414 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 introduces an amplification-free MERFISH-based pooled screening method that significantly enhances the detection of genetic perturbations and endogenous RNAs in intact tissues, enabling the systematic mapping of both cell-autonomous and cell non-autonomous phenotypic responses across millions of cells in a genetic mosaic mouse liver model.
By screening 4,000 yeast deletion mutants, this study reveals that the tardigrade Dsup protein confers cadmium resistance through a dose-dependent mechanism that shifts from broadly buffering cellular processes at low stress levels to targeting specific genes at higher doses, thereby identifying host genetic factors that influence Dsup-mediated protection.
This study develops and validates rapid, high-throughput genome-based multilocus sequence typing (MLST) schemes for *Histoplasma capsulatum* using 406 genome assemblies, demonstrating their ability to reproducibly distinguish all seven major lineages and six sublineages without requiring high-performance computing resources.
This study utilizes whole-genome sequencing of 249 *Plasmodium falciparum* isolates from 2023 to characterize Uganda's high genetic diversity and low population structure while identifying specific haplotypes associated with artemisinin and partner drug resistance, thereby establishing a baseline for coordinated genomic surveillance across Uganda and neighboring countries.
This study analyzes the evolutionary dynamics of the IS6110 insertion sequence across 10,000 *Mycobacterium tuberculosis* complex strains using a reference-free detection tool and ancestral state reconstruction, revealing that its distribution is shaped by a combination of non-random insertion into specific DNA motifs and purifying selection, ultimately governed by a niche constraints model where insertions accumulate only in genomic regions with suitable properties and minimal functional impact.
This study utilizes single-nucleus RNA sequencing of the human prefrontal cortex to reveal that the co-occurrence of alcohol use disorder and smoking synergistically expands cell-type-specific molecular alterations—particularly neuroinflammation, proteostatic stress, and post-transcriptional remodeling—across diverse neuronal and glial populations, leading to a more severe and widespread cortical dysfunction than either condition alone.
The authors developed PfPHAST, a streamlined 56-target amplicon sequencing panel derived from the comprehensive MAD4HatTeR tool, which offers a scalable, lower-cost alternative for routine public health malaria genomic surveillance while maintaining comparable performance in detecting drug resistance, diagnostic failures, and vaccine targets.
By analyzing haplotype-resolved long-read genome assemblies from 292 donors, this study reveals that HERV-K(HML-2) exhibits significant structural polymorphism and variable coding capacity across human pangenomes, demonstrating that standard reference genomes and short-read sequencing often fail to accurately capture the intact proviral structures and functional alleles present in individuals.
This study identifies a novel postmeiotic route to polyploidy in *Saccharomyces cerevisiae* called Sporulate-Endoreplicate-Mate (SEM), where a spore undergoes endoreplication before mating with a sibling to form triploids and tetraploids, suggesting this mechanism is a major natural pathway for polyploid genome formation in yeast and potentially other eukaryotes.
This study utilized the high-throughput SSRseq method to develop highly polymorphic and reliable microsatellite markers for *Glossina palpalis gambiensis* and *G. p. palpalis*, revealing high genetic diversity and extensive movement across three sleeping sickness foci in Guinea and Côte d'Ivoire while highlighting potential evolutionary responses to vector control measures.