Stefano Monti

Age-based shifts in multicellular community organization and abundance in HPV-Negative Head and Neck Cancer

This study identifies age-related changes in cellular composition and organization in HPV-negative head and neck cancer using single-cell data, highlighting MDK as a key factor in stromal remodeling and immunosuppression.

Metabolic dysfunction and metformin modify plasma extracellular vesicle signaling to prostate cancer cells

This study investigates how metabolic dysfunction and metformin affect plasma extracellular vesicle signaling to prostate cancer cells, identifying specific miRNAs and their effects on tumor progression.

Signature Recontextualization: Mapping perturbational signatures across biological contexts

This paper introduces a benchmarking framework for predicting perturbation signatures across biological contexts, showing that projection and network-based methods perform well across diverse datasets and contexts.

hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models

hypeR-GEM connects metabolite signatures to enzyme-coding genes using genome-scale metabolic models, showing concordance with proteomic and transcriptomic data in real-world applications.

Sub-phenotypes of pneumonia defined by pulmonary histopathological features

The paper defines sub-phenotypes of pneumonia using histopathological features from human lung samples and validates them in mouse models.

Environmental chemical mixtures reprogram mammary epithelial development to epigenetic states associated with breast cancer

This study shows that environmental chemical mixtures disrupt mammary development and induce epigenetic changes linked to breast cancer, particularly invasive lobular carcinoma.

METABOLOMIC SIGNATURES OF EXTREME OLD AGE: FINDINGS FROM THE NEW ENGLAND CENTENARIAN STUDY

The paper identifies metabolomic signatures associated with extreme old age using data from the New England Centenarian Study and links them to biological age and mortality risk.

A highly resolved integrated single-cell atlas of HPV-negative head and neck cancer

The paper integrates six single-cell datasets to create a high-resolution atlas of HPV-negative HNSCC, revealing new cell populations and associations between transcriptional signatures and clinical outcomes.

Whole blood transcriptional signatures of age and survival identified in Long Life Family and Integrative Longevity Omics Studies

This study identifies age and survival-related transcriptomic signatures in longevity-enriched cohorts using RNAseq data from blood samples.

A highly resolved integrated single-cell atlas of human breast cancers

This study creates a large integrated single-cell RNA-seq atlas of human breast cancers, revealing tumor microenvironment heterogeneity and survival-associated cell states across multiple datasets.

Dietary Serine Restriction Impacts H3K27 and H3K4 Methyl Epigenomes to Impede Head and Neck Cancer Cell Plasticity and Tumor Growth

This study shows that dietary serine restriction alters H3K27me3 and H3K4me3 histone modifications, reducing tumor growth and plasticity in head and neck cancer.

IPSC-based modeling of resiliency in centenarians reveals longevity-specific signatures

The paper uses iPSC-derived neurons from centenarians to identify resilience signatures associated with longevity, showing enhanced stress response and specific transcriptional programs.

Plasma exosomes from individuals with type 2 diabetes drive breast cancer aggression in patient-derived organoids

This study shows that exosomes from type 2 diabetes patients promote breast cancer aggressiveness in organoids by expanding immunosuppressive cells and increasing tumor heterogeneity and invasiveness.

Plasma Exosomes in Insulin Resistant Obesity Exacerbate Progression of Triple Negative Breast Cancer

This study shows that plasma exosomes from obese mice enhance TNBC aggressiveness by inducing epithelial-mesenchymal transition and Rac1 activation.

Learning Gaussian Graphical Models from Correlated Data

This paper introduces a Bootstrap algorithm to infer Gaussian Graphical Models from correlated data, showing it controls Type I error better than conventional methods in simulations and a real family-based study.

DDR1 regulates RUNX1-CBFβ to control breast stem cell differentiation

This study shows DDR1 regulates RUNX1-CBFβ to drive breast stem cell differentiation into multiple lineages and tissue structures.

Robust Serum Proteomic Signatures of APOE2

The paper validates and expands a serum protein signature associated with APOE genotypes, identifying new protein associations and potential targets for Alzheimer's disease prevention.

LSD1 inhibition corrects dysregulated MHC-I and dendritic cells activation through IFNγ-CXCL9-CXCR3 axis to promote antitumor immunity in HNSCC

This study shows LSD1 inhibition enhances antitumor immunity in HNSCC by upregulating MHC-I and activating the IFNγ-CXCL9-CXCR3 axis through dendritic cells and CD8+ T cells.

Insulin Resistance Increases TNBC Aggressiveness and Brain Metastasis via Adipocyte-derived Exosomes

This study shows insulin-resistant adipocyte exosomes promote TNBC aggressiveness and brain metastasis via miRNA pathways.

The Aryl Hydrocarbon Receptor Controls IFNγ-Induced Immune Checkpoints PD-L1 and IDO via the JAK/STAT Pathway in Lung Adenocarcinoma

This study shows the aryl hydrocarbon receptor (AhR) mediates IFNγ-induced PD-L1 and IDO1 in lung adenocarcinoma via JAK/STAT, leading to immunosuppression and tumor growth.

Cross-platform proteomics signatures of extreme old age

The paper validates and expands a serum protein signature of extreme old age using LC-MS/MS, identifying 80 conserved proteins across platforms associated with aging pathways.

yQTL Pipeline: a structured computational workflow for large scale quantitative trait loci discovery and downstream visualization

The paper introduces yQTL Pipeline, a tool for QTL discovery and visualization, applied to metabolomics data from NECS, identifying 14,983 mQTLs with improved efficiency.

Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer.

This study uses total RNA sequencing to compare gene expression and microbial profiles between oral premalignant lesions, cancer, and healthy tissues, identifying shared molecular and microbial features associated with progression to cancer.

Bayesian Differential Analysis of Cell Type Proportions

This paper introduces a Bayesian multinomial regression method for analyzing cell type proportions without requiring a reference cell type, using the rjags package in R.

Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data

The paper introduces K2Taxonomer, an unsupervised algorithm for identifying molecular subgroups in bulk and single-cell transcriptomics data, and applies it to breast cancer TILs to find a shared transcriptional program associated with better prognosis.

Structure Learning for Hierarchical Regulatory Networks

SHINE improves network structure learning from high-dimensional data with limited samples by leveraging shared structural information across multiple networks.

hypeR: An R Package for Geneset Enrichment Workflows

hypeR provides an R package for geneset enrichment workflows with flexible analysis, visualization, and reporting features.

Pipeliner: A Nextflow-based framework for the definition of sequencing data processing pipelines

Pipeliner provides a Nextflow-based framework for creating flexible and reproducible sequencing data processing pipelines, supporting bulk RNA-seq, scRNA-seq, and DGE data.

The Carcinogenome Project: In-vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity

The paper develops an in-vitro gene expression screening method to predict chemical carcinogenicity and genotoxicity using HepG2 cells and machine learning models.

iEDGE: integration of Epi-DNA and Gene Expression and applications to the discovery of somatic copy number-associated drivers in cancer

iEDGE integrates epi-DNA and gene expression data to identify cis and trans driver genes in cancer, showing enrichment for known oncogenes and tumor suppressors.