Publications

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 https://doi.org/10.1093/nar/gky486


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

Trends in Biotechnology [December, 2017] Danny Incarnato and Salvatore Oliviero https://doi.org/10.1016/j.tibtech.2016.11.002


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 https://doi.org/10.1093/nar/gkx617


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 https://doi.org/10.1093/nar/gkw810

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 https://doi.org/10.1038/nprot.2016.063 * 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 https://doi.org/10.1093/bioinformatics/btv571

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 https://doi.org/10.1016/j.celrep.2015.01.008 * 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 https://doi.org/10.1186/s13059-014-0491-2

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 https://doi.org/10.1093/nar/gkt629