400 papers
This study presents a single-cell atlas of cerebrospinal fluid and peripheral blood that elucidates the pathogenesis of neuropsychiatric systemic lupus erythematosus (NPSLE) by revealing key immune dysregulations, including BAM-CCL3 enrichment and T-cell clonal expansion, while establishing a publicly available resource for future CNS disease research.
This study systematically identifies and characterizes 23 candidate PCOS-associated lncRNAs (PDEGALs) by integrating genetic, transcriptomic, and evolutionary data, highlighting HELLPAR and four other lncRNAs as high-priority targets for future functional validation and therapeutic development in polycystic ovary syndrome.
This study presents a high-quality genome assembly of the red alga *Delisea pulchra*, revealing genetic expansions related to stress responses and identifying candidate genes for its unique halogenated furanone defenses, thereby establishing a foundational resource for investigating chemical host-microbe interactions in marine algae.
This study validates the accuracy of computational variant effect prediction tools in *Brachypodium distachyon* using a novel mutant population, demonstrating that protein language models like ESM effectively predict missense variant fitness while genomic models like PlantCAD outperform traditional regulatory assays for gene-proximal variants.
This paper introduces FindMetapeaks, a machine learning-based approach that analyzes a massive, uniformly reprocessed collection of histone modification ChIP-seq datasets to identify a concise set of genomic "metapeaks" that serve as predictive epigenetic landmarks for distinguishing cell states and regulatory regions.
StrataBionn is a novel supervised neural network framework that outperforms traditional methods in classifying microbial communities into community state types across diverse anatomical sites by effectively capturing complex, non-linear taxonomic signatures to provide more robust and accurate microbiome stratification.
The paper introduces GrAdaBeam, a hybrid optimization algorithm that combines gradient-derived attention maps with adaptive beam search to outperform existing methods across 17 diverse nucleic acid design tasks in the new NucleoBench benchmark, demonstrating superior generalization and biological signal recovery.
This study characterizes over 100 autosomal loci called Inactivation/Stability Centers (I/SCs) that exhibit stochastic, mitotically stable, allele-specific epigenetic regulation of gene expression and replication timing, creating cellular mosaicism that impacts numerous dosage-sensitive genes associated with human diseases.
An analysis of 12 soil viromics datasets reveals that temperate bacteriophages consistently exhibit significantly higher microdiversity than virulent ones, suggesting that lysogeny promotes or preserves genetic variation within phage populations.
This study of the CANDLE cohort reveals that prenatal exposure to air pollution alters infant DNA methylation patterns linked to transient wheeze, but these adverse epigenetic changes can be partially mitigated by higher maternal intake of specific micronutrients and overall diet quality.
This study demonstrates that existing human whole-genome sequencing data from saliva can be effectively repurposed for robust, population-scale oral microbiome profiling by leveraging deep sequencing depth to overcome extraction biases, thereby unlocking vast archives of discarded microbial reads for dual host-microbiome research.
The authors present TrIdent, an R package that automates the time-consuming manual inspection of transductomics data by using pattern-matching algorithms to efficiently and reproducibly identify virus-mediated DNA mobilization, revealing that specific low-abundance bacterial families are heavily involved in this horizontal gene transfer process.
The paper introduces scGRIP, a scalable and interpretable graph variational autoencoder framework that integrates prior cis-regulatory knowledge with single-cell multi-omics data to infer cell-specific gene regulatory networks, demonstrating superior performance in identifying disease-associated regulatory mechanisms in Alzheimer's disease compared to existing methods.
This study defines a polyclonal-to-monoclonal evolutionary trajectory in lung squamous cell carcinoma driven by JNK pathway inhibition and cytoskeletal dysregulation, identifying specific mutational signatures and genes that correlate with poor prognosis and offer new targets for precision therapeutics.
By leveraging a complete diploid human genome and ultra-long-read DiMeLo-seq, this study reveals that DNA methylation acts as a principal regulator of centromere organization, where hypomethylation erodes discrete CENP-A subdomains while hypermethylation consolidates them into broader tracts, thereby maintaining balanced chromatin architecture across haplotypes despite underlying sequence variation.
BioWorldModel introduces a single, dynamic architecture that models phenotype generation as a multi-layered biological process modulated by environment and time, significantly outperforming static predictive methods across bacteria, fungi, animals, and plants by capturing how organisms interpret their genomes rather than merely associating genotypes with outcomes.
This study demonstrates that cardiac-specific deletion of Gpx4 in mice recapitulates human cardiomyopathy by inducing ferroptosis-driven transcriptional changes, thereby identifying key pathways and potential therapeutic targets for heart disease.
This study utilizes pangenome variation graphs alongside phylogenetic and gene-level analyses to reveal distinct evolutionary histories between goatpox and sheeppox viruses, highlighting how structural variation at inverted terminal repeats drives genomic diversity and host specificity in these economically important pathogens.
X-Plat is a cross-platform data transformation tool that utilizes per-gene second-degree polynomial regression to convert legacy microarray expression and methylation data into high-throughput sequencing formats (and vice versa), demonstrating superior accuracy compared to existing methods across multiple organisms and enabling the integration of heterogeneous biological datasets.
This study demonstrates that while soil viral biogeography is influenced by dispersal opportunities, the activity of host communities—rather than their specific taxonomic composition—is the primary driver shaping viral diversity and distribution in both bulk and rhizosphere soils throughout a tomato growing season.