses and prevalence …
Read PDFStatistically rigorous and computationally efficient chromatin stripe detection with Quagga
Chromatin stripes are architectural chromatin features in which a singular loop anchor interacts with a contiguous region of DNA so, at the bulk sequencing level, it appears as a long stripe on chromatin contact matrices. …
Read PDFNutrigenomics of Obesity: Integrating Genomics, Epigenetics, and Diet-Microbiome Interactions for Precision Nutrition
Obesity is a highly complex, multifactorial disease influenced by dynamic interactions among genetic, epigenetic, environmental, and behavioral determinants that explicitly position genetics as the core. While advances in multi-omic integration have revolutionized our understanding of …
Read PDFIntegrative Transcriptomic Analysis Decodes the Interplay Between Aging, Senescence, and Cancer
Cancer risk increases with age, and cellular senescence may be a major contributor to cellular carcinogenesis. Enormous efforts have been made to investigate the interrelation between aging and tumors, but little is known about the …
Read PDFMachine Learning for Predicting Stroke Risk Stratification Using Multiomics Data: Systematic Review
<h4>Background</h4>Stroke is a complex, multidimensional disorder influenced by interacting inflammatory, immune, coagulation, endothelial, and metabolic pathways. Single-omics approaches seldom capture this complexity, whereas multiomics techniques provide complementary insights but generate high-dimensional and correlated feature spaces. …
Read PDFCharacterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources
Cytosine methylation, a crucial epigenetic modification, plays a vital role in genomic regulation. Leveraging the advancements in long-read sequencing, we investigate the methylation patterns of polymorphic transposable element (TE) insertions of human lymphoblastoid cell lines …
Read PDFThe functional significance of vascular DNA hypermethylation in atherosclerosis: a historical perspective
A decade ago, independent mechanistic and descriptive epigenomics data demonstrated for the first time that vascular DNA hypermethylation is a landmark of and causal factor in human and murine atherosclerosis. Since then, a flurry of …
Read PDFThe role of gene-environment interactions in endocrine-sensitive life stages for shaping mental health: focus on the RE-MEND project
The number of people seeking help for mental illness is increasing across all ages, creating a major burden for individuals, families, and the society. While personalized medicine is advancing in other fields, diagnosis and treatment …
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