Federico Andrea Santoni

IVA, a locally deployable Intelligent Variant Analyser based on a small language model for complete case-level and trio-based genomic interpretation.

IVA uses a small language model to perform local genomic variant interpretation, achieving high sensitivity but lower precision in identifying pathogenic variants.

COLSTATS: an interactive web platform for systematic colocalization of GWAS and QTL summary statistics

COLSTATS provides a web platform for colocalizing GWAS and QTL summary statistics to identify shared genetic determinants.

Interdependent Dynamics of mRNA Expression and HIV-1 Viral Load: Insights from Transcriptomics and Mendelian Randomization

The paper identifies 792 genes associated with HIV load using transcriptomics and confirms TRABD2A as a viral restriction factor through Mendelian Randomization.

GenMasterTable: A user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants

GenMasterTable is a desktop application that filters, summarizes, and visualizes large-scale annotated genetic variants, offering a user-friendly interface for non-programmers.

Understanding the genetic complexity of puberty timing across the allele frequency spectrum

This study identifies genetic signals associated with age at menarche, highlights genes involved in pubertal development, and links reproductive timing to later life disease risk.

Pseudospatial transcriptional gradient analysis of hypothalamic ependymal cells: towards a new tanycyte classification

The paper analyzes hypothalamic ependymal cells using single-cell RNA sequencing to classify tanycyte subpopulations and reveal their functional heterogeneity under different fasting conditions.

Transcriptomic profiling of murine GnRH neurons reveals developmental trajectories linked to human reproduction

This study profiles GnRH neurons in mice to uncover developmental gene expression patterns linked to human reproductive processes.

CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications

CoverageMaster detects and visualizes CNVs in exome and genome data using wavelet compression and HMM, potentially replacing probe-based methods.

Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome

This paper introduces revTWMR, a method to determine causal relationships between gene expression and complex traits, finding that traits more strongly influence gene expression than vice versa.

Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2

The paper identifies a dominant monoallelic PAK2 variant causing Knobloch syndrome type 2 with intellectual disability and retinal degeneration.

Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma

This study identifies a genetic variant near CXCL12 associated with increased susceptibility to HIV-related non-Hodgkin lymphoma.

The role of gene expression on human sexual dimorphism: too early to call

The paper investigates sex-specific cis-eQTLs in whole blood RNA-seq data and finds they do not systematically translate into detectable sex-specific trait associations due to limited power and compensatory effects.

Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts.

The paper uses single-cell allele-specific expression to identify novel XCI escapees and reveals cellular heterogeneity in XCI driven by XIST.

Time and space dimensions of gene dosage imbalance of aneuploidies revealed by single cell transcriptomes.

The paper uses single-cell transcriptomes to analyze gene dosage imbalance in aneuploidies, revealing both temporal and spatial dimensions of gene expression changes in trisomies.