DNA methylation

The MarR-family regulator TilR links biosynthesis of enterotoxin tilimycin with physiologic adaptation in Klebsiella oxytoca

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

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

SARDINE unlocks EWAS summary statistics for large-scale epigenetic biomarker analysis

SARDINE uses EWAS summary statistics to estimate epigenetic clock-phenotype associations without individual-level data, revealing heterogeneity in biomarker associations with aging and diseases.

Temporal changes in genetic variation during the invasion of Lygodium japonicum in North America

This study uses herbarium specimens to analyze genetic variation in Lygodium japonicum during its invasion of North America, identifying Asia as the source and finding evidence of rapid adaptation and reduced non-coding diversity.

Epigenome-informed Polymer Modeling Reveals Chromosome Folding Landscapes across Distinct Genetic and Epigenetic Contexts

This study uses epigenome-informed polymer modeling to generate chromosomal conformational ensembles from epigenomic data, revealing how genetic and epigenetic contexts shape chromosome folding landscapes.

Asymmetric division and polar growth define a non-canonical cell cycle in Bradyrhizobium.

This study describes the asymmetric cell division and polar growth in Bradyrhizobium, revealing a unique cell cycle program with distinct nucleoid dynamics and chromosome organization.

Evolutionary dynamics of the pan-centromere architecture in oaks

The paper analyzes centromere evolution in oaks, showing lineage-specific expansion of QuCEN146 satellite drives turnover, while LTR-rich centromeres show low polymorphism due to suppressed recombination.

Quantum Entanglement as a Physical Determinant of Genomic Instability in TP53

The paper explores whether quantum entanglement, measured via von Neumann Entropy, influences TP53 mutation patterns, finding elevated entropy at known mutational hotspots but cautioning about limited validation.

Hybrid RY-mers increase aDNA alignment sensitivity

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

Long-read DNA sequencing reveals global hypomethylation and focal hypermethylation in SDHx-deficient pheochromocytoma and paraganglioma

The paper uses long-read sequencing to analyze DNA methylation patterns in SDHx-deficient PPGLs and finds global hypomethylation with focal hypermethylation at specific CpG islands.

A three-factor model can explain symmetry breaking and the n-1 rule during X-chromosome inactivation

This paper introduces a three-factor mathematical model to explain symmetry breaking and the n-1 rule in X-chromosome inactivation by integrating Xist, an X-linked activator, and SPEN.

Learning Strand-Equivariant Tokenizations of DNA with MirrorDNA

This paper introduces MirrorDNA, a DNA language model with a strand-equivariant tokenizer that improves prediction consistency across DNA strands.

2'-O-Methylated ncRNA condensates form a recombination center for IgH synapsis

This study shows that FBL-mediated 2'-O-methylation of GLTs forms condensates that drive IgH synapsis and CSR in B cells.

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

This study compares how genomic and epigenomic relationships contribute to genotype-by-environment interaction in grapevine clones, finding that epigenomic factors capture more GEI variance than genomic factors.

Widespread Saccharomyces hybridization in agave fermentations arises repeatedly from asymmetric parental diversity

The paper identifies widespread Saccharomyces hybridization in agave fermentations, showing multiple independent origins and asymmetric parental genetic diversity.

Rates of molecular and morphological evolution are uncoupled across the eukaryote Tree of Life

The paper investigates correlations between molecular and morphological evolutionary rates across eukaryotes and finds little evidence of a link, suggesting differing evolutionary dynamics at genomic and phenotypic levels.

The long noncoding RNA FOSIL shapes the dynamics of FOS induction

This study shows that the lncRNA FOSIL regulates the timing and resolution of FOS induction by modulating chromatin structure and nuclear speckle dynamics.

An unprecedented codon reassignment and two new genetic code variants in ciliates

The paper identifies new genetic code variants in ciliates, including an unprecedented codon reassignment in Licnophora and a previously unreported reassignment in Balantidium ctenopharyngodoni.

Joint protein-DNA language modeling enables prediction and engineering of DNA recognition specificity

This paper introduces PDLMs, protein-DNA language models that jointly represent protein and DNA sequences to predict and engineer DNA recognition specificity.

Phenotypic and Molecular Characterization of Potentially New Shigella boydii Serotype in Bangladesh

The paper characterizes a unique cluster of Shigella-like organisms in Bangladesh, identifying them as potentially a new serotype of S. boydii based on phenotypic, genotypic, and serological analyses.

HiSpoT: a novel one-tube dual-barcode PCR method for NGS spoligotyping amplicon library preparation in Mycobacterium tuberculosis complex

HiSpoT is a PCR-based method for preparing NGS libraries for spoligotyping MTBC isolates, offering high-throughput, low-cost, and accurate strain typing with open-source tools for analysis.

memVar: an integrated resource for interpreting human membrane protein variation in molecular and disease contexts

memVar links human membrane protein variants to molecular contexts and disease, revealing enrichment of pathogenic variants in transmembrane regions and interaction sites.

Epigenetic reprogramming by promoter hypomethylation is linked to aberrant gene expression and transcriptomic plasticity in colorectal cancer

The paper identifies promoter hypomethylation as a driver of transcriptomic plasticity and aberrant gene expression in colorectal cancer, linking it to distinct cell states and metastatic behavior.

RNA Polymerase Backtracking Promotes Type III-A CRISPR DNA Targeting

The paper shows RNA polymerase backtracking promotes type III-A CRISPR DNA targeting by inhibiting GreA anti-backtracking factors, which suppress Cas10-Csm activity.

TIGRdisco: a tool for the discovery of TIGR arrays and TIGR-associated Tas proteins from nucleotide sequences

TIGRdisco identifies TIGR arrays and Tas proteins from nucleotide sequences, recovering most array units and uncovering unannotated loci across datasets.

PartiDesign: A structure-sequence co-design paradigm for practical all-to-all biomolecules design

PartiDesign is a structure-sequence co-design model that generates molecular structures and sequences for proteins, nucleic acids, and small molecules, achieving high design throughput across benchmarks.

A Bias Correction Method for Substructure Estimation with Small Reference Sample Sizes

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

Phage-Inducible Chromosomal Jumbo Islands (PICJIs) spreading antimicrobial resistance, host-adaptation factors and defense systems, a novel satellite family of nucleus-forming Chimalliviridae

The paper identifies PICJIs as large mobile genetic elements in E. coli and Salmonella that spread antimicrobial resistance and defense systems via a specific bacteriophage.

Polygenic polymorphisms cooperate to drive expansion of HCMV adaptive NK cell and NK-like T cell populations

This study identifies genetic polymorphisms in NKG2C, CD16a, and HLA-E that influence NKG2C expression and ADCC capacity in HCMV-infected individuals.

Predicting single-molecule chromatin distribution from DNA sequence

This paper introduces a sequence-to-distribution framework to predict single-molecule chromatin states from DNA sequence, revealing new regulatory mechanisms and variant effects.