407 papers
This study reveals that the population structure and evolutionary history of the bacterial leaf blight pathogen *Xanthomonas oryzae* pv. *oryzae* in Africa were shaped by the independent domestication of African rice (*Oryza glaberrima*) and its subsequent replacement by Asian rice (*Oryza sativa*), driving distinct genetic diversification and host adaptation mechanisms in the pathogen.
This study demonstrates that ultra-conserved CpG dinucleotides, which are enriched in brain-expressed genes and developmental pathways, co-localize with age-related differentially methylated regions, thereby linking functional components of DNA methylation ageing to conserved developmental mechanisms.
By integrating experimental measurements of aneuploidy rates and fitness in budding yeast with computational modeling, this study establishes a unified model revealing that while canonical reversion rarely impacts population dynamics, a distinct, chromosome-specific mechanism involving unresolved linkages and breakage-driven repair drives high-frequency reversion for specific chromosomes.
This study demonstrates that using donor-specific assemblies significantly enhances the detection of somatic structural variants in complex and repetitive genomic regions compared to linear reference genomes, thereby improving the identification of cancer-associated mutations.
This study presents the first transcriptome time-course of the *Plasmodium knowlesi* A1-H.1 strain grown in human erythrocytes, revealing strong genome-wide conservation of temporal gene expression with *P. vivax* and providing an interactive webtool to facilitate comparative functional studies using *P. knowlesi* as a model for *P. vivax*.
This study elucidates the conserved regulatory mechanisms governing fruit shape in peach and apple by demonstrating how Ovate Family Proteins (OFPs) interact with brassinosteroid signaling and microtubule dynamics to orchestrate distinct flat versus oblong phenotypes, thereby providing a refined framework for breeding fruit morphology in Rosaceae crops.
This study utilizes nanopore sequencing to reveal substantial genomic and epigenomic variability between MCF-7 breast cancer sublines, highlighting significant differences in structural variants, single-nucleotide variants, and allele-specific DNA methylation patterns that affect key cancer driver genes and transposable elements.
The authors developed TEExplorer, an interactive web portal that provides accessible visualization of transposable element and histone mark associations across 57 human cell types from the EpiATLAS dataset while enabling users to upload and compare their own ChIP-seq data.
Through the community-driven manual curation of over 7,500 gene models in *Pristionchus pacificus*, this study highlights critical limitations in current automated annotation pipelines—such as assembly errors, artificial transcript fusions, and homology-based error propagation—and offers valuable insights to improve future genome annotation efforts across diverse species.
This study utilizes a multidimensional analysis of a multiparental interspecific tomato (ToMAGIC) population to identify key genomic regions and transgressive lines associated with drought resilience, offering valuable insights for breeding water-efficient tomato cultivars.
This study demonstrates that treating small-cell lung cancer patients with the hypomethylating agent guadecitabine induces global DNA hypomethylation in peripheral blood mononuclear cells, alters key immune-related signaling pathways, and significantly shifts immune cell populations, highlighting the potential of blood-based methylomic analysis for monitoring treatment response.
This study utilizes single-nucleus RNA sequencing to construct a cell-type-resolved atlas of the bovine mammary gland, revealing that heat stress impairs lactational performance by disrupting epithelial cell differentiation, inducing proteostasis pressure, and rewiring intercellular signaling networks.
The paper introduces ADAPRE, an adaptive instrumental variable framework that leverages Perturb-seq data to accurately infer causal, potentially cyclic gene regulatory networks by accounting for heterogeneous CRISPRi knockdown efficiencies, thereby outperforming existing methods in reconstructing biologically relevant interactions.
OncoBERT is a context-aware language model trained on large-scale clinical sequencing data that captures complex somatic mutational patterns to enhance patient stratification, predict therapeutic responses, and link mutational landscapes to tumor biology for precision oncology.
The paper introduces PanExonNet, a deep learning framework that integrates RNA-binding protein expression with DNA sequence to predict cell-type-specific splicing patterns with superior generalization to unseen cellular contexts compared to existing models.
Portello is a novel assembly-based mapping tool that transfers read alignments from de novo assembly contigs to a standard reference genome, thereby unifying assembly and reference-based inferences to improve variant calling accuracy, enable direct read-level review, and facilitate the interpretation of complex genomic regions for rare-disease whole genome sequencing.
By applying the Minimum Description Length principle and maximum parsimony, this study reveals that regulatory demands scale nonlinearly with tissue specificity—peaking in intermediate-specificity genes—and uncovers distinct regulatory strategies where selective genes function as on/off switches while ubiquitous genes act as fine-tuning knobs, all of which vary systematically with gene age.
This study reveals that the evolutionary history and global dispersal of the rice bacterial blight pathogen *Xanthomonas oryzae* pv. *oryzae* (Xoo) in Asia closely mirror the domestication and spread of rice, with distinct ancestral lineages emerging in China and India and a third lineage arising through recombination and trade.
By integrating whole-genome sequencing with paleoclimate history, this study reveals how Andean climatic oscillations shaped distinct demographic trajectories and genetic risks in Ecuadorian pumas, providing a framework for targeted conservation strategies that balance corridor restoration with genetic rescue.
The paper introduces GFMBench-API, a modular Python interface that standardizes the evaluation of Genomic Foundation Models by decoupling model-specific processing from task-specific data and metrics to enable reproducible and consistent benchmarking.