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The paper identifies a link between bacterial horizontal gene transfer and transposable element proliferation in nut weevils, contributing to genome expansion and molecular innovation.

The paper investigates methyltransferases (MTs) in CPR genomes, finding they are primarily associated with restriction-modification systems for DNA defense and nucleotide scavenging rather than antimicrobial resistance.

The paper generates a single-cell transcriptomic atlas of coral during heat stress and recovery, revealing cell type-specific transcriptional responses and symbiont dynamics.

The paper maps long-range correlations in the complete telomere-to-telomere human genome, revealing heterogeneous genomic structure and chromosome-specific scaling.

scWeave translates between gene expression and chromatin structure at single-cell resolution using deep learning, improving cross-modality inference across multiple datasets.

This study uses whole-genome resequencing and GWAS to identify genomic regions under selection associated with yield and adaptability traits in groundnut.

The paper presents a haplotype-resolved genome assembly of the pomegranate cultivar 'Wonderful' using DNA from haploid pollen grains and long-read sequencing technologies.

The paper examines chromosomal rearrangements in Carex helodes, identifying genomic features associated with karyotypic evolution and environmental adaptation.

This study examines drought-induced phenotypic and transcriptomic plasticity in Dianthus inoxianus, identifying plastic genes and regulatory mechanisms underlying drought tolerance.

The paper identifies a new wild clownfish hybrid in the Philippines and characterizes its genomic and phenotypic traits, showing it is a backcrossed descendant of A. sandaracinos and A. perideraion.

The paper identifies and characterizes CpG islands in 3'UTRs, showing their conservation, methylation patterns, and association with cancer-related gene expression changes.

The paper introduces iCLIP3, a streamlined protocol for mapping RBP-RNA interactions at single-nucleotide resolution, with improvements in visualization, RNA isolation, and multiplexing.

This paper introduces GO-CRE, a method for designing cell-type-specific cis-regulatory elements by reconstructing sequence-grammar trajectories and using reinforcement learning with predictor guidance.

The paper investigates enhancer-promoter interactions in a native chromatin context, revealing transcription factor synergy and the role of facilitators and repressive promoters in regulating gene activation.

The paper assembles and annotates the Tainung 67 rice genome, tracing its japonica and indica ancestries through gene analysis and repeat composition.

The paper shows that blood DNA methylation can predict gene expression based on regulatory mode and enhancer architecture, with lineage genes being more predictable than stimulus-responsive genes.

The paper presents a chromosome-scale genome assembly of Cycas revoluta and identifies genes related to sex determination and thermogenesis, offering insights into cycad diversification.

The paper demonstrates that long-read sequencing detects more mitochondrial genome variants than short-read sequencing or microarrays in a Korean population.

The paper introduces a spatial transcriptomics method for whole-transcriptome and isoform-resolved analysis of single cells in mouse brain tissue, revealing spatial diversity and cell-type-specific isoform usage.

This study quantifies sequence determinants of human programmed stop codon readthrough using deep mutational scanning and identifies gene-specific and context-dependent effects.