DNA methylation

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.

ctDNA-BERT scores individual bisulfite reads for cell-free DNA methylation analysis, achieving high accuracy in cancer staging without cohort-specific retraining.

This study develops epigenetic clocks for mule deer and a multi-species clock for the Odocoileus genus to analyze age-associated DNA methylation patterns and aging dynamics.

The paper presents a chromosome-scale genome and methylome assembly for table beet, identifies candidate genes for geosmin production, and compares it with sugar beet.

This study identifies two CREBBP variants causing Menke-Hennekam syndrome that increase HAT activity but disrupt phase separation differently, with HAT inhibition restoring condensate dynamics in one variant.

This study reconstructs the plant organellar homologous recombination pathway in Arabidopsis, showing that AtRecA1-mediated recombination is enhanced by plant-specific ssDNA-binding proteins, while AtRecA2 and AtRecA3 require these proteins for activity.

This study shows that KMT2C and KMT2D regulate skeletal development through epigenetic control of chondrogenesis, with redundancy in their function during bone formation.

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

The paper introduces MEMAR, a Maximum Entropy model for predicting m6A methylation in human transcripts and influenza A viral segments, showing improved performance over existing methods.

DAPE-PD adapts a genomic foundation model into a diffusion model to generate functional cis-regulatory DNA sequences across three non-model gut commensals.

This study uses landscape genetics to analyze sloth bear populations in the Indian Terai, finding agriculture and proximity to water as key barriers to gene flow and highlighting low genetic diversity.

This study identifies DHX30 as an R-loop helicase that resolves RNA:DNA hybrids, prevents replication stress, and maintains genome stability in human and zebrafish cells.

This study models human MLH1 and MLH3 variants in mice, revealing MutLγ's roles in meiotic DNA repair and ovarian reserve maintenance through multiple mechanisms.

This paper introduces Mimic, a unified neural network architecture for genomic sequence modeling, showing it outperforms existing models in protein-DNA interactions and enhancer activity.

The paper develops a framework to analyze long-term sequence dynamics from context-dependent mutation processes, applied to somatic hypermutation in antibodies, revealing mutational biases and their effects on sequence evolution.

The paper identifies genomic features of domoic acid biosynthesis in Pseudo-nitzschia diatoms, revealing expanded toxigenic diversity and environmental expression patterns.

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.

CROP-1 predicts gene activity based on DNA sequence and regulatory state, enabling context-specific edit design in plants with higher accuracy than sequence-only models.

This study identifies diffuse centromere organization in Cryptosporidium parvum, distinct from regional centromeres in related apicomplexans, suggesting an independent evolutionary origin.

The paper shows that telomerase elongates a second substrate formed by spontaneous replication fork collapse in budding yeast, significantly contributing to telomere length homeostasis.

The paper resolves a 245-year-old taxonomic confusion between Ganoderma lingzhi and G. lucidum using a historical specimen and genomic analysis, showing they diverged over 12 million years ago.

The paper proposes a genetic divergence threshold for demarcating orthoflavivirus species, identifying 25 new Euflavivirus and 33 new Fusivirus species.

The paper develops a cost-effective and sensitive method for detecting microchimerism using custom genotyping and qPCR assays, validated in two populations.

This study uses genomic data to analyze the genetic diversity and management history of French local horse breeds, showing distinct patterns of kinship and inbreeding linked to different management practices.

This paper introduces Akita Semifreddo, a framework for designing DNA sequences that produce specific 3D genome folding patterns, demonstrating the ability to create boundaries, dots, and flames with controlled strengths.

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 identifies climate-associated genomic variation in European beech across life stages, revealing population-specific adaptive responses to temperature and precipitation changes.

This study identifies 73 annexin genes in alfalfa and shows MsANN22 improves drought tolerance by enhancing antioxidant capacity and reducing oxidative stress.