Publications

This section lists peer-reviewed publications, conference papers, and associated open research outputs produced within the RNA2Fun project.

Journal Articles

• Floris E., …, Ballarino M., Chimenti I., Pagano F.
  Effect of the cardiac long non-coding RNA Charme depletion on the maturation and paracrine signaling of resident cardiac fibroblasts
  Cell Death & Disease, in press (CDD-25-1570).

• Buonaiuto G, Santini T, Ballarino M.
  Protocol for the simultaneous detection of nuclear long non-coding RNAs and proteins in human iPSC-derived cardiomyocytes
  STAR Protocols, 7(1):104351, Jan 28, 2026.
  

• Matarrese M. A. G., Quadrini M., Luchetti N., Di Petta F., Durante D., Ballarino M., Chiodo L., Tesei L.
  Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure
  Briefings in Bioinformatics, Vol. 27, Issue 1, 2026.
  

• Buonaiuto G., Taliani V., Nicoletti C., Desideri F., Ballarino M.
  LncRNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyogenesis via splicing regulation
  Nature Communications, 16, Article number: 7880, 2025.
  

• Quadrini M., Hierro Canchari P., Rosati P., Tesei L.
  TARNAS: A Software Tool for Abstracting and Translating RNA Secondary Structures
  International Journal of Molecular Sciences, 26(12), 5728, 2025.
  

• Palma A., Buonaiuto G., Ballarino M., Laneve P.
  Genome biology of long non-coding RNAs in humans: A virtual karyotype
  Computational and Structural Biotechnology Journal, 27, 575-584, 2025.
  

• Desideri F., Grazzi A., Lisi M., Setti A., Santini T., Colantoni A., Proietti G., Carvelli A., Tartaglia G. G., Ballarino M., Bozzoni I.
  CyCoNP lncRNA establishes cis and trans RNA–RNA interactions to supervise neuron physiology
  Nucleic Acids Research, 2024; 52(16):9936–9952.
  

• Silvestri B., Mochi M., Mawrie D., de Turris V., Colantoni A., Borhy B., Medici M., Anderson E. N., Garone M. G., Zammerilla C. P., Simula M., Ballarino M., Pandey U. B., Rosa A.
  HuD impairs neuromuscular junctions and induces apoptosis in human iPSC and Drosophila ALS models
  Nature Communications, 15, Article number: 9618, 2024.
  

Book Chapters

• Quadrini M., Merelli E., Tesei L.
  Abstractions for RNA Secondary Structure Analysis
  In: Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2025) Lecture Notes in Computer Science, 2026. Springer, Cham, in press.

• Loreti M., Quadrini, M. , Scoccia M., Tesei L.
  A Formal Approach to Identify Structural Patterns in RNA
  In: Computational Methods in Systems Biology (CMSB 2025) Lecture Notes in Computer Science, vol 15959, 2025. Springer, Cham.
  

• Quadrini M., Hierro Canchari P., Rosati P., Tesei L.
  TARNAS, a TrAnslator for RNA Secondary Structure Formats
  In: Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2024) Lecture Notes in Computer Science, vol 15276, 2025. Springer, Cham.
  

Preprints

• Quadrini M., Tesei L.
  PhyloRNA: a database of RNA secondary structures with associated phylogenies
  BioRxiv preprint. BioRxiv, 2026.
  

• Tesei L., Levi F., Quadrini M., Merelli E.
  Alignment of RNA Secondary Structures with Arbitrary Pseudoknots using Structural Sequences
  Research Square preprint. Research Square, 2024.
  

• Palma A., Ballarino M.
  Transcriptional profiling of human brain cortex identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis
  BioRxiv preprint. BioRxiv, 2024. https://doi.org/10.1101/2024.03.18.585481.