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.
This study establishes that human endogenous retroviruses (HERVs) serve as pervasive, family-specific building blocks of RNA regulatory architecture by embedding distinct RNA-binding protein motifs, contributing to thousands of long non-coding RNAs, and forming unique antisense configurations that influence post-transcriptional gene regulation and immune responses.
MethylBench provides a comprehensive cross-platform benchmark of six DNA methylation profiling technologies using GIAB and human samples, demonstrating that while sequencing-based methods offer superior genome-wide coverage and long-read platforms enable phasing, all methods consistently identify robust epigenetic hotspots in promoters and introns when coverage and annotation redundancies are properly addressed.
The authors introduce CoCUT&Tag, a single-molecule, single-cell method for mapping linked chromatin states, and apply it to demonstrate that bivalent chromatin in human hematopoiesis defines a distinct regulatory class that enhances gene expression through increased enhancer demand and preferential derepression.
By benchmarking six local ancestry inference methods on Neolithic European genomes, this study demonstrates that while multi-method validation can robustly identify selection signals in genes related to pigmentation and metabolism, inferred ancestry patterns and selection signatures are highly sensitive to the specific method used, particularly in complex regions like the HLA.
This study presents the first genome-wide association study (GWAS) of the sugar kelp *Saccharina latissima*, identifying both major-effect loci and polygenic traits for morphological and metabolic characteristics to provide a genomic foundation for future aquaculture breeding programs.
The paper introduces SCADS, a scalable computational framework that integrates single-cell ATAC-seq data with GWAS summary statistics to identify disease-relevant cell populations and regulatory programs by quantifying the polygenic enrichment of chromatin co-regulatory regions.
By integrating subgenome-resolved genome assemblies with large-scale citizen science data, this study reveals that rapid urban adaptation in the octoploid *Oxalis corniculata* is driven by a repeat-length polymorphism in a MYB transcription factor that modulates leaf color and heat tolerance.
This study presents a comprehensive, haplotype-resolved DNA methylation atlas for 106 individuals across 19 Chinese provinces using nanopore long-read sequencing, revealing that genomic structural variants and habitat altitude are key determinants of methylation patterns and identifying specific altitude-responsive genes.
This study presents a new phased genome assembly of the Antarctic spiny plunderfish (*Harpagifer antarcticus*) and comparative analyses revealing that lineage-specific bursts of transposon activity, segmental duplications of antifreeze glycoprotein genes, and diversifying selection in antioxidant and proteostasis pathways were key drivers of notothenioid adaptation to extreme cold.
This study establishes a modular platform for eukaryotic genome minimization by engineering an essential neo-chromosome III in the Sc2.0 yeast strain that relocates essential genes to enable extensive SCRaMbLE-mediated deletions, while demonstrating the viability of orthogonal regulatory elements and the stability of highly synthetic chromosome architectures.