MONICA BALLARINO
Associate Professor
Deputy Coordinator of the PhD in Genetics and Molecular Biology
Sapienza University, Facoltà di SMFN
Principal Investigator
Research Laboratory “ RNA Lab – Decoding Non-Coding RNAs in Development and Disease”
Sapienza University, Dept. of Biology and Biotechnologies "Charles Darwin" Rome (Italy)
Discipline: Genetics and Molecular Biology
Investigation of the biogenesis and regulatory logic of noncoding RNAs, with a focus on how these mechanisms control cell lineage specification, cell fate transitions, and morphogenesis. Development and application of innovative cellular and molecular approaches - including transcriptomics, CRISPR-Cas9 - based perturbations, and advanced imaging - to dissect stem cell behaviour, proliferation, and differentiation. Experimental systems range from in vitro cell models (primary cultures, iPSC-derived cardiomyocytes, myocytes, motoneurons, and neuromuscular organoids) to ex vivo tissues and in vivo animal models, enabling multi-scale analyses of development and neuromuscular biology.
PROFESSIONAL EXPERIENCE
2024 Habilitation Full Professor, 05/E2 - MOLECULAR BIOLOGY
ASN 2023/2025
2019 - to date Associate Professor
Sapienza University, Dept. of Biology and Biotechnologies "Charles Darwin", Rome (Italy)
Academic Courses:
MOLECULAR BIOLOGY (CFU:6) - Physics
MOLECULAR BIOLOGY AND GENOMICS (CFU:6) - Bioinformatics
GENOMICA (CFU:3) - Scienze Biologiche
2016 - 2019 Assistant Professor (Researcher RTDB)
Sapienza University, Dept. of Biology and Biotechnologies "Charles Darwin", Rome (Italy)
▪Research Project: “Non-coding RNAs in muscular and neuromuscular systems development and diseases”
2012 - 2015 Researcher RTDA
Sapienza University, Dept. of Biology and Biotechnologies "Charles Darwin", Rome (Italy)
▪Research Project: “Long non-coding RNAs in cellular differentiation and disease”
2010 Visiting Scientist
Institut de Biologie de l'ENS, Paris, France. Host: Prof. Olivier Bensaude.
▪Research Project: “Single cell detection of TAF15 and mRNAs by Fluorescence In Situ Hybridization in osteosarcoma U2OS cells”
2009 – 2012 Research associate (Chercheur)
Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, (France). Host: Prof. Laszlo Tora.
▪Research Project: “Normal and oncogenic functions of the RNA binding protein, TAF15 in human”
2005 - 2009 Post-doctoral Fellow
Sapienza University of Rome (Italy), Dept. of Genetics and Molecular Biology. Host: Prof. Irene Bozzoni.
▪Research Project “Analysis of microRNA biosynthesis and function during myeloid cell differentiation”
EDUCATION AND TRAINING
2002-2005 PhD Programme
Sapienza University of Rome, School of Molecular Medicine and Biology
▪Genetics and Molecular Biology, Thesis: “The Factory of small non-coding RNAs”
2003 Biologist state assesment examination
Università degli Studi della Tuscia, Viterbo, Session2/ Autumn 2002 (150/150)
1999-2001 Master’s degree
Sapienza University of Rome, Centro Acidi Nucleici-CNR
▪Graduated with honors in Biological Sciences (Molecular Biology)
ACTIVITIES
Awards
2025 Women at the Top leadership certification, GSoM POLIMI - Politecnico di Milano
