Hi-C

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.

Decoding Cell-type Specific Gene Regulation with CellReg3D by Integrating DNA Large Language Models and 3D Genome Structure

CellReg3D integrates DNA language models and 3D genome structure to model cell-type-specific gene regulation, achieving state-of-the-art performance in predicting epigenetic marks and gene expression.

Reference-Guided De Novo Retrieval of 3D Chromatin Organizational Features with Representation Learning

The paper introduces C-Fetch, a framework that retrieves 3D chromatin features using reference examples, showing improved enrichment for biologically relevant contacts compared to existing methods.

Local chromatin, 3D genome folding and transposon cargo shape Sleeping Beauty transposition

This study identifies factors influencing Sleeping Beauty transposition, showing chromatin context, cargo size, and transcriptional activity affect efficiency and reintegration patterns.

A generative network model reveals hierarchical structural memory guiding post-mitotic 3D genome inheritance

The paper introduces HiCONA, a Bayesian framework that identifies mitotically preserved chromatin interactions guiding post-mitotic 3D genome reassembly and epigenetic memory.

scSTEC: Annotating Chromatin Subcompartments from Individual Single-Cell Hi-C Data via Direct Two-Dimensional Embedding and Chromosome-wise Consensus

scSTEC directly annotates chromatin subcompartments from individual single-cell Hi-C matrices without imputation or cross-cell sharing, achieving results comparable to scGHOST with greater interpretability.

Continuous Topological Accessibility (RFA) as a 3D-Aware GRN Filter: Anticorrelation with eQTL and No Prediction of ΔRNA

This paper introduces RFA, a 3D-aware GRN filter, and finds it anticorrelates with eQTL via local distance-decay but does not predict ΔRNA.

Diversity-generating retroelements enable phages to expand their host range in the human gut.

The paper tracks phage-host interactions in the human gut and finds that DGR-encoding phages interact with multiple bacterial species and show increased nucleotide diversity in their receptor-binding proteins.

Pre-existing genome architecture partitions viral takeover in the smallest free-living eukaryote

The paper tracks viral infection in Ostreococcus tauri, showing pre-existing genome architecture dictates viral positioning and transcriptional changes during infection.