DNA methylation

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

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

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

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.

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

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.

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

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.

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

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

UMR-seq reveals epigenetic variation in plant hypomethylomes, showing UMRs are enriched in regulatory loci and improve genomic prediction and trait association mapping in wheat.

This study investigates how PWO1 and PWO2 proteins interact with circadian and epigenetic signaling to regulate flowering time in Arabidopsis.

The paper identifies native T-DNA transfer systems in rhizobia that deliver cargo genes into legume nodules, showing they share similarities with Agrobacteria-mediated transformation but have distinct regulatory mechanisms.

The paper identifies CD200R1 as a marker for an immature NK-cell precursor in tonsils, distinguishing between oligopotent and more restricted developmental stages.

This paper introduces dreems, a graph neural network that efficiently estimates effective migration surfaces from genetic data, achieving lower error and faster computation than existing methods.

The paper shows that neural RNA splicing models rely on reading frame information that the splicing machinery cannot access, leading to errors in predicting poison exons.

This study examines parallel evolution of nuclear OXPHOS genes in threespine stickleback across freshwater populations and identifies mitonuclear evolutionary coupling in specific functional modules.

This study compares epigenomic signatures of longevity between a giant tortoise and humans, finding shared methylation patterns linked to telomere biology.

The paper introduces the segmentome, a DNA methylome representation using a Bayesian HMM, and shows it can group cell types and identify cell-of-origin in DNA samples.

The paper investigates the mcm4Chaos3 mutation in yeast, showing it causes genome instability by impairing specific centromere-proximal origins.

The paper shows that most hnRNP proteins are excluded from DNA double-strand breaks, with hnRNPH1's exclusion dependent on its GYR domain and independent of recruitment pathways.

This study shows FoxO1 and HNF1α work together to change nucleosome structure and stability to activate transcription.

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.

The paper identifies tandem repeats in methanogenic archaea and their viruses, showing they contribute to genomic diversity and adaptation potential.

The paper identifies methylation changes associated with dysplasia and cancer progression in Barrett's esophagus using whole-genome methylation profiles.

The paper models tumor volume and ctDNA dynamics in HPV-associated anal cancer to predict immunotherapy response using patient-specific parameters.

This study compares the genotoxic effects of BrdU and EdU in trypanosomatids, finding EdU more genotoxic and revealing species-specific responses to DNA damage.