2024 Best poster IIM Meeting 2024, Assisi. Marco Simula (*), PhD XXXIX cycle
2024 Best poster SIBBM2024, Trento. Giulia Buonaiuto (*), PhD XXXVI cycle
2022 FSE – Regione Lazio Contributo premiale per ricercatori
2020 Best PhD Thesis in Genetics and Molecular Biology. Fabio Desideri (*), PhD XXXII cycle
2019 Recognition of Excellent university teaching, Sapienza University of Rome
2015-19 ANVUR-VQR Recognition of 3/4 “Excellent-extremely relevant” 1/4 “Excellent” publications
2017 FFABR-ANVUR (GU n.297 21-12-2016 Sup Ord n.57), MIUR
2016 Poster Prize XIX CONGRESSO NAZIONALE SIGU, Torino Rossella Tita (*), PhD XXIX cycle
2015 Best Poster Telethon XVIII Scientific convention, Riva del Garda
2010 Long-Term Fellowship Espoirs de la Recherche “FRM - Fondation pour la Recherche Medicale”
2009 Best Poster SIROCCO Annual meeting, UK
2005 Premio di Studio Fondazione Telethon
2004 Long-Term fellowship by Istituto Pasteur-Fondazione Cenci-Bolognetti
2003 Short-Term fellowship by Istituto Pasteur-Fondazione Cenci-Bolognetti
2002 Long-Term fellowship by Consiglio Nazionale delle Ricerche (CNR), Bando n. 113.50 BO.2
(*) PhD advisor, Monica Ballarino
Appointments and Memberships
Since 2025 Departmental Representative for Dual-Use Research, Dept. BBCD, Sapienza University
Since 2025 Member of Gender Equality Plan Commission, Dept. BBCD, Sapienza University
Since 2024 Departmental Representative for institutional relations Dept. BBCD–IBPM/CNR
Since 2024 Responsible Mobility Area (RAM) Erasmus, Facoltà di Farmacia e Medicina
Since 2023 Deputy Coordinator of the PhD in Genetics and Molecular Biology, Sapienza University
Since 2022 Member of CIVIS-EU University. Experimental Models in Molecular Biomedicine
Since 2021 Member of Giunta (Council) of the Dept. BBCD, Sapienza
Since 2021 Departmental Representative VQR (2015-2019; 2020-2024), Dept. BBCD, Sapienza
Since 2020 Member of “SPBA-Centro Ricerca e Servizi sperimentazione preclinica”, Sapienza
Since 2019 Member of Accademia Medica of Rome https://www.accademiamedicadiroma.it/soci/
Since 2018 Member of SIBBM society https://www.sibbm.org/soci
Since 2017 Member of PhD Board of the doctoral programme in Genetics and Mol. Biology, Sapienza
Since 2012 Member of the Academic Committee for bachelor’s and master’s degrees final examination, Faculty of SMFN, Sapienza
Scientific organization
2026 Co-organiser of GLASS - Gender & Leadership in Academia - Sapienza School advanced course SASS Sapienza
2025 Co-organiser PhD EMBL-Sapienza lectures “Neurobiology and Epigenetics”, Sapienza
2025 Co-organiser of GLASS - Gender & Leadership in Academia - Sapienza School advanced course SASS Sapienza
2025 Co-organiser Minisimposio Disparità di genere in accademia - SASS Sapienza
2023 Co-organiser EMBO Practical Course on Fishing for RNAs, EMBL Heidelberg, Germany
https://www.embl.org/about/info/course-and-conference-office/events/FIS23-01/#vf-tabs__section-85822261-2f19-40aa-ad0c-f263a918ea17
2023 Co-organiser PhD EMBL-Sapienza lectures “Neurobiology and Epigenetics”, Sapienza, Rome
2021 Co-organiser PhD Workshop “Cutting-edge molecular technologies: a Sapienza/EMBL joint effort to share complementary expertise”, Sapienza, Rome
