DNA methylation

The paper examines thermal adaptation in bacterial chaperone mRNAs, finding no strong structural differences but a significant shortening of the groL coding sequence in thermophiles.

The paper evaluates genomic methods to detect outbreaks of a vancomycin-resistant Enterococcus faecium lineage, finding that lower allelic thresholds improve outbreak detection.

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

The paper evaluates how small reference sample sizes affect substructure estimation and proposes bias corrections for improved accuracy.

NPlasmid-seq detects sub-percent contamination and sequence heterogeneity in plasmid preparations using Cas9-encoded terminal signatures, revealing structural variants missed by consensus-based methods.

This paper adapts ACMG/AMP variant classification criteria for the non-protein-coding gene RMRP, resulting in a framework for classifying variants in cartilage-hair hypoplasia.

This study evaluates the conservation of antifungal dsRNA target genes across fungal plant pathogens at siRNA-length resolution, finding limited conservation beyond closely related species.

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

The paper analyzes the structure and evolution of a selfish centromere in monkeyflowers, identifying genomic expansions and gene content differences that may contribute to meiotic drive.

The paper establishes a genomic baseline for six aquatic species in the Netherlands using SNP data to assess population structure, diversity, and conservation priorities.

This study identifies Nuc1, a mitochondrial enzyme, as a regulator of an RNA surveillance system in yeast that limits replication of the L-A mycovirus.

GBactPro improves cross-species bacterial promoter prediction using element-resolved promoter definitions, achieving high AUROC across multiple species and outperforming existing predictors.

This study identifies genomic and environmental factors affecting circular single-stranded DNA (cssDNA) yield in engineered E. coli and improves production efficiency.

The paper shows introgression from black kites into red kites increased genetic diversity and reduced genetic load in northern red kites by 18%.

This study evaluates the performance of three large language models on basic bioinformatics tasks compared to human performance, finding LLMs match human accuracy in some areas but struggle with complex tasks like sequence alignment.

The paper detects malignant hematopoietic stem cells (HSCs) in myelodysplastic neoplasms (MDS) using low-input sequencing and shows they predict relapse after transplantation.

The paper develops a cell-free system using Xenopus egg extracts to study TMEJ, showing that Pol theta and Cyclin B-CDK1 are essential for efficient DNA joining.

This study identifies regulators that control ECA biosynthesis in E. coli, showing ECA's role in acid and reactive nitrogen species stress resistance.

OddCAPS improves dCAPS by using three primers in one PCR reaction to detect SNVs with more engineered base changes and flexibility in restriction enzyme selection.

This study identifies AtSUV3 as a mitochondrial RNA helicase involved in DNA repair and shows its role in mitigating DNA damage in Arabidopsis.

The paper identifies and characterizes U6 promoters in Ulva prolifera, showing their dual transcriptional activity and utility for CRISPR-Cas9 genome editing.

KmerSignificance Score (KSS) prioritizes viral k-mers by integrating strain-distinguishing capacity, mutation impact, and functional importance, achieving superior classification performance and cross-dataset comparability.

The paper identifies horizontal gene transfer of the Drosomycin antimicrobial peptide gene across insect species, suggesting HGT contributes to immune system novelty and defense capabilities.

The paper analyzes early genetic contexts of blaNDM-1 in Acinetobacter and Enterobacterales isolates to understand its spread and resistance mechanisms.

The paper develops an epigenetic enrichment method for fetal cfDNA using a first-trimester methylome reference, increasing fetal fraction from 5.1% to 28.4%.

The paper develops and optimizes two protocols for purifying ssDNA from filamentous phages using chaotropic salts and silica columns, achieving high recovery and purity comparable to commercial kits.

The paper analyzes parasite genotypes in sympatric mosquito species to show divergent selection on Plasmodium falciparum mediated by different vectors.

This paper introduces DSP as a reversible fixative for microbial cells that enables fluorescence imaging and DNA extraction, improving targeted microbial genomics.