407 papers
The paper introduces MitoDrift, a probabilistic framework that leverages somatic mitochondrial DNA mutations to achieve high-precision, engineering-free single-cell lineage tracing in humans, thereby revealing critical insights into clonal dynamics during aging and disease that were previously undetectable.
This study identifies miR-199-5p as a key post-transcriptional regulator that suppresses *ifi27l2a* expression in European seabass, thereby modulating resistance to viral nervous necrosis and serving as a promising biomarker for aquaculture breeding.
This study demonstrates that nanopore metagenomic sequencing can accurately link antimicrobial resistance genes to their specific bacterial hosts in clinical samples by exploiting DNA methylation patterns, thereby enabling culture-free, rapid pathogen and resistance surveillance.
This study presents high-quality, chromosome-level reference genomes for *P. falciparum*, *P. ovale wallikeri*, and *P. malariae* derived directly from natural infections using advanced sequencing technologies, thereby resolving previously inaccessible genomic regions and providing a critical foundation for global malaria elimination efforts.
This study characterizes the global diversity of the sourdough yeast *Mauriziozyma humilis*, revealing a complex evolutionary history driven by hybridization and ploidy variation that shapes its phenotypic landscape more significantly than ploidy level alone.
CLM-X is a novel multimodal single-cell foundation model based on a flexible multi-way Transformer architecture that unifies the analysis of scRNA-seq and scATAC-seq data, demonstrating superior performance over existing methods in tasks such as cross-modal translation, cell type annotation, and perturbation prediction.
By analyzing nearly 9,000 tumors from The Cancer Genome Atlas, this study reveals that the frequency of two-hit inactivation in tumor suppressor genes is driven by a complex interplay of mutation functional impact, chromosomal context, and aneuploidy biases, offering a refined framework for understanding the heterogeneity of tumor suppressor behavior and its clinical implications.
By integrating human genetic data with mouse single-cell transcriptomics, this study identifies distinct cochlear cell types—specifically hair cells for sensory and spiral ganglion neurons for metabolic components—underlying different subtypes of age-related hearing loss, while revealing that age-related transcriptional heterogeneity shifts the expression patterns of risk genes in supporting cells and stria vascularis intermediate cells.
This study presents the first chromosome-scale, haplotype-resolved genome assembly of the citral-rich lemongrass *Cymbopogon flexuosus* var. Krishna, generated using PacBio HiFi and Omni-C technologies, which provides a foundational genomic resource for advancing molecular breeding and metabolic engineering in aromatic grasses.
This paper introduces HERVarium, a comprehensive interactive database that systematically annotates the protein-domain architecture and regulatory landscape of over 400,000 human endogenous retrovirus LTRs, revealing distinct functional specializations and structural preservation patterns across the human genome.
This study utilizes Visium HD high-resolution spatial transcriptomics to generate a detailed, sub-cellular resolution map of gene expression in healthy adult and pediatric human livers, revealing spatially distinct cellular heterogeneity and providing a valuable resource for identifying disease signatures and therapeutic targets.
Whole-genome resequencing of Pacific gray whales reveals that the currently small Western North Pacific stock possesses unexpectedly high genetic diversity resulting from historical admixture between the Eastern and Western stocks, challenging previous assumptions about their extirpation and highlighting the role of gene flow in recovering genetic variation.
The paper introduces Mahi, a scalable and interpretable multi-modal graph neural network that integrates diverse molecular features within tissue-specific contexts to outperform sequence-based models in predicting gene essentiality, modeling perturbation responses, and identifying therapeutic targets for precision medicine.
This study demonstrates that early exposure to estradiol confers a protective effect against neuronal network hyperexcitability and associated behavioral deficits in a subset of autism and neurodevelopmental disorder risk genes, potentially explaining the male sex bias in autism spectrum disorder.
This study compares manual and automated transposable element annotation methods in *Drosophila melanogaster* and *Aedes albopictus*, concluding that while automated pipelines are efficient for large-scale comparative analyses, manual curation remains superior for detailed population genomics and studies of recent TE activity, particularly in complex genomes.
By leveraging fully phased telomere-to-telomere pedigree assemblies and matched long-read epigenomes across cell-fate transitions, this study reveals that while human centromeric dip regions maintain positional stability across generations and differentiation, their epigenetic architecture exhibits remarkable plasticity, characterized by dynamic methylation changes during reprogramming and differentiation, insulation from X-chromosome status, and a distinct pattern of de novo mutations that are enriched in centromeric regions but depleted within functional cores.
Using enhanced Hi-C Capture Analysis (eHiCA) on frontal cortex and microglia data, this study elucidates the complex regulatory architecture of the PICALM-EED locus in Alzheimer's disease, revealing that PICALM is the primary causal driver interacting with specific cis-regulatory elements and demonstrating how distinct SNPs within a risk haplotype exhibit unique chromatin interactions.
This study employs specialized mathematical and computational estimation approaches to demonstrate that classical non-parametric techniques outperform model-based methods in predicting undiscovered phage species, thereby providing a framework to optimize future isolation efforts for combating antimicrobial resistance.
This study utilizes bulk segregant analysis on historical *Anopheles gambiae* crosses to map the genomic architecture of early metabolic DDT resistance, revealing that amino acid substitutions and promoter variations in the GSTe gene cluster on chromosome 3R established a metabolic resistance foundation that persists in East African mosquito populations today.
This study employs a comparative multi-omics approach to demonstrate that *Mycobacterium bovis* drives distinct epigenomic reprogramming in bovine alveolar macrophages compared to other *M. tuberculosis* complex bacteria, revealing specific host-pathogen interaction mechanisms and identifying candidate genes that could inform breeding strategies for enhanced tuberculosis resilience in cattle.