Probing the dynamic RNA structurome and its functions

Nature Reviews Genetics [November, 2022] Robert C. Spitale & Danny Incarnato

SHAPE-guided RNA structure homology search and motif discovery

Nature Methods [March, 2022] - Supporting data Edoardo Morandi, Martijn J. van Hemert & Danny Incarnato

Genome-scale deconvolution of RNA structure ensembles

Nature Methods (cover image) [February, 2021] - Supporting data - Behind the Paper Edoardo Morandi, Ilaria Manfredonia, Lisa M. Simon, Francesca Anselmi, Martijn J. van Hemert, Salvatore Oliviero & Danny Incarnato

A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

Nucleic Acids Research [January, 2021] - Supporting data Tycho Marinus, Adam B. Fessler, Craig A. Ogle, Danny Incarnato

Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies

Biochemical Society Transactions [December, 2020] Ilaria Manfredonia and Danny Incarnato

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

Nucleic Acids Research [November, 2020] - Supporting data Ilaria Manfredonia, Chandran Nithin, Almudena Ponce-Salvatierra, Pritha Ghosh, Tomasz K. Wirecki, Tycho Marinus, Natacha S. Ogando, Eric J. Snider, Martijn J. van Hemert, Janusz M. Bujnicki, Danny Incarnato

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

Nucleic Acids Research [May, 2019] - Supporting data Lisa M. Simon, Edoardo Morandi, Anna Luganini, Giorgio Gribaudo, Luis Martinez-Sobrido, Douglas H. Turner, Salvatore Oliviero, Danny Incarnato

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

Nucleic Acids Research [June, 2018] Danny Incarnato, Edoardo Morandi, Lisa M. Simon, Salvatore Oliviero

The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications

Trends in Biotechnology [December, 2017] Danny Incarnato and Salvatore Oliviero

In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

Nucleic Acids Research [July, 2017] Danny Incarnato, Edoardo Morandi, Francesca Anselmi, Lisa M. Simon, Giulia Basile, Salvatore Oliviero

High-throughput single-base resolution mapping of RNA 2'-O-methylated residues

Nucleic Acids Research [February, 2017] Danny Incarnato, Francesca Anselmi, Edoardo Morandi, Francesco Neri, Mara Maldotti, Stefania Rapelli, Caterina Parlato, Giulia Basile, Salvatore Oliviero

Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis

Nature Protocols [July, 2016] Francesco Neri*, Danny Incarnato*, Anna Krepelova, Caterina Parlato, Salvatore Oliviero * equal contribution

RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data

Bioinformatics [February, 2016] Danny Incarnato, Francesco Neri, Francesca Anselmi, Salvatore Oliviero

Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics

Cell Reports (cover image) [February, 2015] Francesco Neri*, Danny Incarnato*, Anna Krepelova, Stefania Rapelli, Francesca Anselmi, Caterina Parlato, Claudio Medana, Federica Dal Bello, Salvatore Oliviero * equal contribution

Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome

Genome Biology [October, 2014] Danny Incarnato, Francesco Neri, Francesca Anselmi, Salvatore Oliviero

MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets

Nucleic Acids Research [October, 2013] Danny Incarnato, Francesco Neri, Daniela Diamanti, Salvatore Oliviero