2017 Co-organiser 1st EMBL-Sapienza "Chromatin and Epigenetics" PhD meeting, Sapienza, Rome
2006 Instructor for ChIP-related techniques, First ROC practical course Regina Elena Cancer Institute CRS-IRE, Rome.
Editorial activity
Associate Editor, Frontiers Molecular Bioscience
Review Editor, Frontiers in Genetics; Frontiers in Cell and Developmental Biology
Reviewer, Nature Communications (16-03872A and 19-11007-T); PLoS ONE (PONE-D-10-04987);
Mol.Cell.Biol. (MCB00840-15); Mol Cell (control n. D-09-01418; D-10-00248); FEBS (F140131); NAR (01452-X-2010); ARS (issue on "NON-CODIN RNAs AND EPIGENETICS”)
Editor of the BBCD Scientific Report, https://bbcd.bio.uniroma1.it/it
Invited presentations
2025 Non-coding RNAs in Health and Disease Workshop, Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest
2025 Consiglio Nazionale delle Ricerche - Ist. di Bioimmag. e Sistemi Biol. Complessi (IBSBC), Milan
Seminar Title: "Questioni di CHARME: dal genoma nascosto a nuove ispirazioni terapeutiche"
2025 RNA-based innovative therapies for neurological disorders, National Center for Gene Therapy and Drugs based on RNATechnology - Spoke 3, Naples
Seminar Title: “Long Noncoding RNAs as a Therapeutic Toolkit for Neuromuscular Disorders
2025 Non-coding RNAs in Health and Disease Workshop, Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest
Seminar Title: “Long non-coding RNAs (lncRNAs) in cell proliferation and differentiation”
2024 Istituti del Polo San Lorenzo, Dottorato in Biologia Cellulare e dello sviluppo e Dottorato in Genetica e Biologia Molecolare, Sapienza University of Rome
Seminar Title: “Lights from the dark matter: noncoding RNAs in neuromuscular physiology and disease'”
2023 International Winter School, Genome integrity and genome organization in physiology and Pathology, Sapienza University of Rome
Seminar Title: “Myogenesis and long non-coding RNAs: a chromatin affair”
2023 EMBO Course FISHing for RNAs: Classical to Single Molecule Approaches, EMBL Heidelberg
Seminar Title: “FISHing for Charme, a lncRNA solution to cell differentiation issue”
2021 PhD School in Genetics and Molecular Biology. Sapienza University of Rome.
Seminar Title: “Methodological issues and challenges for probing the function of long noncoding RNAs”
2021 EMBO Course “FISHing for RNAs: Classical to Single Molecule Approaches”. EMBL Heidelberg
Seminar Title: “FISHing for Charme, a long noncoding solution to cell differentiation issues”
2020 2nd CCP Phenogenomics, Conference Vestec, Prague
Seminar Title: "A comprehensive glimpse on Charme long noncoding RNA”
2019 PhD School in Biology and Molecular Medicine, Sapienza University of Rome
Seminar Title: “A noncoding solution to cell differentiation issues: the Charme example”
2018 Scuola Superiore di Studi Avanzati Sapienza - SSAS - Rome
Seminar Title: “New and improved methodologies to detect RNA/protein interactions with chromatin”,
2018 EPIGEN Final Meeting. San Servolo, Venice
Seminar Title: “Non-coding regulation of myogenic chromatin”
2018 SIBBM “When and where: temporal and spatial regulation of biological processes”, Rome
Seminar Title: “Non-coding regulation of myogenic chromatin”
2017 Unità di Terapia Intensiva Cardiologica-Ospedale S.Andrea, Rome
