368 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.
The study introduces SnakeHichipTF, a scalable framework integrating HiChIP analysis and AI-based footprinting to decode how distinct transcription factor programs govern region-specific enhancer-promoter wiring in the human brain, linking these regulatory architectures to psychiatric and metabolic traits as well as human evolutionary adaptations.
This study utilizes whole-genome resequencing of 94 farmer-maintained cacao trees across Costa Rica to reveal a complex genetic landscape containing both Criollo-derived lineages and unique local diversity, highlighting the critical role of smallholder farming systems as reservoirs for the crop's conservation and future breeding.
This paper introduces MystraColoc, a novel Bayesian algorithm designed to efficiently perform multi-trait colocalisation across hundreds or thousands of GWAS datasets, demonstrating superior clustering performance and deeper biological insights compared to existing methods.
This systematic review of 90 studies from the past 25 years reveals that rapid urbanisation significantly alters freshwater microbiomes by reducing overall bacterial diversity while increasing the abundance of Proteobacteria, Cyanobacteria, and Coliform bacteria, alongside a proliferation of antimicrobial resistance genes and pathogens, thereby posing critical risks to human health and ecosystem sustainability.
By leveraging a complete diploid human genome and ultra-long-read DiMeLo-seq, this study reveals that DNA methylation acts as a principal regulator of centromere organization, where hypomethylation erodes discrete CENP-A subdomains while hypermethylation consolidates them into broader tracts, thereby maintaining balanced chromatin architecture across haplotypes despite underlying sequence variation.
BioWorldModel introduces a single, dynamic architecture that models phenotype generation as a multi-layered biological process modulated by environment and time, significantly outperforming static predictive methods across bacteria, fungi, animals, and plants by capturing how organisms interpret their genomes rather than merely associating genotypes with outcomes.
This paper identifies critical artifacts in existing tools for studying cellular IRESes, such as false positives from back-splicing plasmids and misidentification of nuclear RNAs by smFISH and qRT-PCR, while proposing and validating more reliable orthogonal methods for accurate transcript annotation and IRES activity assessment.
This study presents a high-quality, haplotype-resolved chromosome-level genome assembly of the bluethroat that utilizes Oxford Nanopore sequencing to reveal complex structural variations and distinct organizational patterns within the hypervariable Major Histocompatibility Complex (MHC) region.
The authors present Novabrowse, an open-source interactive framework that bridges the gap between sequence-level homology and chromosome-scale synteny to enable high-resolution ortholog detection and gene signal discovery, successfully validating its utility by resolving the presence or absence of specific genes in the newt *Pleurodeles waltl* genome.
This study demonstrates that genomic markers, specifically a conserved 7 kb prophage region encoding a DNA invertase, can distinguish high-risk *Salmonella* Agona lineages from low-risk foodborne strains, enabling a shift from treating all isolates as equivalent hazards to a genomics-informed framework for predictive risk stratification and improved public health responses.