407 papers
This paper introduces a controlled benchmarking framework to evaluate DNA foundation models like Evo2, revealing systematic blind spots in their ability to capture essential biological signals and challenging their current readiness for clinical variant-effect prediction.
By analyzing near-complete long-read assemblies from human and ape genomes alongside organoid data, this study elucidates the evolutionary history, structural diversity, and regulatory landscape of human-specific NOTCH2NL duplications, revealing their independent origins, copy number variations, and distinct regulatory elements that likely contributed to human brain expansion.
This study provides the first nuclear genome profiling of *Epidendrum anisatum* and *Epidendrum marmoratum* by integrating flow cytometry and k-mer analysis to reveal that both species are diploid with highly repetitive genomes dominated by Ty3-gypsy retrotransposons, where the significant 2.3-fold genome size difference is primarily driven by the expansion of these transposons and a species-specific 172 bp satellite in *E. anisatum*.
The paper introduces GeoAdvAE, a geometry-aware adversarial autoencoder that successfully integrates unpaired single-cell morphology and transcriptomics data to reveal novel biological insights into microglial form-function relationships in Alzheimer's disease, outperforming existing methods in cross-modal cell-type matching.
This study reveals that non-recombining UV mating-type chromosomes in diverse phytoplankton species undergo extensive genomic erosion through chromatin-mediated splicing deficiency and intron retention rather than gene loss, offering a novel model for understanding how recombination suppression compromises RNA processing fidelity over deep evolutionary time.
This study reveals that proliferating facioscapulohumeral muscular dystrophy (FSHD) myoblasts exhibit a transient, stage-specific architectural chromatin accessibility state characterized by widespread remodeling of non-coding and heterochromatic regions, which is largely resolved upon differentiation and appears largely uncoupled from canonical DUX4-driven programs.
This study introduces CollapsedChrom, a novel bioinformatic pipeline that leverages read depth profiling and karyotypic data to successfully resolve and rescue collapsed chromosomal segments, thereby generating high-quality, chromosome-level reference genomes for the complex polyploid grass species *Brachypodium phoenicoides* and *B. boissieri*.
The paper introduces BacPT, a bacterial proteome foundation model trained on tens of thousands of genomes that leverages unsupervised deep learning to generate contextualized gene embeddings, thereby significantly enhancing the prediction of enzyme activities, metabolic traits, and ecological interactions across diverse bacterial taxa.
This study introduces a novel short-read genotyping method to detect Robertsonian translocations in large biobank cohorts, revealing a consistent carrier frequency of approximately 0.11–0.12% and uncovering previously uncharacterized structural variations in distal junction regions of acrocentric chromosomes.
This study reveals that histone-protamine replacement during spermiogenesis is orchestrated within a compartment-centered framework where transient genome-wide chromatin accessibility facilitates PRM1 loading in A-compartments, a process essential for maintaining sperm genome stability and preventing DNA fragmentation.
This study demonstrates the feasibility of non-invasive whole genome sequencing of humpback whales by collecting exhaled blow samples via drone, successfully generating high-quality genetic data sufficient for population genomics without the need for invasive tissue sampling.
This study utilizes longitudinal data from birth to adulthood to identify dynamic genetic variants that regulate DNA methylation in an age-dependent manner, revealing that these influences often increase over time and are enriched in developmental pathways.
This paper presents a novel RNA-seq annotation pipeline that leverages massive public data to significantly improve mouse and rat genome annotations by identifying tens of thousands of previously unannotated genes and hundreds of thousands of new transcripts, which are now available in standard formats for functional analysis.
This study demonstrates that supervised aerobic exercise induces specific skeletal muscle transcriptomic and DNA methylation changes related to immunomodulation and tissue remodeling in sedentary individuals, regardless of their age or COPD status.
This study demonstrates that the 10X Genomics GEM-X Flex assay, combined with a "chop-fix" preprocessing protocol, outperforms standard fresh-frozen and single-nuclei methods in generating high-quality single-cell transcriptomic data from fixed clinical trial samples, thereby overcoming logistical barriers to broader scRNA-seq implementation in clinical research.
By applying PacBio HiFi long-read sequencing to a large four-generation family, this study comprehensively profiles nearly eight million tandem repeat loci to identify key genomic and parental factors—such as locus length, motif continuity, heterozygosity, and paternal age—that drive de novo mutagenesis and reveal the existence of hyper-mutable tandem repeat regions.
This study presents a high-quality, chromosome-level genome assembly of the parthenogenetic nematode *Acrobeloides nanus*, generated through integrated Nanopore, PacBio HiFi, and Hi-C sequencing, to serve as a foundational resource for investigating its unique asexual reproduction, developmental differences from *C. elegans*, and extreme desiccation resistance.
This study presents an optimized iMAP CRISPR perturbation platform that overcomes previous recombination biases to systematically map the tissue-specific essentiality of RNA modification factors across 46 mouse tissues and identify Thg1l as a therapeutic target for enhancing NK cell-mediated tumor killing.
This study demonstrates that an extremely small, isolated population of the Aeolian wall lizard can persist with record-low genomic diversity because its realized genetic load remains comparable to that of larger populations, suggesting that severe bottlenecks do not necessarily lead to immediate extinction if the burden of deleterious mutations stays within tolerable limits.
This study reveals that a widespread network of C2H2 zinc finger proteins interacts extensively at chromatin loop anchors to regulate higher-order genome organization and gene expression, with many of these sites overlapping somatic mutations in cancer genomes.