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.
SuSiNE is an enhanced genetic fine-mapping method that extends SuSiE by incorporating signed functional priors and multi-basin ensembling to improve causal variant recovery, resolve linkage disequilibrium ambiguity, and provide robust diagnostics while avoiding the pitfalls of purity filtering.
This study reveals that during erythropoiesis, specific cis-regulatory elements termed "matchmakers" concentrate cohesin-mediated loop extrusion to strengthen chromatin interactions and drive the expression of key genes, thereby shaping the 3D genome organization required for red blood cell differentiation.
Using nanorate sequencing in *Arabidopsis*, this study reveals that DNA repair pathways like NER and MMR are less efficient in heterochromatin and transposable elements compared to accessible regions, while mutations in chromatin remodelers and RNA-directed DNA methylation components significantly elevate genome-wide mutation rates through mechanisms likely involving transcriptional changes or genomic instability rather than localized repair defects.
By integrating long-read genomic and transcriptomic data from diverse human samples, this study characterizes the human pangenome's protein-coding duplicated genes to discover thousands of novel copy number polymorphic genes, refine existing gene models by reclassifying pseudogenes as functional, and reveal that evolutionary constraints are predominantly found in ancestral rather than recently derived duplicated genes.
This study demonstrates that adult porcine intestinal organoids, while exhibiting a relatively immature transcriptional state and reduced immune spatial patterning, successfully retain substantial regional epithelial identity and preserve animal-specific regulatory signatures, thereby validating their utility as controlled models for functional follow-up of candidate genes and variants in farm animals.
This paper presents a standardized whole-genome variant dataset comprising approximately 9.1 million SNPs and 0.77 million INDELs for 547 diverse grapevine accessions from the INRAE Bordeaux collection, generated through uniform sequencing and analysis to serve as a harmonized resource for grapevine genetics, breeding, and population genomics research.
This paper introduces the Trajectory Uncertainty Framework (TUF), a modular, open-source tool that quantifies single-cell trajectory uncertainty through Temporal Entropy and Trajectory Divergence scores to identify transitional states and reveal context-specific transcriptional drivers across diverse biological systems.
Using single-cell RNA sequencing, this study reveals that *Wolbachia* infection in *Drosophila* follows a multiphasic trajectory involving distinct transcriptional waves that reprogram host cell cycles, organelle function, and immune responses to establish a stable chronic infection.
Omega-seq is an ultra-low-background RNA sequencing method that utilizes USER-excisable template-switching oligonucleotides and a specialized dT primer to eliminate phantom UMIs and poly-T artifacts, enabling faithful molecular counting and precise transcript-end mapping even in minute samples like single Drosophila neuroblasts.
By applying a reference-free pangenome approach to 465 near-complete human assemblies, this study reveals that high-identity pseudo-homologous regions organize chromosome ends into sequence communities that facilitate recurrent ectopic exchange, driving the concerted evolution of human subtelomeres across the genome.