407 papers
The paper introduces PatchDNA, a flexible, biologically-informed approach that replaces fixed tokenization with evolutionary conservation-guided patching to create more efficient DNA language models that achieve state-of-the-art performance with significantly smaller architectures while allowing dynamic adjustments without retraining.
This study presents a complete, custom diploid genome assembly and comprehensive annotation for the KOLF2.1J reference iPSC line, offering a more accurate genomic resource than traditional references to improve the investigation of neurodegenerative disease mechanisms and establish a framework for future high-value cell line references.
This study demonstrates that persistent SARS-CoV-2 Spike protein in the gut tissues of Long COVID patients drives localized immune dysregulation characterized by specific gene expression changes, myeloid and T-cell enrichment, and a dysfunctional pro-inflammatory microenvironment, particularly within the colon.
The paper introduces ACE-OF-Clust, a scalable four-step workflow that addresses the clustering alignment problem in single-cell omics by integrating multiple clustering solutions, comparing models against annotations, and identifying informative features to enhance the interpretability and robustness of cellular heterogeneity analysis.
This study reveals that the histone-to-protamine exchange during spermiogenesis is not a stochastic process but a highly programmed event dictated by the 3D chromatin architecture of round spermatids, which establishes a specific spatiotemporal blueprint for sperm epigenome assembly.
This study presents a high-quality, chromosome-level genome assembly of the South African lion (Panthera leo melanochaita) generated using PacBio HiFi and Omni-C technologies, providing a critical genomic resource to support future population genomic and conservation efforts for this threatened species.
The paper introduces ChromSMF, a novel method that utilizes antibody-guided tethering and Nanopore sequencing to simultaneously profile histone modifications, protein-DNA interactions, nucleosome occupancy, and DNA methylation on individual multi-kilobase DNA molecules, thereby enabling the integrated analysis of combinatorial epigenetic regulation across entire cis-regulatory landscapes.
BenchDrop-seq is a novel, microfluidics-free benchtop platform that combines particle-templated partitioning with Oxford Nanopore sequencing to enable scalable, cost-effective, and isoform-resolved single-cell long-read RNA sequencing using standard laboratory equipment.
The paper introduces paired plus-minus sequencing (ppmSeq), a highly efficient and accurate method that partitions and amplifies both DNA strands on single beads to achieve superior duplex recovery rates and ultra-low error rates, enabling sensitive, tumor-naive circulating tumor DNA detection for clinical applications.
This study demonstrates that while incorporating data-driven genotype-to-phenotype structures into individual Graph Attention Networks did not consistently improve genomic prediction for maize flowering time, ensembling models across a continuum of such structures significantly enhanced prediction performance by integrating complementary information from diverse biological representations.
By integrating extensive COFRADIC proteomics with the high-sensitivity sel-TRAP approach, this study constructs the most comprehensive map of the human and yeast Nt-acetylomes to date, revealing refined Nat substrate specificities and uncovering hundreds of previously hidden cryptic substrates generated by alternative translation initiation.
This study defines the comprehensive interactome of the pioneer factor Zelda in *Drosophila* embryos, revealing that it recruits a diverse array of co-activators, chromatin remodelers, and the transcriptional machinery to orchestrate zygotic genome activation while coordinating transcription with early mitotic cycles.
By analyzing complete genome assemblies of 151 global *Mycobacterium tuberculosis* isolates, this study reveals that recurrent gene conversion within paralogous regions, particularly in virulence-associated PE, PPE, and ESX gene families, acts as a primary driver of significant antigenic and virulence diversity in this otherwise genetically conserved pathogen.
This study presents a large-scale, cross-organ single-cell transcriptomic meta-analysis of over five million cells from human heart, liver, kidney, and lung tissues to construct a unified fibrosis atlas that identifies both shared and organ-specific gene expression programs, ultimately providing an open resource to accelerate the discovery of antifibrotic therapies.
This study demonstrates that the URINN rapid metagenomic workflow accurately identifies uropathogens, resistance genes, and virulence factors from urine samples within four hours, enabling early tailored therapy and improved antimicrobial stewardship for complicated urinary tract infections.
This study demonstrates that unsupervised, explainable AI analysis of oligonucleotide usage patterns in the human genome reveals approximately 2,000 distinct functional zones that align with high-resolution prophase chromosome bands, effectively bridging classical cytogenetics and modern genomics by predicting banding structures from sequence data alone.
This study presents the first draft genome assembly of the invasive decaploid species *Ludwigia grandiflora* subsp. *hexapetala*, validated through gene expression analysis, providing a foundational resource for evolutionary and functional genomics within the Onagraceae family despite challenges posed by high fragmentation and repetitive regions.
This study utilizes single-cell whole-genome methylation data to demonstrate that aging is a heterogeneous, cell-specific process characterized by accelerated Average Polycomb CpG Methylation in rapidly proliferating cells, which correlates with distinct changes in immune response, translation regulation, and tumorigenesis.
The paper introduces scDEcrypter, an uncertainty-aware penalized two-way mixture model that leverages partial infection labels and cell type information to overcome sparse viral reads and bystander effects, thereby improving the accuracy of differential expression analysis in viral infection scRNA-seq studies.
This study demonstrates that the histone chaperone HIRA-mediated deposition of histone variant H3.3 is essential for preserving hepatocyte cell identity and metabolic function during aging in non-proliferating cells, a role that can be compensated for by canonical histone deposition during tissue regeneration-induced proliferation.