Nicolae Radu Zabet

This paper introduces a framework to quantify DNA methylation heterogeneity and detect co-methylated loci using native Nanopore sequencing, revealing patterns obscured by average methylation summaries.

HiCPotts is an R/Bioconductor package that identifies significant chromatin interactions in Hi-C data while modeling biases using a zero-inflated Negative Binomial distribution.

The paper develops AI models to predict enhancers in human and mouse cell lines, identifying H3K18ac as a new enhancer marker and annotating enhancers using a combination of epigenetic marks.

The paper identifies a conserved global control region for Hox gene regulation in annelids and shows convergent evolution of cluster-wide regulatory mechanisms in vertebrates and spiralians.

The paper identifies stable and variable DNA methylation loci in human whole blood using the IlluminaEPIC array, showing their genomic distribution and genetic control.

The paper shows gene body methylation reduces gene expression noise in Arabidopsis thaliana by linking methylation levels to expression variability.

This study shows that DNA methylation changes in Arabidopsis thaliana under fluctuating light conditions compared to square light, affecting gene expression and transposable elements.

The paper identifies epigenetic regulation of key pathways and novel druggable targets in glioblastoma by comparing chromatin remodelling in neoplastic and neural stem cells.

This study generates human cerebellar organoids to model medulloblastoma subgroups G3 and G4, showing their ability to sustain tumor growth and respond to anti-tumour compounds.

The paper develops a statistical model to predict TF binding to chromatin and finds that about one third of TFs bind independently of chromatin accessibility.

The paper shows H4K16ac activates LINE1 and LTR transcription, contributing to cis-regulatory function by maintaining active chromatin at TEs.

ZipHiC identifies enriched interactions and experimental biases in Hi-C data using a Bayesian framework with hidden Markov random field and approximate Bayesian computation.

The paper identifies sex-associated differentially methylated CpG sites and regions in whole blood using the Illumina EPIC array, revealing their genomic locations and enrichment for sex-related transcription factors.

This study shows that depletion of architectural proteins affects TAD organisation and gene expression in Drosophila, linking TAD reorganisation to changes in gene expression.

The paper develops a method to generate locus-specific chromatin profiles at transposable elements using HiChIP and PAtChER, revealing epigenetic variation in young TEs in mouse and human cells.

The paper introduces ChIPanalyser, a statistical thermodynamics model for predicting TF-DNA binding, showing differences in binding mechanisms across TFs and cell lines.

The paper presents high-resolution contact maps of Drosophila neuronal cells and identifies TAD rearrangements during differentiation, showing enhanced long-range interactions and CTCF enrichment at cell-type-specific borders.

The paper identifies DNA sequence features that predict susceptibility to epiallelic switching in Arabidopsis and verifies these findings in rice.