407 papers
This study identifies p63 as a critical molecular switch that maintains the glucocorticoid receptor's tumor-suppressive function in prostate cancer, revealing that its loss reprograms the receptor into an oncogene via GATA2 and FRA1-mediated transcriptional changes, thereby driving antiandrogen resistance and disease progression.
This study establishes a comprehensive atlas of mammalian non-canonical open reading frames (ncORFs) by analyzing ribosome profiling data from hundreds of tissues, revealing that thousands of these elements are evolutionarily conserved, highly translated, and functionally integrated into the proteome through co-translation with canonical coding sequences.
This study of Uruguayan infants reveals that the mode of delivery (vaginal vs. cesarean) significantly shapes gut microbiota composition and its distinct correlations with breast milk components and maternal stress even during exclusive breastfeeding at a mean age of 5.4 months.
This study demonstrates that LINE-1 retrotransposition directly drives genomic instability and cancer evolution by inducing diverse chromosomal rearrangements, such as translocations and inversions, through illegitimate recombination of double-strand breaks, which subsequently fuel complex genetic alterations via breakage-fusion-bridge cycles.
This study establishes a unifying developmental framework for DNA methylation programming by integrating cross-species data from mice and humans to reveal how genetic variants disrupt transcription factor binding to shape tissue-specific and developmental epigenetic landscapes, thereby linking sequence variation to gene regulation and disease.
GALA is a unified, landmark-free framework that leverages genetic algorithm-guided large deformation and modality-aware rasterization to achieve robust, accurate, and efficient spatial alignment of transcriptomic and histological data across diverse resolutions, modalities, and tissue coverage scenarios.
This study utilizes long-read metagenomic sequencing to generate the largest Lecanoromycetes genomes to date, revealing that high transposable element content and their associated gene adaptations are key drivers in the evolution of Peltigerales lichen symbionts.
This paper presents a scalable, modality-agnostic AAV-based in vivo screening platform coupled with a human disease signature-matching analysis framework to identify and validate therapeutic targets across diverse species and organ systems, successfully demonstrating its efficacy in murine pulmonary fibrosis and equine osteoarthritis models.
By integrating multiomic data from over 5.4 million immune cells across nearly 2,000 individuals, this study reveals that tandem repeat variation is a major, cell type-specific regulator of gene expression and a key driver of complex immune and hematological traits.
This study demonstrates that genomic selection for flax seed yield is ready for routine breeding deployment, as using breeding-oriented training populations and moderate-density SNP panels enables high prediction accuracy, significantly reduces field evaluation costs, and accelerates breeding cycles.
This study presents a high-quality, chromosome-scale consensus genome sequence for the social amoeba *Dictyostelium giganteum* derived from six Indian strains, revealing its AT-rich composition, extensive synteny with related dictyostelids, and a conserved Amoebozoan core alongside lineage-specific adaptations that illuminate the evolutionary roots of aggregative multicellularity.
This paper presents iCLIP3, an optimized, non-radioactive protocol that streamlines the generation of high-resolution, transcriptome-wide maps of protein-RNA interactions from low-input material through key improvements in visualization, RNA isolation, and library multiplexing.
The paper introduces UTOPIA, a model-agnostic framework that provides statistically calibrated, multiscale confidence scores for virtual spatial transcriptomics predictions, thereby enhancing interpretability and preventing false biological conclusions across varying spatial resolutions and biological granularities.
This study introduces a de novo workflow to identify non-autonomous LTR retrotransposons in sugar beet without prior sequence information, revealing a vast, previously overlooked diversity of families that exhibit modular evolution and are largely missed by current annotation methods.
This study utilizes single-cell multi-omics analysis of 580,353 cells from the prefrontal cortex, amygdala, and cerebellum to reveal that while HIV primarily activates immune pathways in glial cells, opioid use disorder specifically impairs neuronal metabolic function and alters calcium channel activity, with comorbid infection exacerbating metabolic dysregulation in cortical glia and uniquely affecting cerebellar cell types.
This paper introduces a contrastive learning framework that aligns single-cell RNA-seq expression with copy number variations to identify dosage-insensitive genes in lung adenocarcinoma, revealing specific regulatory escape and compensation mechanisms that persist despite genomic alterations.
This study establishes that the evolution of complex multicellularity is characterized by a scaling law where genome growth is driven primarily by noncoding DNA expansion rather than a proportional increase in coding genes, which saturates beyond approximately 40 Mb of genic content.
The ROME pilot study established a network of eDNA-based observatories across four French estuarine ecosystems to demonstrate how integrating coastal microbiome monitoring within a One Health framework enables high-resolution surveillance of microbial biodiversity and early detection of risks to human, oyster, and environmental health.
This study leverages the BakRep repository to analyze 37,970 *Streptococcus agalactiae* genomes, revealing global trends in serotype distribution, lineage-specific virulence, and widespread antimicrobial resistance while highlighting critical gaps in metadata that currently limit comprehensive epidemiological insights.
This study reconstructs a comprehensive, transcript-resolved catalogue of human enhancer RNAs (eRNAs) across diverse tissues and disease contexts, revealing reproducible, cell-type-specific splicing patterns and providing a new annotation framework to enable functional investigation of eRNA biology.