CUT&Tag

METTL3 Uncouples Chromatin Accessibility from Transcription during Retinal Development

This study investigates METTL3's role in retinal development by integrating multi-omics data, revealing its impact on m6A regulation and chromatin accessibility independent of transcription.

Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data

The paper develops MultiXray, a Bayesian method for multi-state and multi-condition protein structure modeling using X-ray crystallography data, improving Rfree values in both simulated and experimental cases.

Nucleosome context regulates chromatin reader preference

The paper investigates how nucleosome context influences chromatin reader binding preferences using biochemical and genomic approaches, revealing that multivalent engagement often has regulatory effects beyond simple additivity.

Merging conformational landscapes in a single consensus space with FlexConsensus algorithm

The paper introduces FlexConsensus, an algorithm that merges conformational landscapes from different CryoEM heterogeneity methods into a shared consensus space to improve reliability and reproducibility.

Structural Basis of Pseudomonas FapC Biofilm-Forming Functional Amyloid Formation

This study determines the structural basis of FapC biofilm formation in Pseudomonas aeruginosa using integrative structural biology methods.

Repurpose of Ritlecitinib Reduces Neointima Formation and Enhances Endothelial Recovery Following Vascular Injury

This study shows that Ritlecitinib reduces neointima formation and enhances endothelial recovery after vascular injury by modulating JAK3 signaling and VEGF-A/TSP-1 pathways.

Trimodal Single-Cell Gene Regulatory Networks Reveal Principles of Stemness Loss and Cell Fate Acquisition in Human Hematopoiesis

The paper establishes dynamic enhancer-based gene regulatory networks in human hematopoiesis, revealing that stemness loss and lineage acquisition are temporally and mechanistically uncoupled.

Comprehensive architecture of the bacterial RNA interactome

The paper introduces TRIC-seq to map bacterial RNA interactions, revealing novel regulatory contacts and stress-related mRNA co-aggregation in Escherichia coli and other bacteria.

Therapeutic Salmonella induces long-term protective trained immunity in NK cells against cancer metastasis

This study shows that a single dose of Salmonella YB1 vaccine induces long-term protective trained immunity in NK cells, enhancing their ability to combat cancer metastasis.

Diverse epigenomic mechanisms underpin transcriptional dysregulation in Polycomb-altered acute myeloid leukemia

This study investigates how PRC2 depletion in AML affects epigenomic and transcriptional changes, revealing altered chromatin accessibility, H3K27me3 levels, and gene expression patterns that impact cell phenotype and treatment response.

Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma.

Integrating Multi-Modal Cancer Data Using Deep Latent Variable Path Modelling

This paper introduces DLVPM, a deep learning method for integrating multi-modal cancer data, showing improved performance in mapping associations between genetic, epigenetic, and histological features.

SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress

SPIDR is a high-throughput method for mapping RNA-protein interactions that identifies 4EBP1's role in selectively repressing mRNA translation under mTOR inhibition.

Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip

Rocketchip improves rigor and reproducibility in ChIP-seq, CUT&RUN, and CUT&Tag data analysis by enabling comparison and swapping of analysis components.

POCALI: Prediction and insight On CAncer LncRNAs by Integrating multi-omics data with machine learning

POCALI identifies cancer lncRNAs by integrating 44 multi-omics features, showing improved sensitivity and strong associations with cancer phenotypes.

The epigenetic regulator TRIM24 controls melanoma cell dedifferentiation and resistance to treatment in melanoma

This study identifies TRIM24 as an epigenetic regulator that promotes melanoma cell dedifferentiation and treatment resistance, with potential as a druggable target.

MagIC-Cryo-EM: Structural determination on magnetic beads for scarce macromolecules in heterogeneous samples

The paper introduces MagIC-cryo-EM, a technique that enables structural analysis of scarce macromolecules in heterogeneous samples with lower concentration requirements, and applies it to study H1.8-associated nucleosomes.

EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer

This study shows that the EZH1Q571R mutation enhances chromatin compaction and PRC2 activity, leading to repression of tumor suppressor genes in follicular thyroid cancer.

NMNAT1 Binding at Promoters and Enhancers Couples NAD+ Synthesis to RNA Polymerase II Engagement

This study identifies NMNAT1's role in transcriptional regulation by showing its binding to gene promoters and enhancers and its impact on RNA Polymerase II occupancy.

Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN

HetSIREN is a deep learning method for CryoEM conformational state reconstruction and refinement, improving structural accuracy by decoupling pose and CTF information from conformational landscapes.

Charting the transition from in vitro gliogenesis to the in vivo maturation of transplanted human glial progenitor cells

This study tracks the in vitro generation and in vivo differentiation of human glial progenitor cells using single-cell RNA and ATAC-seq, revealing how the host environment influences their maturation into astrocytes and oligodendrocytes.

StACKER, A TOOL FOR SYSTEMS LEVEL ANALYSIS OF BASE STACKING IN NUCLEOTIDE-RICH STRUCTURES

The paper introduces StACKER, a Python tool for analyzing base stacking in nucleic acid structures, and applies it to ribosome simulations to reveal conformational changes linked to translation phenotypes.

A Combined Multi-Omics and Supervised Learning Strategy Uncovers an Epithelial Signature of Radiotherapy Response in Colorectal Cancer

The paper identifies a 101-biomarker signature predicting radiotherapy response in colorectal cancer using multi-omics and supervised learning, achieving 89% accuracy.

DEK::NUP214 acts as an XPO1-dependent transcriptional activator of essential leukemia genes

This study identifies DEK::NUP214 as an XPO1-dependent transcriptional activator of leukemia genes, showing selective response to XPO1 inhibitors in t(6;9) AML cases.

Chemical inhibition of RPA gap protection sensitizes BRCA1-deficient cancers to PARP inhibition

This study shows that inhibiting RPA gap protection enhances PARP inhibitor efficacy in BRCA1-deficient cancers by increasing genomic instability and reducing tumor growth.

CLCluster: a redundancy-reduction contrastive learning-based clustering method of cancer subtype based on multi-omics data

CLCluster uses contrastive learning with multi-omics data to cluster cancer subtypes, showing improved performance over existing methods and identifying AS events linked to patient survival.

Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome

The paper predicts and annotates alternative transcription starts and promoter shifts in the chicken genome using CAGE data, revealing that housekeeping genes may use single sharp promoters and undergo significant promoter shifts.

CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

This study benchmarks CUT&Tag against ENCODE ChIP-seq for histone modifications, finding 54% average recall of known peaks and comparable peak caller performance.

FROM CANCER MOLECULAR SUBTYPE TO AI HYPE: BENCHMARKING AI IN CANCER MOLECULAR SUBTYPING

This study benchmarks 35 AI classifiers across 153 cancer datasets to evaluate their performance in molecular subtype classification, identifying optimal data configurations and model types for different omics modalities and cancer types.

Non-coding structural variants identify a commonly affected regulatory region steering FOXG1 transcription in early neurodevelopment

The paper identifies a regulatory region affecting FOXG1 transcription in neurodevelopment through structural variants and chromatin analysis.