ATAC-seq

The epigenomic landscape of deep lineage divergence: The case of the European sea bass

The paper identifies regulatory variation driving lineage divergence in European sea bass by analyzing epigenomic and genomic data from Atlantic and Mediterranean populations.

Prioritizing Non-coding Variants in Rice GWAS Loci with a Chromatin-Informed DNA Language Model

This paper introduces a method to prioritize non-coding variants in rice GWAS loci using a chromatin-informed DNA language model, demonstrating its utility through case studies.

TRIM28 preserves ovarian identity by stabilising lineage-specific transcription factor hubs

This study identifies TRIM28's role in preserving ovarian identity by stabilizing lineage-specific transcription factor hubs rather than through H3K9me3-dependent heterochromatin.

Genome-wide multi-layered epigenomic profiling across human aging

This study investigates the relationship between age-related epigenetic changes in DNA methylation, chromatin accessibility, and histone modifications across human aging using integrated WGBS and ATAC-seq data.

An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid

The paper constructs a multi-omics single-cell atlas of human RPE and choroid, identifying cell types, aging patterns, and genetic risk factors for AMD.

GatorPrism: Prototype-Conditioned Routing across Coalition Graph Experts for Spatial Multi-Omics Integration

GatorPrism integrates spatial multi-omics data by balancing cross-omics consensus with modality-specific signals, achieving strong performance across clustering metrics and revealing tissue structure organization.

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

Epigenetic and 3D genome reprogramming during the aging of human hippocampus

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

Single-cell chromatin state transitions during epigenetic memory formation

The paper investigates chromatin state transitions during epigenetic memory formation by analyzing single-cell gene expression and chromatin structure changes after repressor recruitment and release.

SpatialJEPA: JEPA-inspired graph-context distillation for spatially aware multiomics integration

SpatialJEPA transfers spatial context from spatial multiomics data to dissociated non-spatial data through graph-context distillation, improving alignment and recovery of spatially organized programs in mouse brain multiomics.

The CoREST complex inhibitor, corin, leads to decreased tumor growth, increased cellular differentiation and extended lifespan in atypical teratoid rhabdoid tumor xenograft models

This study shows that corin, a CoREST inhibitor, reduces ATRT tumor growth, increases differentiation, and extends lifespan in xenograft models.

Lineage-specific change in craniofacial genetic networks of syngnathid fishes revealed by integrating multiomics across fishes

The paper investigates craniofacial genetic network evolution in syngnathid fishes using multiomics data, finding conserved core networks with localized changes contributing to morphological diversity.

Deep learning design and in vivo validation of Müller glia-specific cis-regulatory elements

The paper designs Müller glia-specific cis-regulatory elements using deep learning and validates their function in vivo.

Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq.

The paper introduces UNIChro-seq, a method for quantifying chromatin accessibility at target loci, and demonstrates its application in analyzing disease risk alleles and genome-edited variants.

BaiZe: A Multi-View Dynamic Framework for Simulating and Interpreting Cellular Responses Across Perturbation Contexts

BaiZe predicts and interprets cellular responses to perturbations using a multi-view framework, showing effectiveness across diverse contexts and improved predictions with ATAC-seq data.

Promoter-associated RNA polymerase III shapes RNA polymerase II-dependent inflammatory gene expression during viral infection

Pol III occupies TATA-enriched, TBP-dependent inflammatory gene promoters, primes basal expression, then restrains Pol II induction during MHV68, HSV-1 and influenza A infection.

Unveiling a missing component of the atypical type IV secretion system required for natural transformation of Helicobacter pylori

The paper identifies a missing component of the ComB T4SS in H. pylori essential for DNA uptake, showing it is a hexameric ATPase interacting with ComB4.

ARSENAL: Learning Transferable Regulatory DNA Representations with Targeted Short-Context Language Models

A 350 bp masked DNA language model trained on ENCODE cCREs with a frequency-domain regularizer recovers TF motifs zero-shot, scores regulatory variants, improves ChromBPNet inputs, and guides sequence design.

Semantic fragment representations for coordinate-free analysis of genomics data

The paper introduces LEAF-1, a fragment-level foundation model for genomics data analysis, showing it can classify cell types and detect cancer from sparse datasets and cell-free DNA.

The MEK inhibitor trametinib incurs mitochondrial injury and induces innate immune responses in the mouse heart

This study shows trametinib causes mitochondrial injury and innate immune activation in mouse hearts, leading to cardiomyopathy and heart failure.

On the state of chromatin in mammalian sperm

The paper shows that properly purified cauda sperm lack somatic contamination and that pretreatment disrupts chromatin structure, validating untreated sperm profiles.

CD117 epitope-shielded hematopoietic stem cell transplantation with toxin-free conditioning and in vivo selection ameliorates β-thalassemia model

This paper demonstrates a method using CD117-blocking antibody and epitope-engineered HSPCs to treat β-thalassemia without myeloablative conditioning.

Synergistic Inhibition of Notch Signaling and Forced Cell Cycle Re-entry Drive Müller Glia Reprogramming in Uninjured Mouse Retina

This study shows that inhibiting Notch signaling and forcing cell cycle re-entry in Müller glia promotes their reprogramming into neurons in uninjured mouse retina.

The BRCA1-A complex restricts replication fork reversal-dependent DNA repair in ATM deficient cells

The paper shows BRCA1-A complex restricts replication fork reversal in ATM-deficient cells, leading to hypersensitivity to Topoisomerase I inhibitors and resistance to PARP1 inhibitors.

Regulation of Human Erythroferrone Expression

This study identifies the transcriptional regulatory mechanisms governing ERFE expression in human erythroblasts using genomic approaches.

Divergent chromatin remodeling in post-sepsis MDSCs underlies MHC class II repression in CCI

The paper profiles chromatin accessibility in post-sepsis MDSCs, showing divergent epigenetic trajectories between rapid recovery and chronic critical illness, with MHC class II repression in CCI.

Graph-based Contrastive Learning Enables Unified Integration and Niche Transfer Across Single-Cell and Spatial Multi-Omics

Garfield integrates single-cell and spatial multi-omics data into a shared space, outperforming existing methods in identifying spatial niches and revealing immune microenvironment heterogeneity.

Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model

The paper investigates molecular mechanisms of maternal-induced embryonic diapause in crickets using genome assembly and time-series transcriptomic analyses, revealing epigenetic and metabolic changes.

Time-resolved inference of gene regulatory networks underlying human cranial neural crest development suggests novel risk genes for orofacial clefting.

Bidirectional modulation of aging-associated cellular phenotypes by mitochondrial genome replacement

This study shows mitochondrial genome replacement can reverse or accelerate aging-related cellular decline in fibroblasts and T cells from mice and humans.