309 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 WaveSeekerNet model accurately predicts influenza A virus host origins and reveals distinct genomic adaptation patterns between avian and mammalian hosts, offering a quantitative framework for assessing zoonotic risk and identifying key adaptive mutations.
This study reveals that while insertion sequence (IS) elements, particularly the IS256 family, drive significant genetic diversification in *Staphylococcus epidermidis* during persistent orthopaedic device-related infections, the strains' high-level multidrug resistance and biofilm-forming capabilities are likely pre-existing traits of epidemic clones rather than results of rapid within-host adaptation.
The paper introduces SpeciMiR, a generative AI framework trained on 2.2 million miRNA-mRNA pairs that synthesizes target-specific siRNA sequences with enhanced on-target potency and minimized off-target effects, successfully recovering binding regions corresponding to FDA-approved liver disease drugs.
This study introduces a Bayesian framework that successfully estimates mosaic loss of chromosome Y (LOY) from bulk male RNA-seq data by modeling reduced Y-linked gene expression, achieving strong correlation with DNA-based measurements for large LOY events while highlighting the method's limitations due to transcriptional confounding and its nature as a probabilistic rather than direct substitute for DNA-based assays.
The paper introduces PerturbPlan, an interactive web application that utilizes a novel, computationally efficient analytical formula to enable the rapid and flexible design of well-powered single-cell CRISPR screen experiments, overcoming the limitations of existing simulation-based tools.
By analyzing over a million somatic mutations across thirteen human tissues, this study reveals that the aging genome exhibits "organized vulnerability" where critical, highly connected genes are systematically protected from mutations through transcription-coupled repair and selective filtering, suggesting that organismal decline is driven not by the total mutational burden but by the specific network locations where mutations accumulate.
This study establishes a comprehensive atlas of snoRNA expression and 2'-O-methylation sites in *Drosophila melanogaster* S2 cells using RibOxi-seq2, revealing widespread modifications in rRNAs, snRNAs, and mRNAs while identifying novel consensus sequences that may guide mRNA methylation despite the absence of canonical guiding snoRNAs.
This study demonstrates that while ambient temperature storage methods (FTA cards and DESS buffer) yield lower sequencing quality for individual parasitic nematode larvae compared to frozen controls, they provide comparable results for pooled samples, offering a viable alternative for whole-genome sequencing in resource-limited settings.
This study presents Jindo1-G-TTAGGA, the first complete, gapless, and haplotype-resolved canine reference genome that meets a stringent TTAGGA standard, featuring a single-contig Y chromosome that resolves approximately 79% of the full-length canine Y and significantly advances the understanding of canine structural variation and sex-chromosome evolution.
This study demonstrates that CDK12 and CDK13 play distinct roles in suppressing intronic polyadenylation to maintain transcript integrity, and reveals that the resulting prematurely terminated transcripts are translationally competent, generating novel intronic peptides that could serve as tumor-specific neoantigens in CDK12/13-deficient cancers.