Andrea Vandelli

A circRNA-derived IRES-like element enables programmable translational activation of the endogenous chaperone HSP90

The paper describes a synthetic circRNA-derived IRES-like element, SynFarsa, that enhances translation of an endogenous protein, HSP90, in trans by targeting its 3'UTR.

The human RNA-DNA interactome is cell type-specific and dynamic

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

Integrating RNA Structure and Protein Interactions to Uncover the Mechanisms of Viral and Cellular IRES Function

The paper develops a computational framework to analyze IRES function by combining mutagenesis and RNA-protein interaction profiling, revealing structural and protein dependency differences between viral and cellular IRESs.

A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.

The paper introduces a spatial long-read sequencing method to study developmental splicing and polyadenylation changes in cortical layers and cell types, finding layer-specific and age-related regulatory patterns.

Rationalizing the Effects of RNA Modifications on Protein Interactions

The paper investigates how RNA modifications affect protein-RNA interactions and introduces an algorithm to predict these effects.

Subgenomic flaviviral RNAs and human proteins: in silico exploration of anti-host defense mechanisms

The paper uses in silico analysis to explore interactions between flaviviral subgenomic RNAs and human proteins, identifying novel host factors involved in viral evasion.

The PRALINE database: Protein and Rna humAn singLe nucleotIde variaNts in condEnsates

PRALINE is a database that catalogs proteins and RNAs in biological condensates, their interactions, and the impact of single-nucleotide variants on condensate properties.

Discovering host protein interactions specific for SARS-CoV-2 RNA genome

The paper identifies host proteins interacting with SARS-CoV-2 RNA ends, highlighting pseudouridine synthase PUS7 and post-transcriptional modifications in viral RNA structure and function.

Interplay between disordered regions in RNAs and proteins modulates interactions within stress granules and processing bodies

The paper investigates the structural properties of proteins and RNAs in stress granules and processing bodies, finding that intrinsic disorder and single-stranded regions mediate dynamic interactions.

Structural analysis of SARS-CoV-2 genome and predictions of the human interactome

The paper analyzes the structural elements of the SARS-CoV-2 genome and predicts human protein interactions, identifying conserved regions and potential host factors involved in viral replication.

CROSSalive: a web server for predicting the in vivo structure of RNA molecules

CROSSalive predicts RNA secondary structure in vivo and assesses the impact of m6A methylation using icSHAPE data and a trained model.