400 papers
This study presents the first telomere-to-telomere, haplotype-resolved diploid reference genome for the widely used human embryonic stem cell line H9, revealing unique structural features like extended telomeres and chromosome inversions while establishing a high-precision resource for allele-specific multi-omic analyses of human development and disease.
This study utilizes Hi-C to reveal that programmed DNA elimination in nematodes involves distinct, species-specific spatial interactions at chromosomal breakage regions that demarcate retained versus eliminated DNA, while demonstrating that the resulting 3D genome reorganization of somatic chromosomes is evolutionarily conserved across *Ascaris* and *Parascaris*.
This study demonstrates that transient delivery of DNA methylation-based epigenome editors to human hematopoietic stem cells enables stable, heritable, and reversible silencing of the platelet integrin ITGB3, resulting in sustained prevention of thrombosis through impaired platelet aggregation.
By leveraging advances in protein structure prediction to explore the metagenome, researchers discovered novel compact RNA-guided nucleases that combine small size with broad PAM diversity, offering superior candidates for in vivo genome editing compared to existing systems.
This study reveals that spaceflight induces a universal "Systemic Genome Correlation Loss," where the regulatory architecture of the transcriptome undergoes profound decoherence and stochasticity, causing survival-critical networks to remain intact while non-essential systems shatter, thereby shifting the paradigm for astronaut health risks from gene abundance changes to the entropic decay of gene-gene synchronization.
MINTsC is a novel computational method that leverages single-cell Hi-C data to infer multi-way chromatin interactions, offering well-calibrated statistical significance and revealing biologically relevant regulatory mechanisms while reducing the multiple-testing burden for association studies.
This study presents the first comprehensive analysis of non-canonical DNA motifs in birds using high-quality genomes, revealing that these structures are uniquely enriched on gene-rich dot chromosomes, play regulatory roles similar to mammals, and pose significant challenges for genome assembly due to their association with sequencing depth limitations.
This study establishes that meiotic cells utilize two distinct DNA repair pathways to direct crossovers away from transcriptionally active genes, thereby safeguarding gene function through an evolutionarily conserved mechanism where early transcriptional context determines whether a double-strand break is resolved as a non-crossover or a crossover.
This paper presents a systematic workflow for identifying and filtering seed-driven off-target effects in CRISPRi Perturb-seq experiments by leveraging transcriptional similarity between cells harboring off-target guides and those with direct on-target perturbations, thereby establishing a principled framework to prevent erroneous gene-pathway associations in genome-wide analyses.
This study analyzes mutation profiles from nearly 12,000 normal human samples across 25 tissues to identify both universal and tissue-specific mutagenic mechanisms, revealing that while clock-like processes and APOBEC activity are widespread, UV-induced mutagenesis is skin-specific and diseased tissues exhibit significantly higher, age-independent mutation accumulation.
This paper introduces a novel window-based SNP-similarity method that enables accurate across-chromosome phasing in unrelated individuals without requiring parental or relative data, achieving up to 95% accuracy when within-chromosome phase errors are minimized.
By integrating multi-omics data from trabecular meshwork cells and retinal ganglion cells, this study identifies ARHGEF12 as a primary open-angle glaucoma effector gene, demonstrating that risk-associated homozygosity leads to reduced expression, morphological defects, and disrupted neuronal activity specifically in retinal ganglion cells.
Pathotypr is a rapid, alignment-free tool that enables harmonized assignment of all 14 recognized *Mycobacterium tuberculosis* complex lineages and high-confidence detection of drug-resistance variants from genomic data, facilitating near real-time, cross-border tuberculosis surveillance.
This study presents a comprehensive single-cell and spatial atlas of prostate cancer from 128 patients that reveals how combinatorial gene modules drive lineage plasticity and metastasis, identifies distinct tumor microenvironment features, and introduces a transformer-based foundation model for automated cell-state classification.
NetTracer3D is a user-friendly, integrated tool that standardizes the analysis, sharing, and visualization of diverse 3D microscopic and medical datasets through three distinct network modalities—connectivity, branch adjacency, and proximity—to reveal structural and physiological relationships across various tissue types and imaging modalities.
This study demonstrates that Oxford Nanopore enrichment-mode adaptive sampling enables the efficient, culture-free, de novo reconstruction of near-complete intracellular *Wolbachia* genomes directly from host tissues, overcoming challenges of low abundance and significant reference divergence to reveal novel genomic features like strain-specific prophage expansions and chromosomal rearrangements.
This study demonstrates that individual-specific recovery of the human skin barrier following disruption is significantly shaped by distinct host-microbe interactions, where specific microbial community stability profiles and functional changes correlate with varying host recovery timelines.
This study demonstrates that environmental gradients, particularly salinity and temperature, combined with taxon-specific metabolic strategies and functional redundancy, govern the abundance, activity, and resilience of hydrocarbon-degrading microbiomes in the Delaware and Chesapeake Bays.
This study presents high-quality, haplotype-resolved genome assemblies of hybrid wheatgrass and bluebunch wheatgrass that elucidate the species' stepwise polyploid origin, reveal the H subgenome's unique evolutionary position and expression dominance driven by selective adaptation, and provide a foundational framework for breeding stress-tolerant crops.
This study demonstrates that replication-associated hypomethylation at solo-WCGW CpGs serves as a shared epigenetic signature of cumulative immune cell proliferation across multiple immune-mediated diseases, while also revealing disease-specific methylation changes in antigen receptor loci that reflect unique immune dynamics.