336 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 utilizes comprehensive phylogenomic and comparative genomic analyses of 104 *Erwinia* strains to resolve evolutionary relationships, identify taxonomic inconsistencies, and demonstrate how lineage-specific genomic plasticity drives ecological adaptation and pathogenicity through diverse combinations of virulence factors.
This study reveals that homologous recombination and genome plasticity drive the evolution and host adaptation of the emerging soft rot pathogen *Pectobacterium jejuense*, as evidenced by global genomic analyses of 214 strains that identified distinct lineages, extensive interspecies gene flow, and unique adaptive features in Hawaiian isolates.
By re-mapping SNP data to a native buffalo reference genome, this study reveals that Nili-Ravi buffalo exhibit selection signatures in a T-cell costimulatory and cytokine-signaling gene network rather than in classical bovine tuberculosis candidate genes, highlighting the critical importance of species-specific genomic resources for accurate disease resistance inference.
This paper presents a gene model for the Density regulated protein (DENR) ortholog in *Drosophila pseudoobscura*, characterized as part of an undergraduate research project investigating the evolution of the Insulin signaling pathway across the *Drosophila* genus.
This study leverages deep RNA-seq and genotype data from 336 human brain samples to identify thousands of short tandem repeats that significantly influence alternative splicing, revealing their potential role in regulating RNA-binding protein interactions and contributing to the genetic risk of brain-related disorders such as Alzheimer's disease and schizophrenia.
This study validates nanopore whole-genome sequencing as a cost-effective tool for clinical carbapenem-resistant Enterobacterales surveillance, demonstrating its superiority over routine diagnostics in resolving genomic context and defining specific sequencing depth requirements (10x to 40x) for accurate species identification, strain typing, and plasmid-level epidemiology.
This paper presents Pan20, a barley pangenome graph built from the MorexV3 reference and global diversity data, which utilizes a novel greedy mapping strategy and Practical Haplotype Graph (PHG) approach to enable accurate sequence alignment, presence-absence variation detection, and efficient genomic imputation beyond the limitations of a single linear reference.
This study introduces BLink-seq, a scalable, low-cost linked-read sequencing framework compatible with standard short-read platforms that enables population-scale generation of chromosome-scale phased haplotypes and structural variant detection in non-model species, as demonstrated through validation in *Drosophila melanogaster* and large-scale application to Atlantic silverside populations.
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.