Abdulrahman Salhab

EpiATLAS - a reference for human epigenomic research

EpiATLAS provides a comprehensive collection of human reference epigenomes to advance epigenomic research and understanding of cellular function and disease.

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation

ESMM improves epigenomic state annotation by integrating DNA methylation and chromatin marks, enhancing the detection of heterochromatic regions and regulatory element boundaries.

EpiSegMix: A Flexible Distribution Hidden Markov Model with Duration Modeling for Chromatin State Discovery

EpiSegMix improves chromatin state segmentation by using a flexible hidden Markov model with duration modeling, outperforming existing tools in predicting gene expression.

Age-associated changes in endothelial transcriptome and chromatin landscape correlate with elevated risk of hemorrhage

The paper investigates age-related changes in endothelial cells of mice, identifying gene and chromatin alterations linked to increased intracerebral hemorrhage risk.

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

The paper characterizes the epigenomic organization of the Paramecium macronuclear genome, revealing broad histone mark domains and unique transcriptional features.

GwEEP - A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes

GwEEP quantifies DNA modifying enzyme efficiencies using HPoxBS data, revealing dynamic changes in methylation and hydroxylation during cellular reprogramming and development.

Vesicle-bound regulatory RNAs are associated with tissue aging

The paper identifies aging-associated differences in vesicle-bound and freely circulating small regulatory RNAs in mice, showing tRNA fragments and miRNAs strongly correlate with aging.

Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data

The paper compares DNase I-Seq, ATAC-Seq, and NOMe-Seq to identify assay-specific features and their impact on chromatin accessibility and gene expression prediction.

DNA methylation signatures of a large cohort monozygotic twins clinically discordant for multiple sclerosis

The paper identifies DNA methylation differences in monozygotic twins discordant for multiple sclerosis, highlighting treatment effects and genetic confounders.

Partially methylated domains are hallmarks of a cell specific epigenome topology

The paper identifies partially methylated domains (PMDs) as widespread epigenomic features across human and mouse cells, showing cell-type specificity and links to gene expression, replication timing, and proliferation.