309 papers
Genomics is the study of an organism's complete set of DNA, offering a deep dive into the biological instructions that shape life. This field explores how genetic information influences traits, health, and evolution, moving beyond single genes to understand the complex interplay within entire genomes. From uncovering the roots of disease to mapping biodiversity, genomics provides the foundational data for many modern medical breakthroughs.
At Gist.Science, we process every new preprint in this category as it appears on bioRxiv, ensuring you stay ahead of the curve. Each paper is accompanied by both a clear, plain-language overview and a detailed technical summary, making cutting-edge research accessible to everyone regardless of their background. Below are the latest papers in genomics, freshly summarized and ready for you to explore.
This paper introduces HERVarium, a comprehensive interactive database that systematically annotates the protein-domain architecture and regulatory landscape of over 400,000 human endogenous retrovirus LTRs, revealing distinct functional specializations and structural preservation patterns across the human genome.
This study utilizes Visium HD high-resolution spatial transcriptomics to generate a detailed, sub-cellular resolution map of gene expression in healthy adult and pediatric human livers, revealing spatially distinct cellular heterogeneity and providing a valuable resource for identifying disease signatures and therapeutic targets.
By leveraging fully phased telomere-to-telomere pedigree assemblies and matched long-read epigenomes across cell-fate transitions, this study reveals that while human centromeric dip regions maintain positional stability across generations and differentiation, their epigenetic architecture exhibits remarkable plasticity, characterized by dynamic methylation changes during reprogramming and differentiation, insulation from X-chromosome status, and a distinct pattern of de novo mutations that are enriched in centromeric regions but depleted within functional cores.
This study establishes a comprehensive comparative atlas of RNA-binding proteins across 19 Leishmania species, revealing a conserved regulatory core, lineage-specific adaptations, and distinct RNA modification machinery, while specifically linking these proteins to life-stage transitions, stress responses, and antimony drug resistance mechanisms in L. braziliensis.
This study presents a high-quality long-read genome sequence of *Digitalis purpurea* that elucidates the molecular mechanisms underlying its flower color variation, caused by a disruptive insertion in the anthocyanidin synthase gene, and its terminal flower morphology, driven by a large insertion in the *DpTFL1/CEN* gene.
This study reveals that allele-specific alternative polyadenylation (asAPA) serves as a critical mechanistic link between noncoding genetic variants and Alzheimer's disease risk by demonstrating how RNA-binding proteins like FMRP regulate 3' UTR usage, with specific asAPA events showing condition-specific shifts in Alzheimer's brains and significant overlap with genetic risk loci for multiple neurodevelopmental and neurodegenerative disorders.
This study demonstrates that HP1 depletion and TGFβ activation exert antagonistic effects on the 3D genome organization of human mammary epithelial cells, where HP1 loss drives a shift toward active chromatin compartments and oncogenic gene upregulation, while TGFβ promotes chromatin compaction and inactive compartments, collectively highlighting how these opposing architectural changes contribute to breast cancer development.
ARSENAL is a short-context DNA language model trained on enriched regulatory data with a novel motif-discovery regularizer that outperforms existing models in motif recovery, zero-shot regulatory variant prediction, and chromatin accessibility modeling.
By combining shotgun metagenomics and single-cell sequencing, this study demonstrates that ceftiofur administration and *E. coli* inoculation significantly remodel the calf fecal microbiome, driving shifts in microbial diversity, nutritional taxa, and the prevalence of antimicrobial resistance genes.
Researchers have produced a high-quality, chromosome-level reference genome for the Bering Sea Pacific herring (*Clupea pallasii*) to address existing genomic data gaps and support the study of this ecologically and economically vital species.