Seminar Title: “Long non coding RNA nella miogenesi e nelle malattie del cuore”
2016 Chromatin, Epigenome, Drug discovery, training-school meeting, Epigen. Chem. Biol, Naples
Seminar Title: “Non-coding answers to differentiation questions”
2015 Joint meeting People Marie Curie, RNA Day, Rome
Seminar Title: “LncRNPs and control of chromatin structure”
2008 Congres de la Sociètè Francaise d’Hematologie, Paris
Seminar Title: “miRNA and hematopoietic differentiation”
Grants
2025 1st ELIXIRxNextGenIT Transnational/National Open Access (TNA/NOA) “MultiOmics in MYC-dependent Medulloblastoma (MoMyc)”, Access granted
2025 Human Technopole 24-LI-PILOT Call for Access to the National Facilities. Ion Imaging in Neuro Muscular Organoids (iNEMO), Access granted
2023 Sapienza Ricerca Bandi Ateneo. EVOMAP: EVOlutive perspectives into cellular differentiation:
identification, conservation, and functional characterization of non-coding RNAs in MAmmals and Plants
RM123188F6B80CE4, PI 12K€
2022 PRIN PNRR “RNA secondary structures and their relationship with function: application to non-coding RNAs (RNA2Fun)” P2022FFEWN, Responsabile di Unità 100K€
2022 PRIN “Study Noncoding RNAs in Organoids for Muscle-Nerve development (NOMeN)”, PI 187K€
2022 PNRR-CN3 Spoke 3, “Studying how lncRNA and circRNA alteration impacts neuromuscular transmission and ALS” CUP B83C22002870006, PI and Task 2.5 leader 160.0 K€
2022 Bando Visiting Professor cat. “Towards a complete map of the non-coding RNA landscape in the Tabula Sapiens Dataset: development of novel single cell pipelines for discovering and studying new long non-coding RNAs”, PI 5.0 K€
2021 Sapienza Ricerca Bandi Ateneo “A muscle perspective into neurodegeneration: dissecting the role of lncRNAs through hiPSC-derived neuromuscular organoids” RM12117A5DE7A45B, PI 14.8K€
2020 POR-FESR Lazio 2020-T0002E0001. “Soluzione Integrata di Microscopia Brillouin Avanzata” A03752020-36389, Co-PI 149.0 K€
2019 Sapienza Ricerca Bandi Ateneo. Contribution of RNA-protein interactions to Charme lncRNA
epigenetic activities” RM11916B7A39DCE5, PI 14.0K€
2017 INFRAFRONTIER "Disease model development and systemic phenotyping" International
consortium, Czech Centre for Phenogenomics, PI 50.0K€
2017 Sapienza Ricerca Bandi Ateneo “Dissecting the role of the long non-coding RNA Charme in
cardiomyogenesis” RM11715C7C8176C1, PI 11.0K€
Other Academic Activities
Since 2025 Responsabile Dipartimentale for Dual-Use Research, Dept. BBCD, Sapienza University
Since 2024 Responsabile accademico mobilità internazionale, Facoltà di Farmacia e Medicina
Since 2021 Referent person VQR (2015-2019; 2020-2024), Dept. BBDC
Since 2021 Referent person E-learning platform, CdS Bioinformatics, Facoltà di Farmacia e Medicina
Since 2021 External reviewer for Doctoral Programmes in:
Molecular Medicine Faculty of Health Sciences, University of Eastern Finland (Dr. Flavia SCOYNI, Unlocking the potential of non-coding RNAs in regulating neurodegeneration. A glimpse into Alzheimer’s disease and ischemic stroke pathophysiology);
Medicina Traslazionale e Molecolare – DIMET, Cycle XXXIV (Dr. Rebecca VADALÀ, Epigenetic role of transposable elements in human T lymphocytes identity and plasticity).
