Matteo A. Pellegrini

Alignment-Free k-mer Analysis Reveals Age-Associated k-mer Signals in Canine Buccal DNA and Cell-Free DNA

This study identifies age-associated k-mer signals in canine buccal and cell-free DNA using alignment-free k-mer analysis and ridge regression models.

Is epigenetics Lamarck's revenge? The evolutionary and ecological impacts of DNA methylation in a California oak

The study investigates DNA methylation's role in Lamarckian inheritance in California oaks, finding environmental induction and gene expression associations but not stable transmission across generations.

Determining the age of single cells using scMLEAge

The paper develops a Bayesian statistical framework to predict single-cell age from transcriptomic profiles and demonstrates its accuracy on Tabula Muris Senis data.

Systematic Comparison of 10X Genomics and Parse Single Cell RNA Technologies across PBMC and CD8+ TEMRA Cells

Side-by-side PBMC and CD8+ TEMRA profiling shows Parse favors longer transcripts but underdetects cytotoxic genes (GNLY, PRF1, GZMB), so 10X Chromium better resolves TEMRA subsets.

Physics-Informed Modeling of Biological Aging through DNA Methylation Entropy

This paper introduces a physics-informed epigenetic clock using DNA methylation entropy and machine learning, achieving high accuracy in age prediction and associating age acceleration with clinical conditions.

Conformal Uncertainty Quantification for BayesAge Epigenetic Age Predictions

This paper applies conformal prediction to BayesAge to provide calibrated uncertainty intervals for epigenetic age estimation from DNA methylation data.

Mucus cell and ionocyte precursors migrate between epithelial cells to disperse through the zebrafish epidermis

The paper shows that mucus cell and ionocyte precursors migrate between epithelial layers in zebrafish epidermis to achieve their scattered distribution.

AlphaFold-Driven Structural Proteomics Reveals Extensive Cellulosome Machinery in Human Ruminococcal Symbionts

The paper uses AlphaFold2 to uncover expanded cellulosome machinery in human-associated Ruminococcus species, revealing previously undetected structures and functions.

MKMC enables reference-free transcriptomic analysis using k-mer representations

MKMC enables reference-free transcriptomic analysis using k-mer representations, detecting isoform-specific events and matching alignment-based methods in differential expression and age prediction.

Novel Synthetic Promoter Armed Oncolytic Herpes Simplex Virus For Treatment of PAX3-FOXO1 Positive Rhabdomyosarcoma

This paper develops a PAX3-FOXO1-targeted oncolytic herpes virus that improves tumor control in immunocompetent mouse models when combined with anti-PD1 therapy.

Improving the Accuracy of Forensic Age Estimation Through Bias Reduction

This study compares age estimation models using DNA methylation data, finding that maximum likelihood estimation reduces bias compared to linear regression and random forest.

Accurate estimation of canine inbreeding using ultra low-coverage whole genomesequencing

This study shows that ultra low-coverage whole genome sequencing can reliably estimate canine inbreeding using runs of homozygosity and inbreeding coefficients.

Inference of admixture in dogs from whole genome sequences

The paper develops a method to estimate admixture in dogs using whole genome sequences and demonstrates its accuracy in both simulated and real data.

Multi-tissue transcriptomic aging atlas reveals predictive aging biomarkers in the killifish

The paper creates a multi-tissue transcriptomic aging atlas in killifish, identifies age-altered pathways, and develops tissue-specific transcriptomic clocks with sex-specific biomarkers for aging prediction.

Rtf1-dependent transcriptional pausing regulates cardiogenesis

This study shows that Rtf1-mediated transcriptional pausing is essential for cardiogenesis, as its disruption leads to cardiac progenitor cell defects and cardiomyocyte absence.

MAGIC: Methylation Analysis with Genomic Inferred Contexts

MAGIC improves differential methylation analysis in WGBS data by modeling genomic heterogeneity with a beta-binomial mixture model, enhancing sensitivity and reducing false positives.

Robust software development practices improve citations of RNA-seq tools

This study shows that better software development practices for RNA-seq tools lead to more citations, as evidenced by a strong statistical association between development quality and citation counts.

TREM2+ macrophages accumulate in alveoli of human pulmonary tuberculosis providing a permissive niche for bacterial growth

This study identifies TREM2+ lipid-laden macrophages in alveolar TB pneumonia that support Mtb survival, contrasting with granulomas, and shows pharmacological reversal of this immunometabolic state.

MicroBayesAge: A Maximum Likelihood Approach to Predict Epigenetic Age Using Microarray Data

MicroBayesAge improves age prediction using microarray data by dividing data into age-specific cohorts and employing a two-stage process, showing better accuracy for younger patients and males.

Genome-wide DNA Methylation Patterns in Daphnia magna are Not Significantly Associated with Age

This study examines DNA methylation in Daphnia magna and finds no significant age-related changes in methylation patterns.

Genetic and anatomical determinants of olfaction in dogs and wild canids

This study investigates the genetic and anatomical basis of olfaction in dogs and wild canids, finding no evidence of human-directed selection for enhanced olfaction in domestic dogs.

BayesAge 2.0: A Maximum Likelihood Algorithm To Predict Transcriptomic Age

BayesAge 2.0 predicts transcriptomic age from RNA-seq data using a maximum likelihood algorithm with Poisson distribution and LOWESS smoothing, improving accuracy and efficiency over traditional models.

BSReadSim: a versatile and efficient simulator to generate realistic bisulfite sequencing reads

BSReadSim generates realistic bisulfite sequencing reads by integrating genetic variants and methylation profiles across multiple sequencing technologies.

An epigenetic clock for Xenopus tropicalis reveals age-associated sites enriched in H4K20me3-marked heterochromatin

This paper develops an epigenetic clock for Xenopus tropicalis using DNA methylation data, finding age-associated CpG sites enriched in heterochromatin marks similar to mammals.

The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation

The paper introduces MSEPM, a multidimensional model for DNA methylation that accounts for age, sex, and cell type, revealing site-specific methylation dynamics influenced by transcription factors.

Fractional Calculus in Epigenetics

This paper introduces a fractional calculus framework to model DNA methylation dynamics, showing improved fit compared to standard exponential models.

Systematic dissection of epigenetic age acceleration in normal breast tissue reveals its link to estrogen signaling and cancer risk

The paper evaluates epigenetic clocks in normal breast tissue, identifies age acceleration linked to estrogen signaling and cancer risk, and highlights cellular heterogeneity's role in age estimation.

Dysfunctional β-cell longevity in diabetes relies on high energy conservation and positive epistasis

The paper identifies PFKFB3-expressing dysfunctional β-cells in T2D, showing their survival via positive epistasis and reduced clearance, and demonstrates PFKFB3 inhibition restores glucose tolerance in mice.

Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis

The paper identifies tissue-informative DNA methylation sites in ALS using targeted sequencing and machine learning, showing accurate prediction of disease status and progression.

BayesAge: A Maximum Likelihood Algorithm To Predict Epigenetic Age

BayesAge predicts epigenetic age using maximum likelihood estimation and binomial models for bulk bisulfite sequencing data, outperforming scAge in accuracy and interpretability.