407 papers
The paper introduces Lorax, a GPU-accelerated, web-native platform that enables real-time, interactive visualization and exploration of biobank-scale ancestral recombination graphs by integrating genomic position, coalescent time, local genealogy, and metadata.
This study presents the first high-quality, chromosome-level genome assembly of the medicinal plant *Helichrysum odoratissimum*, generated using Oxford Nanopore long-read and Hi-C sequencing technologies, to serve as a foundational resource for understanding its bioactivity, evolution, and commercial potential.
This study introduces TimeFlies, a deep learning-based single-nucleus RNA sequencing aging clock for the *Drosophila melanogaster* head that identifies long non-coding RNAs as key biomarkers and reveals distinct sex-specific aging pathways driven by X chromosome dosage compensation.
Through a cross-platform meta-analysis of Hi-C and micro-C datasets following protein depletion, this study demonstrates that functional insulators are distinct from static TAD boundaries and are defined by their ability to dynamically prevent the formation of new, cohesin-dependent enhancer-promoter loops that drive gene activation.
This study utilized whole-genome sequencing of CRFK and PG-4 feline cell lines to infer the coat and iris phenotypes of their original donor cats, thereby elucidating their previously unknown genetic backgrounds and providing a foundation for more accurate interpretation of feline cell data and future genome-editing research.
This paper presents a scalable workflow that integrates large-scale experimental data and predictive models to reclassify the majority of existing variants of uncertain significance (VUS) and preclassify future unobserved variants for 40 disease-associated genes, thereby significantly advancing the clinical application of genomic medicine.
This study presents a reproducible, interpretable pipeline that combines SHAP-guided CpG selection with a stacked ensemble of deep learning and tree-based models to achieve high-accuracy, cross-tissue epigenetic age prediction supported by robust biological annotations.
Pixel2Gene is a deep learning framework that leverages co-registered histology images to denoise, reconstruct, and predict spatial gene expression across diverse high-resolution platforms, thereby overcoming current limitations in cost, coverage, and data quality to enable comprehensive, whole-tissue spatial transcriptomics.
REMAP is a deep learning framework that integrates single-cell RNA-seq data with spatial transcriptomics references to reconstruct multi-scale tissue spatial architecture, outperforming existing methods in resolving cellular neighborhood heterogeneity and identifying disease-relevant subpopulations across diverse biological contexts.
This paper introduces modFDR, a rigorous framework utilizing negative controls to evaluate nanopore sequencing reliability, revealing that while the technology effectively detects abundant DNA modifications, it suffers from significant false-positive rates for rare modifications and false negatives for 5mCpG, necessitating its adoption in future studies and a shift toward prioritizing abundant targets in biomedical applications.
This study demonstrates that genome size, replichore length, and nucleotide compositional skew are significant predictors of bacterial growth rates, with the latter potentially facilitating replication fork progression, although the strength of this association diminishes over evolutionary time as organisms diversify.
The paper proposes CLADES, a contrastive learning framework that leverages evolutionary orthologs as positive pairs to pre-train sequence representations, enabling accurate and interpretable prediction of differential splicing changes across diverse biological contexts.
This study presents two high-quality, regionally representative reference genome assemblies for Australian giant kelp (*Macrocystis pyrifera*), revealing significant genetic and functional divergence from Northern Hemisphere populations and providing essential resources for the conservation and restoration of remnant Southern Hemisphere forests.
This study identifies a single Nepl15 transcript in Oregon-R Drosophila melanogaster that contains minor coding sequence variations compared to the FlyBase reference, suggesting the need for further research into the physiological impact of these differences.
By comparing genome assemblies across seven canine lineages, this study estimates that new LINE-1 and SINEC retrotransposon insertions occur at rates of 1/184 and 1/22 births, respectively, revealing that the high levels of dimorphic retrotransposons in dogs primarily reflect long-standing genetic variation rather than recent rapid mobilization.
By integrating ATAC-seq, molQTL, and GWAS data across 202 porcine skeletal muscle samples, this study reveals distinct developmental shifts in chromatin accessibility between fetal and postnatal stages, identifying stage-specific regulatory variants that prioritize causal mechanisms for agronomically important traits.
This study validates an optimized workflow for generating accurate, genome-wide polymorphism datasets from individual, minute hookworm larvae using whole-genome amplification, enabling the detection of reduced genetic diversity and distinct population structures in laboratory strains compared to field-collected samples.
This study identifies a novel stepwise mechanism called Sporulate-Endoreplicate-Mate (SEM), where spores undergo endoreplication and mating to incrementally generate triploid and tetraploid *Saccharomyces cerevisiae* strains, establishing this iterative process as the predominant natural route to polyploidy in yeast.
This study constructs a reference-free Simmental cattle pangenome from five high-quality haplotype-resolved assemblies to identify crossover events at basepair resolution, demonstrating that integrating structural variants and long-read methylation data with phased SNPs enables the detection of recombination events beyond traditional SNP markers.
This study utilizes a three-population simulation framework to demonstrate that the Southeast-to-Northwest gradient of Neanderthal ancestry in Europe was established by early hunter-gatherer expansion and the Neanderthal range limit, then preserved through subsequent Neolithic migrations despite significantly higher admixture rates between human populations compared to Neanderthal-human interbreeding.