CUT&Tag

Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility

Ryder: Epigenome normalization using a two-tier model and internal reference regions

Ryder normalizes epigenomic bigWig tracks against stable internal reference regions such as invariant CTCF sites, correcting background and signal separately, recovering expected perturbation effects that depth-only normalization obscured.

mV2G: a multiomic atlas for tissue-specific variant-to-gene prioritization

A web atlas counts evidence from 24 types for 188,634,118 variant-gene pairs across 50 human tissues; 1,530,420 pairs pass a high-confidence cutoff, 87% of them tissue-specific.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

Multi-omic Profiling of Recurrence Risk Across Breast Cancer Subtypes

This study identifies subtype-specific molecular and immune features associated with recurrence risk in breast cancer using multi-omic analysis of 340 tumors and validates predictive models in an external cohort.

Programmable Nucleic Acid Sensing in Human Cells Using Circularizable ssDNA

This paper introduces SONAR, a platform for detecting nucleic acids and triggering gene expression in human cells, demonstrating its ability to sense DNA and RNA and express various protein payloads.

A multiscale chromatin collapse underlies vascular pathology in Hutchinson -Gilford progeria syndrome

This study identifies chromatin reorganization and histone mark changes in HGPS VSMCs, linking them to vascular pathology through disrupted enhancer-promoter interactions.

Cross-assay RNA modeling reveals cancer biomarkers

This paper integrates multiple transcriptomics assays to identify cancer biomarkers, finding GBP4 as a predictor of recurrence and immune remodeling.

Genomic and epigenomic maps of mouse centromeres and pericentromeres

This study generates genomic and epigenomic maps of mouse centromeres and pericentromeres using long-read sequencing and epigenetic analyses, revealing satellite DNA composition and chromatin state differences.

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.

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.

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.

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.

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.

Mapping eukaryotic chromatin accessibility and histone modifications with DNA deaminase

The paper introduces two new methods, ChrODIE and ANDIE, for mapping chromatin accessibility and histone modifications without enzymatic cleavage, enabling multi-omics integration.

Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping

The paper uses G4-DNABERT to map G-quadruplexes to enhancer and promoter regions, supporting their role in chromatin looping and gene regulation.

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

DiffModeler uses diffusion models to accurately model protein complex structures from low-resolution cryo-EM maps, achieving high TM-Scores across various resolutions.

Alternative promoters in CpG depleted regions pervasively account for epigenetic misregulation of cancer transcriptomes

The paper identifies alternative promoters in cancer transcriptomes that are associated with epigenetic misregulation due to DNA methylation changes in CpG-depleted regions.

Deep learning based on multi-omics integration identifies potential therapeutic targets in breast cancer

The paper develops a deep learning model integrating multi-omics data to stratify breast cancer patients by prognosis and identify potential therapeutic targets.

FILER: large-scale, harmonized FunctIonaL gEnomics Repository

FILER provides a large-scale, harmonized functional genomics data catalog with streamlined access to over 50,000 datasets and efficient querying capabilities.

Multi-omics Topic Modeling for Breast Cancer Classification

This paper uses multi-omics topic modeling to classify breast cancer subtypes, showing improved accuracy by integrating mRNA, microRNA, and copy number variation data.

An integrated mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons.

The paper develops an integrated resource to analyze small RNA profiles in mosquitoes, revealing evolutionary dynamics and host responses to viruses and transposons.

Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures

MESSI infers coevolution rates of base-pairing interactions in nucleic acid sequences and identifies functionally important substructures.

Control of human testis-specific gene expression

The paper analyzes testis-specific genes to identify regulatory features and patterns associated with differentiation levels in human testis cells.

Module analysis captures pancancer (epi)genetically deregulated cancer driver genes for smoking and antiviral response

This paper introduces AMARETTO, a multi-omics integration algorithm that identifies pancancer driver genes related to smoking and antiviral responses by analyzing eleven cancer types.

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

The paper introduces seqOutBias to correct enzymatic sequence bias in sequencing data, improving the identification of molecular signatures from protein/DNA interactions.

OncoScape: Exploring the cancer aberration landscape by genomic data fusion

OncoScape integrates five genomic data types across 11 cancer types to identify new candidate cancer genes and reveals discrepancies between cell line and tumor aberrations.