403 papers
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.
This study presents the first chromosome-level genome assembly of the invasive erythrina gall wasp (*Quadrastichus erythrinae*) and its *Wolbachia* endosymbiont, providing a foundational resource for comparative evolutionary and pest management research.
This study demonstrates that heat stress induces locus-specific DNA hypomethylation in the blood of lactating Holstein cows, particularly within regulatory regions of immune-related genes such as MSN and MECP2, thereby revealing a novel epigenetic mechanism underlying the modulation of the dairy cow immune system under environmental stress.
By integrating genomic and transcriptomic data across 23 Solanoideae species, this study reveals that a centralized pangenome architecture driven by lineage-specific tandem and proximal duplications, rather than broad diversification or whole-genome duplication, orchestrates the asymmetric evolution and functional differentiation of NLR immune receptors to combat biotic stress.
This study reveals that enzymatic methylation sequencing (EM-seq) suffers from a reproducible fragment-level over-conversion error that creates false-positive unmethylated signals, thereby significantly limiting its specificity for cell-free DNA methylation analysis compared to bisulfite and nanopore methods.
This study establishes a comprehensive genomic database of 2,658 *Desulfovibrio* genomes to reveal species-specific functional traits, such as flagellin-mediated immune modulation and disease-exclusive metabolic pathways, that link strain variation to inflammatory diseases.
This study presents GmHapMap-II, a comprehensive global soybean haplotype map derived from 1,278 accessions, which serves as a powerful genomic resource for discovering novel trait associations, characterizing structural variations, and accelerating the development of improved cultivars through enhanced genomic prediction and breeding strategies.
This study presents a high-quality, telomere-to-telomere assembly of the Lumpy skin disease virus (LSDV) Oman 2009 isolate using a hybrid short- and long-read sequencing approach, which resolves complex telomeric structures, corrects previous misassemblies, and establishes a robust reference for future genomic surveillance and evolutionary analysis.
By integrating large-scale genomic data, a genomic language model, and deep mutational scanning, this study develops the NMDetective-AI framework to quantitatively predict nonsense-mediated mRNA decay across human genes, revealing that NMD follows graded, gene-dependent rules shaped by transcript architecture and local sequence context rather than simple binary thresholds.
This study suggests that temperate and filamentous bacteriophages may drive the emergence of virulence in stony coral tissue loss disease (SCTLD) by integrating into bacterial genomes and transferring virulence genes, offering a potential mechanistic explanation for the disease's pathology despite the unknown primary etiological agent.
This study presents the first telomere-to-telomere reference genome and a pangenome for the common marmoset, resolving complex genomic regions like centromeres and the MHC to significantly enhance its utility as a biomedical model and deepen our understanding of primate evolution.
The paper introduces PlasBin-HMF, a novel multi-flow approach formulated as a Mixed-Integer Linear Program that outperforms existing state-of-the-art methods in accurately binning circular plasmids from short-read assembly graphs while maintaining explainability.
This study demonstrates that the onset of adaptive immunity triggers a rapid physiological reprogramming of *Mycobacterium tuberculosis* from a metabolically active state to an immune-constrained one, thereby explaining the divergent drug efficacy observed between high-dose and low-dose mouse infection models and highlighting the need for therapeutic strategies targeting both bacterial states.
The paper introduces LAMBDA, a comprehensive benchmark designed to evaluate the predictive capabilities of genomic language models through phage-bacteria sequence discrimination, revealing critical insights into the importance of training data quality and domain-specific training for effective prophage detection.
This paper evaluates seven Genomic Foundation Models across 52 tasks and finds that randomly initialized models often serve as strong baselines, with pretraining offering only modest, tokenizer-dependent gains while failing to capture clinically relevant genetic mutations.
This study systematically compares three mouse models of menopause—intact aging, VCD-induced follicle depletion, and Foxl2 haploinsufficiency—using multi-omics and machine learning to define their shared and distinct molecular and phenotypic features, thereby providing a framework for selecting context-appropriate preclinical models to study ovarian aging and its systemic health consequences.
This paper proposes using perplexity, an entropy-based metric that incorporates all isoforms regardless of abundance, as a more interpretable and reproducible alternative to arbitrary expression thresholds for quantifying isoform diversity across human cell types using long-read RNA-sequencing data.
The paper introduces KLinterSel, a Python-based software tool that employs two complementary statistical tests to rigorously evaluate whether overlaps in candidate genomic regions detected by different selective sweep methods exceed random expectations, thereby distinguishing genuine methodological concordance from artifacts caused by underlying genomic structure.