DNA methylation

CodonBench: separating gene context, exon position, and variant-specific component in synonymous-variant classification

The paper evaluates models for classifying synonymous variants by separating gene context, exon position, and variant-specific effects, finding that gene identity and position are more predictive than the variant itself.

Scalable methylome-transcriptome profiling resolves clonal organization in human hematopoiesis

This paper introduces Droplet-MT, a method for joint methylome and transcriptome profiling, enabling clonal organization analysis in human hematopoiesis with high scalability and resolution.

TRF2 mediates force-resistant bridging of distal telomeric DNA repeats

This study shows TRF2 mediates force-resistant tethering of telomeric DNA repeats, which may be a step in T-loop formation.

A unified framework for quantitative splicing and transcript prediction

This paper introduces SpliceAI2, a deep learning model that improves identification and quantification of splice-altering variants and their effects on transcripts and disease.

DNA methylation-based prediction of differentiation state at cell-type resolution reveals an age-associated epigenetic mesenchymal drift

This paper introduces EpiDiff, a DNA methylation-based tool to predict cell differentiation states, revealing age-related epigenetic drift in mesenchymal lineages and cancer risk associations.

A base-modifying enzyme extends the range of anti-phage defense provided by DNA glycosylases

Brig3, a DNA glycosylase from a soil metagenome, excises 5-hydroxymethylcytosine from T-even phage DNA; the glucose hydrolase BapA extends defense to glucosylated genomes such as wild-type T4.

Robust V(D)J Recombination in the Absence of SA1/2-mediated Chromatin Loops

This study shows that SA1/2 are not essential for V(D)J recombination in G0/G1-arrested cells, but their absence disrupts chromatin loops and long-range Igh recombination, while Ig{kappa} recombination remains functional.

PhageHost-GNN: novelty-aware and locally adaptable strain-level Klebsiella-phage prediction

PhageHost-GNN predicts strain-level Klebsiella-phage interactions using a novelty-aware framework, achieving high AUPRC scores in in silico evaluations and showing advantages in handling novel data.

Linking somatic variants to altered methylation profiles in nanopore-derived breast and pancreatic cancer genomes using unduliner

This paper introduces unduliner, a framework that links somatic variants to methylation changes in cancer genomes using nanopore sequencing data.

CRISCross: Integration of Epigenetic Information for Deep-Learning-Based Prediction of CRISPR-Cas9 Off-Targets Across Cell Types

CRISCross improves CRISPR-Cas9 off-target prediction by integrating epigenetic features with sequence data across cell types, showing better performance than sequence-only models.

Disrupted chromatin architecture blocks B lymphopoiesis in Down syndrome

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales

GenDiMug is a multigraph framework for analyzing genomic organization and multi-omics data across scales, revealing gene expression clumping and circadian regulation in a photosynthetic alga.

Linking UV absorption of DNA with base pair sequences

This study investigates the sequence dependence of UV absorption in DNA using computational methods and finds that cytosine- and guanine-rich sequences absorb more UV than adenine-thymine-rich ones.

EvSpark: Lossless Speculative Decoding for Hybrid DNA Foundation Models

EvSpark improves decoding speed for hybrid DNA models by speculative decoding with parallel verification, achieving significant speedups across real and synthetic prompts.

GLARE: Genomic Language model for Automated Repetitive Element classification

GLARE is a TE classifier that outperforms existing methods across multiple taxonomic groups and sequence quality conditions using a genomic language model fine-tuned on harmonized reference data.

Pooled progeny sequencing effectively estimates polyandry in species with large families

This paper develops a likelihood-based method to estimate polyandry using pooled progeny sequencing and applies it to Drosophila melanogaster, finding 57% of families were sired by a single male.

A chimeric infection program and epigenetic conflict underpin endogenous giant virus latency

The paper investigates how a giant virus maintains latency in a green alga by analyzing its genomic architecture and epigenetic regulation.

Maternal hyperglycemia impairs postnatal skeletal muscle growth and induces stage-dependent gene expression changes in mouse offspring

This study shows maternal hyperglycemia impairs skeletal muscle growth in offspring at 4 and 8 weeks, with distinct gene expression changes at each stage.

Beyond ERCs: exploring catastrophic forms of rDNA instability in aging yeast

The paper investigates rDNA instability in aging yeast, identifying new forms of instability beyond ERCs that contribute to lifespan variability.

Comparison of intracellular and encapsidated viral RNA reveals selective constraints on reovirus recombination

The paper compares recombination rates in intracellular and encapsidated reovirus RNA, finding higher recombination in intracellular RNA and suggesting recombination occurs more frequently during plus-strand synthesis.

A modular DNA toolkit for single-molecule biophysics

The paper introduces a modular DNA toolkit for creating long, customizable DNA molecules with user-defined sequences for single-molecule biophysics applications.

The Red Blood Cell Surface Defines a Distinct Tumor DNA Compartment for Liquid Biopsy

This study identifies RBC-bound tumor DNA as a distinct compartment for liquid biopsy, showing it is more abundant and concordant with tumor tissue than plasma DNA.

Sequence-Dependent DNA Base Selection Fidelity: A Kinetics-Based Model and its Validation

The paper develops a kinetics-based model for sequence-dependent DNA base selection fidelity and validates it against mutation spectra from mismatch repair-deficient organisms.

A context-aware analytical framework for DNA methylation biomarker discovery

This paper introduces a context-aware framework for DNA methylation biomarker discovery, showing it identifies context-dependent candidate regions and validates them with PCR assays in independent cohorts.

Gene-level evolutionary conservation and human constraint decline at comparable rates across the age of onset of Mendelian disease

The paper compares the rate of decline in gene-level evolutionary conservation and human constraint scores with disease onset age across Mendelian diseases.

Transcription factor interactions promote binding to non-cognate DNA sites

This study shows how transcription factor interactions enable binding to non-cognate DNA sites by bridging across nucleosomal DNA gyres.

scPRIME-seq uncovers synchronized multimodal molecular collapse facilitated by pre-neoplastic epigenetic burden in prostate cancer

The paper introduces scPRIME-seq, a multimodal single-cell platform, and finds pre-neoplastic epigenetic changes drive tumor progression in prostate cancer.

Ethanol stress induces siRNA-mediated epimutations and phenotypic variability in fission yeast

This study shows ethanol stress increases siRNA-mediated epimutations in fission yeast, leading to transposon expression changes and phenotypic variability.

Probing Genomic Foundation Models with Splice-Variant Perturbations

This paper evaluates genomic foundation models using splice-variant perturbations, finding they match task-specific networks and generalize across mutation types.

DNA 6mA marks transcriptionally active chromatin in malaria parasites

The paper identifies 6mA methylation in Plasmodium falciparum, showing it is associated with active chromatin and transcription, and identifies a methyltransferase involved in this modification.