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 paper introduces LAMBDA, a comprehensive benchmark designed to evaluate the predictive capabilities of genomic language models through phage-bacteria sequence discrimination, revealing critical insights into the importance of training data quality and domain-specific training for effective prophage detection.
By analyzing whole-genome sequencing data from African and South American samples, this study reveals the existence of two genetically distinct yet recombining cryptotypes of *Plasmodium malariae* across Africa, characterized by specific adaptive signatures that contribute to the parasite's persistence and transmission.
The paper introduces Point Cloud Local Ancestry Inference (PCLAI), a novel method that replaces discrete ancestry labels with continuous coordinate-based representations to model genetic variation at the haplotypic level, enabling time-stratified insights into how genomic segments have migrated across space and time.
This study presents a high-quality, chromosome-level genome assembly of the biocontrol strain *Fusarium oxysporum* FO12, generated using Nanopore and Hi-C sequencing, which serves as a valuable resource for advancing agricultural applications of this effective biological control agent.
By applying metatranscriptomic sequencing to 300 PCR-negative severe acute respiratory infection samples in New Zealand, this study uncovered a diverse array of co-infecting viral, bacterial, and fungal pathogens missed by routine diagnostics, demonstrating the critical value of genomic approaches for improving diagnostic accuracy and public health surveillance.
This study demonstrates that standalone Oxford Nanopore sequencing of native DNA is sufficiently accurate for routine foodborne pathogen surveillance when supported by a new quality control framework, alpaqa, which identifies and mitigates systematic assembly errors caused by specific DNA modifications.
This study presents the first comprehensive analysis of genetic diversity in *Apis mellifera* Cytochrome P450 genes across 1,467 individuals from 18 subspecies, revealing that positive selection has driven adaptive variation in detoxification-related CYP3 clan genes, thereby establishing a foundational pharmacogenomic resource to predict pesticide vulnerabilities and enhance pollinator resilience.
This study presents a single-cell atlas of pig-to-monkey kidney xenotransplantation that reveals macrophage chimerism and identifies an epithelial-derived IFN-ε axis as a critical orchestrator of a graft-protective immune niche, offering new insights into xenograft adaptation and potential therapeutic targets.
By leveraging multi-modal epigenomic profiling across a telomere-to-telomere human genome reference, this study reveals that transposable elements, particularly SVA and specific Alu and LTR subfamilies, engage in an evolutionary arms race with host defense systems primarily by escaping H3K9me3-mediated heterochromatinization and progressively invading CTCF-rich regulatory regions to drive genomic innovation.
The paper introduces TEsingle, a computational tool that overcomes challenges in repetitive sequence alignment and intron retention to enable accurate, locus-specific analysis of transposable element expression in single-cell transcriptomes, revealing cell-type-specific TE dysregulation in Parkinson's disease.