400 papers
This study presents a pseudo-phased, chromosome-level genome assembly of the coffee leaf rust pathogen *Hemileia vastatrix* (isolate Hv178a), revealing a unique isolate-specific trisomy of chromosome 17 that likely underlies its increased virulence.
This study presents the first high-quality nuclear genome assembly of *Chaetoceros muelleri*, derived from resurrected Baltic Sea sediments, which reveals extensive gene duplication, transposable element-driven plasticity, and lineage-specific innovations that underpin the diatom's evolutionary adaptability and ecological success.
This study utilizes comparative genomics to characterize the distinct genomic architectures, metabolic capabilities, and safety profiles of two hydrogen-oxidizing bacteria, *Cupriavidus necator* H16 and *Xanthobacter* sp. SoF1, thereby establishing a scientific foundation for selecting and engineering robust, food-grade microbes for scalable, land-independent protein production on Earth and in space.
This study demonstrates that current DNA methylation clocks lack portability and accuracy in predicting age and Alzheimer's disease risk across genetically admixed populations, particularly those with African ancestry, due to widespread differences in methylation patterns and higher frequencies of methylation-associated genetic variants (meQTLs) in these groups.
This paper presents a novel workflow for isolating unfixed nuclei from frozen human and mouse brain tissue, enriching specific cell types via fluorescence-activated nuclei sorting (FANS) based on DNA-bound proteins, and performing low-input epigenomic profiling using nanoCUT&Tag to enable cell-type-specific analysis of the neurovascular unit in both healthy and neurodegenerative contexts.
This study demonstrates that integrating the DNA language model GROVER with chromatin and regulatory features reveals that while cell-type specific information is crucial, much of the genome stability landscape governing double-strand break sensitivity is inherently encoded within the DNA sequence itself.
DenMark is a novel Bayesian hierarchical model that leverages Hilbert space Gaussian process approximations to jointly model cell locations and gene expression in single-cell-resolution spatial transcriptomics, enabling the robust identification and uncertainty quantification of genes whose expression correlates with local cell density across diverse tissues and platforms.
This study integrates ATAC-STARR-seq, CRISPR screens, and high-resolution chromatin mapping to demonstrate that enhancer hubs, organized through CTCF-independent interactions and driven by key elements like Batf, govern the 3D chromatin topology essential for establishing and maintaining Th17 cell identity.
This study presents a comprehensive single-nucleus RNA-seq atlas of 6.7 million nuclei from mouse F1 hybrids across eight tissue groups, revealing that while cis-acting regulatory variation drives divergence, trans-acting effects are highly cell-type-specific and often masked in bulk tissue analyses, thereby establishing a foundational framework for understanding the complex interplay between genetic variation and cell-type-specific gene regulation.
By reconstructing an ancestral placental mammal karyotype and recombination map, this study reveals that while autosomal recombination landscapes are not conserved across species like the X chromosome, ancestral regions with low recombination rates are under stronger purifying selection and enriched for cellular functions, whereas high-recombination regions are less constrained and associated with regulatory and immune systems.
LoRTIA Plus is a chemistry-agnostic software suite that outperforms existing tools in annotating and reconstructing long-read transcriptomes across diverse genomes and library chemistries by employing adapter-aware filtering and quality-based criteria to achieve superior recall and precision for transcription start sites, end sites, and novel isoforms.
This paper reanalyzes the *Rauvolfia tetraphylla* yohimbane biosynthesis pathway by demonstrating that previous findings were compromised by a lack of haplotype phasing and whole-genome triplication awareness, leading to the identification of chimeric genes and revealing a more complex, homeolog-specific enzymatic organization than previously reported.
This study utilizes a novel whole-genome sequencing method on single human colon crypts to analyze complex insertion-deletion events repaired by non-homologous end joining, thereby providing insights into the mechanisms of naturally occurring DNA damage repair within a physiologically relevant context.
The paper introduces NanoPlasmiQC, a cost-effective, automated workflow utilizing Oxford Nanopore long-read sequencing to sequence and analyze full plasmids within a single day, offering a superior alternative to traditional Sanger sequencing.
This study demonstrates that gene expression dispersion is a distinct, genetically encoded regulatory feature reflecting transcriptional fidelity, which is structured by biological function, enriched for cis-regulatory control, and operates independently of mean expression levels.
This study demonstrates that an epigenetic index of adult cognition ("Epigenetic-g") captures distinct genetic and environmental variation in children's cognitive and academic performance that is not reflected by polygenic indices, showing plasticity in early childhood and moderate stability by adolescence without predicting longitudinal cognitive growth.
The paper introduces ICePop, a novel framework that bridges the gap between statistical power and cellular resolution by performing disease-cell type associations at the metacell level, thereby enabling the detection of heterogeneous disease signals within specific cellular states that are missed by existing methods.
This study reveals that the global rise of pneumococcal serotype 12F following vaccine introduction is driven by both distinct regional lineages and a multidrug-resistant global clone, while also identifying reversible strand-slippage mutations in the *wciJ* gene as a novel mechanism for phase variation that allows subpopulations to evade vaccine-induced antibody killing.
This study generates high-quality genomic resources for two Australian arid-zone marsupials, the Wongai ningaui and the slender-tailed dunnart, revealing contrasting demographic responses to historical climate change that highlight the importance of local adaptation for future species resilience.
This study utilizes genome-wide CRISPR screening and genomic profiling in pancreatic beta cells to identify novel mediators of ER stress responses, revealing that pro-survival genes are significantly enriched for type 2 diabetes risk variants and highlighting DTNB as a validated therapeutic target for preserving beta cell function.