Matteo A. Pellegrini

This study shows that IL-1B-mediated inflammation drives ineffective erythropoiesis in early-stage MDS and that canakinumab can reduce transfusion dependence in patients with DNMT3A and TET2 mutations.

The paper identifies three genetic loci influencing mitochondrial proteins and heart hypertrophy in mice using proteomics and association mapping.

The paper identifies age-associated DNA methylation changes in Xenopus tropicalis using whole genome bisulfite sequencing and develops a cost-effective epigenetic clock assay.

This study compares transcriptomic profiles of porcine and human colonic enteric nervous system to identify conserved regional programs and their response to vagal nerve stimulation.

This study examines how age, sex, weight, and breed influence DNA methylomes in canids, finding strong associations with age, sex, and sterilization status, and showing genetic and physiological factors moderate epigenetic aging.

This study presents a high-quality genome and methylome analysis of Quercus lobata, identifying genomic features linked to oak evolutionary success, including gene duplications and methylation patterns.

This study uses pseudotime analysis to show DNA methylation aging follows exponential trends linked to mortality timescales.

The paper develops a mammalian methylation array to profile methylation levels at conserved sequences across species, enabling cross-species comparisons and epigenetic biomarker development.

The paper identifies heterogeneous pdgfrβ+ cells critical for coronary vessel development and heart regeneration in zebrafish.

The paper uses single-cell RNA sequencing to study ductus arteriosus closure in mice, identifying vimentin as critical for vascular remodeling and closure.

The paper compares the epigenetic pacemaker (EPM) to traditional epigenetic clocks, finding EPM more sensitive in detecting factors affecting epigenetic age.

This study uses ChIP-Seq to profile H3K4 methylation across the Chlamydomonas cell cycle, revealing distinct patterns of mono- and trimethylation at gene promoters and their relationship to gene expression.

The paper introduces uscfDNA-seq, a method to sequence single-stranded cell-free DNA in plasma, revealing a novel population of ultrashort cfDNA with a modal size of 50nt.

This study evaluates ten deconvolution tools on 4,000 clinical and synthetic samples, finding EPIC performs best on Framingham data and HPCA references are generally accurate.

BSBolt is a bisulfite sequencing analysis platform that provides accurate and fast alignment and methylation calling, outperforming existing tools.

The paper develops epigenetic clocks and pacemaker models to predict age in plains zebras and other equids using DNA methylation data from blood samples.

GEDIT estimates cell type abundances from gene expression data, outperforming existing tools across multiple platforms and tissue types.

Single-cell RNA sequencing reveals that heterogeneity in Chlamydomonas bulk cultures is largely driven by diurnal cycle phases.

This study develops pan-primate epigenetic clocks and sex predictors using DNA methylation data from 37 primate species, achieving high accuracy for age estimation across species.

This study uses single-cell transcriptomics to show that ATOH7 and Neurog2 regulate human retinal progenitor states and neuroblast fate by modulating bHLH factor expression.

This paper develops a rat epigenetic clock (DNAmAge) that correlates with age and phenotypic aging, and identifies histone modifications linked to its signal.

The paper investigates cell expansion and proliferation in Fucus embryos, showing correlations between cell wall mechanics, alginate biochemistry, and growth patterns, with transcriptomic data supporting gene expression changes related to wall stiffness.

The paper curates a dataset of physical molecular interactions between SARS-CoV-2, SARS-CoV-1, and other Coronaviridae proteins, providing a resource for studying virus-host interactions.

This study shows that glucose metabolism enhances neonatal heart regeneration by increasing glucose uptake, glycogen storage, and cardiomyocyte proliferation in mice.

ACTINN is a neural network that automatically identifies cell types in scRNA-seq data by learning features from annotated datasets, outperforming manual methods in speed and accuracy.

The paper develops a model to characterize non-linear epigenetic aging trends across the entire lifespan, finding a logarithmic relationship between epigenetic age and chronological age.

The paper introduces MREBS, a method for DNA methylation estimation that reduces sequencing costs while improving coverage compared to existing methods.

The paper presents a dataset of 28,000 annotations describing how amino acid mutations affect protein interactions, available through the IntAct website.

The paper identifies the synaptic m6A epitranscriptome in mouse forebrain and shows its role in synaptic function and disease-related pathways.