238 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 the personalized variant effect predictor (pVEP) framework, which demonstrates that an individual's genetic background significantly alters AI-predicted clinical variant effects, revealing that many variants are pathogenic in some genetic contexts but benign in others.
This study presents a pseudo-phased, chromosome-level genome assembly of the coffee leaf rust pathogen *Hemileia vastatrix* (isolate Hv178a), revealing a unique isolate-specific trisomy of chromosome 17 that likely underlies its increased virulence.
This study presents the first high-quality nuclear genome assembly of *Chaetoceros muelleri*, derived from resurrected Baltic Sea sediments, which reveals extensive gene duplication, transposable element-driven plasticity, and lineage-specific innovations that underpin the diatom's evolutionary adaptability and ecological success.
This study demonstrates that integrating the DNA language model GROVER with chromatin and regulatory features reveals that while cell-type specific information is crucial, much of the genome stability landscape governing double-strand break sensitivity is inherently encoded within the DNA sequence itself.
This study integrates ATAC-STARR-seq, CRISPR screens, and high-resolution chromatin mapping to demonstrate that enhancer hubs, organized through CTCF-independent interactions and driven by key elements like Batf, govern the 3D chromatin topology essential for establishing and maintaining Th17 cell identity.
By reconstructing an ancestral placental mammal karyotype and recombination map, this study reveals that while autosomal recombination landscapes are not conserved across species like the X chromosome, ancestral regions with low recombination rates are under stronger purifying selection and enriched for cellular functions, whereas high-recombination regions are less constrained and associated with regulatory and immune systems.
The paper introduces NanoPlasmiQC, a cost-effective, automated workflow utilizing Oxford Nanopore long-read sequencing to sequence and analyze full plasmids within a single day, offering a superior alternative to traditional Sanger sequencing.
This study demonstrates that gene expression dispersion is a distinct, genetically encoded regulatory feature reflecting transcriptional fidelity, which is structured by biological function, enriched for cis-regulatory control, and operates independently of mean expression levels.
This study demonstrates that an epigenetic index of adult cognition ("Epigenetic-g") captures distinct genetic and environmental variation in children's cognitive and academic performance that is not reflected by polygenic indices, showing plasticity in early childhood and moderate stability by adolescence without predicting longitudinal cognitive growth.
This study reveals that the global rise of pneumococcal serotype 12F following vaccine introduction is driven by both distinct regional lineages and a multidrug-resistant global clone, while also identifying reversible strand-slippage mutations in the *wciJ* gene as a novel mechanism for phase variation that allows subpopulations to evade vaccine-induced antibody killing.