RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning

Nature Communications [March, 2026] - Supporting data Chundan Zhang, Ivana Borovská, Teona Iobashvili, Edoardo Morandi, Marta Lionnez, Oluwatosin S Olayinka, Rinse de Boer, Massimiliano Clamer, Martin D Witte, Klaus Pors, John S Schneekloth Jr & Danny Incarnato https://doi.org/10.1038/s41467-026-70801-9

Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis

Nature Biotechnology [July, 2025] - Supporting data Ivana Borovská, Chundan Zhang, Sarah-Luisa J. Dülk, Edoardo Morandi, Marta F. S. Cardoso, Billal M. Bourkia, Daphne A. L. van den Homberg, Michael T. Wolfinger, Willem A. Velema & Danny Incarnato https://doi.org/10.1038/s41587-025-02739-0

Structural and biophysical dissection of RNA conformational ensembles

Current Opinion in Structural Biology [October, 2024] Steve L. Bonilla, Alisha N. Jones & Danny Incarnato https://doi.org/10.1016/j.sbi.2024.102908

SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data

Nucleic Acids Research [July, 2024] Niek R Scholten, Dennis Haandrikman, Joshua O Tolhuis, Edoardo Morandi & Danny Incarnato https://doi.org/10.1093/nar/gkae348

Probing the dynamic RNA structurome and its functions

Nature Reviews Genetics [November, 2022] Robert C. Spitale & Danny Incarnato https://doi.org/10.1038/s41576-022-00546-w

SHAPE-guided RNA structure homology search and motif discovery

Nature Methods [March, 2022] - Supporting data Edoardo Morandi, Martijn J. van Hemert & Danny Incarnato https://doi.org/10.1038/s41467-022-29398-y

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 https://doi.org/10.1038/s41592-021-01075-w

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 https://doi.org/10.1093/nar/gkaa1255

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 https://doi.org/10.1042/BST20200670

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 https://doi.org/10.1093/nar/gkaa1053

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 https://doi.org/10.1093/nar/gkz318

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