Riccardo Delli Ponti

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.

Phase Separation Potential of Marsupial RSX RNA Reveals Convergent Evolution of X-Chromosome Inactivation Mechanisms

The paper identifies RSX interactors and shows they form phase-separation-prone networks, suggesting convergent evolution of XCI mechanisms through biophysical principles rather than sequence or structure.

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.

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.

Computationally-inferred structural landscape of the complete genomes of Dengue serotypes and other viral hemorrhagic fevers

The paper computationally analyzes RNA secondary structures of viral genomes from multiple hemorrhagic fever species, finding structural differences linked to virulence and human protein 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.

A method for RNA structure prediction shows evidence for structure in lncRNAs

The paper introduces CROSSalign, a method for RNA secondary structure prediction and comparison, showing it outperforms covariance models in identifying conserved structures in lncRNAs and viruses.

An integrative study on ribonucleoprotein condensates identifies scaffolding RNAs and reveals a new player in Fragile X-associated Tremor/Ataxia Syndrome

The paper identifies scaffolding RNAs and a new player, TRA2A, in Fragile X-associated Tremor/Ataxia Syndrome by studying RNA-RBP interactions and their aggregation.