Matteo D'Antonio

Publications

• Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer
• In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms
• Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease
• Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments.
• Regulatory variants active in iPSC-derived pancreatic progenitor cells are associated with Type 2 Diabetes in adults
• Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression
• NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes.
• Integrated analysis of recurrent properties of cancer genes to identify novel drivers
• Network of Cancer Genes (NCG 3.0): Integration and analysis of genetic and network properties of cancer genes
• Modification of gene duplicability during the evolution of protein interaction network
• Extraction, integration and analysis of alternative splicing and protein structure distributed information
• Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants
• Improving the predictive power of polygenic risk scores for cardiovascular disease: leveraging genetics, environmental factors and local ancestry within genome-wide association studies
• eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk
• Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
• Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
• Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats
• Properties of structural variants and short tandem repeats associated with gene expression and complex traits
• Author Correction: Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants
• Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease
• Author Correction: Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease
• Network Of Cancer Genes: A web resource to analyze duplicability, orthology and network properties of cancer genes
• Recessive cancer genes engage in negative genetic interactions with their functional paralogs
• EVOLUTION OF PROTEIN INTERACTION NETWORKS THROUGH GENE DUPLICATION
• Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels
• PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3.
• iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
• High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells.
• Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.
• Insights into the mutational burden of human induced pluripotent stem cells using an integrative omics approach
• In-depth genetic analysis of 6p21.3 reveals insights into associations between HLA types and complex traits and disease
• Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats
• Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
• Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics
• In heart failure reactivation of RNA-binding proteins drives the transcriptome into a fetal state
• Insights into genetic factors contributing to variability in SARS-CoV-2 susceptibility and COVID-19 disease severity
• Enhancer release and retargeting activates disease-susceptibility genes
• Genetic analysis of elevated levels of creatinine and cystatin C biomarkers reveals novel genetic loci associated with kidney function.