Gilles Gasparoni

MethylBench: A comprehensive benchmark of DNA methylation profiling methods across diverse sequencing platforms

MethylBench benchmarks DNA methylation profiling methods across sequencing platforms, finding consistent DMC hotspots and highlighting platform-specific strengths and limitations.

Increasing TET expression and 5-hydroxymethylcytosine formation by a carbocyclic 5-aza-2'-deoxy-cytidine antimetabolite

This study shows that the carbocyclic antimetabolite cAzadC increases TET2 expression and 5hmdC levels, leading to reactivation of anti-tumor responses in AML models.

Dynamic transcriptional remodeling in alcohol use disorder reveals immune dysregulation and adaptive shifts in coagulation during therapy

The paper analyzes transcriptomic changes in peripheral blood of AUD patients during withdrawal therapy, finding partial normalization of gene expression but persistent immune and coagulation dysregulation.

Mitochondrial protein import stress causes progressive neurodegeneration opposed by PERK - eIF2α signalling

The paper shows that mitochondrial import stress causes neurodegeneration, which is opposed by PERK-eIF2α signaling, with PERK overexpression protecting against it.

Self-assembly of hybrid 3D cultures by integrating living and synthetic cells

The paper develops hybrid 3D cancer cultures using synthetic and natural cells to mimic tumor immune microenvironments and identify immune evasion mechanisms.

Crosstalk between the Methyl-Cytosine Dioxygenase TET3 and the Methyl-CpG-binding protein MECP2 Controls Neuronal Maturation

The paper shows TET3 and MECP2 interact to regulate neuronal maturation, with TET3 critical for functional development and MECP2 inhibiting TET3 activity.

Gut miRNA regulates gut microbiome and Alzheimer pathology in App-knock-in mice

This study shows that gut miRNA depletion in App-knock-in mice alters microbiome composition, reduces Aβ load, and induces anxiety, suggesting miRNA manipulation could influence AD pathogenesis.

Identification of targetable vulnerabilities of PLK1-overexpressing cancers by synthetic dosage lethality

The paper identifies synthetic dosage lethality targets for PLK1-overexpressing cancers using genome-wide screens and validates key hits to show their therapeutic potential.

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.

Two Piwis with Ago-like functions silence somatic genes at the chromatin level

The paper investigates the role of two Piwi proteins in transgene-induced silencing in Paramecium, showing they have distinct but overlapping functions in generating and processing siRNAs for chromatin-level gene silencing.

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

The paper introduces MAGAR, a framework to identify methylation quantitative trait loci (methQTLs) and distinguish common from cell-type-specific effects using DNA methylation and genotyping data.

A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex

This study performs a meta-analysis of DNA methylation data from Alzheimer's disease patients to identify differentially methylated loci across brain regions and cortex.

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.

Integrative analysis of single cell expression data reveals distinct regulatory states in bidirectional promoters

The paper integrates single cell RNA-seq with bulk epigenomic data to identify distinct regulatory states in bidirectional promoters and their associations with structural features and TF binding.

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.

normR: Regime enrichment calling for ChIP-seq data

normR normalizes ChIP-seq data to improve enrichment calling in different histone modification regimes.

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

This paper introduces TEPIC, a method that combines open-chromatin data with TF binding affinities to predict gene expression, achieving results comparable to TF ChIP-seq.