President of the TOLC-B examining committee AA 2020-21, Facoltà di Scienze Matematiche, Fisiche e Naturali (SMFN), Sapienza
Since 2016 III Mission activities, Facoltà di SMFN, Sapienza:
JOB PLACEMENT E INCUBATORI DELLA RICERCA: Editor for Dept. BBDC Brochure https://bbcd.bio.uniroma1.it/bbcd/sites/default/files/allegati_notizie/SCIENTIFIC_REPORT_DIPBBCD_2021_0.pdf);
EDUCAZIONE E DIVULGAZIONE SCIENTIFICA: Eventi Mass media (YOUTUBE interview “La tua carriera da Biologo Molecolare”; Attività seminariale scuole primarie e secondarie (Cellule nella ricerca biomedica, Istituto Cristo Re, Roma
EDUCAZIONE E DIVULGAZIONE SCIENTIFICA: Identificazione di HSCHARME e suo ruolo nella regolazione dei cardiomiociti e nella salute del cuore", a cura di Ester Trevisan, Giornale dei Biologi (FNOB), Ott. 2025; - 34 - https://www.fnob.it/2025/10/31/online-il-numero-di-ottobre-2025-del-giornale-dei-biologi/
EDUCAZIONE E DIVULGAZIONE SCIENTIFICA: Intervista per ITALPRESS, Video News, Pillole, Salute https://www.italpress.com/cardiomiopatieidentificato-gene-finora-sconosciuto/
Since 2012 Supervisor of around 100 students during their Thesis and PhD projects, Facoltà di SMFN, Sapienza
ADDITIONAL INFORMATION
Scientific Production and Metrics
Number of total publications in peer-reviewed journals 45, Preprints 6, Articles in revision 5
source SCOPUS
Last 10-years publications in peer-reviewed journals
JIF (Journal Impact Factor 5 years); source ISI Web of Science
1.Grandioso A, Tollis P, Pellegrini FR, Falvo E, Palma A, Migliaccio F, Belvedere A, Rea J, Tisci G, Carissimo A, Bozzoni I, Trisciuoglio D, Ballarino M, Ceci P, Laneve P. The MYC-dependent lncRNA MB3 inhibits apoptosis in Group 3 Medulloblastoma by regulating the TGF-β pathway via HMGN5. Cell Death Dis. 2025 Nov 6;16(1):800. doi: 10.1038/s41419-025-08097-8.
JIF 9.8
2.Buonaiuto G, Desideri F, Setti A, Palma A, D'Angelo A, Storari G, Santini T, Laneve P, Trisciuoglio D, Ballarino M. LncRNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyogenesis via splicing regulation. Nat Commun. 2025 Aug 23;16(1):7880. doi: 10.1038/s41467-025-62754-2. PMID: 40849301; PMCID: PMC12374974.
JIF 17.2
3.Palma, A., Buonaiuto, G., Ballarino, M*, Laneve, P* Genome biology of long non-coding RNAs in humans: A virtual karyotype. Comput Struct Biotechnol J. (2025) Jan 31;27:575-584. DOI: 10.1016/j.csbj.2025.01.026. PMID: 39989619; PMCID: PMC11847481.
JIF 6.3
4.Silvestri, B., Mochi, M., Mawrie D, de Turris V, Colantoni A, Borhy B, Medici M, Anderson EN, Garone MG, 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 (2024) Nat Commun. Nov 7;15(1):9618. DOI: 10.1038/s41467-024-54004-8.
JIF 14.7
5.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 (2024) Nucleic Acids Res. Sep 9;52(16):9936-9952. DOI: 10.1093/nar/gkae590.
JIF 16.6
6.Taliani, V., Buonaiuto, G., Desideri, F., Setti, A., Santini, T., Galfrè, S., Schirone, L., Mariani, D., Frati, G., Valenti, V., Sciarretta, S., Perlas, E., Nicoletti, C., Musarò, A., Ballarino, M. The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart (2023) eLife, 12, art. No. e81360. DOI: 10.7554/elife.81360 ISSN: 2050084X
JIF 8.3
7.Buonaiuto, G., Taliani, V., Nicoletti, C., Desideri, F., Ballarino, M. Preparation of Cardiac Extracts from Embryonal Hearts to Capture RNA–protein Interactions by CLIP (2023) Bio-protocol, 13 (20), art. No. e4857. DOI: 10.21769/BioProtoc.4857 ISSN: 23318325
JIF 1.3
8.Ballarino, M., Pepe, G., Helmer-Citterich, M., Palma, A. Exploring the landscape of tools and resources for the analysis of long non-coding RNAs (2023) Computational and Structural Biotechnology Journal, 21, pp. 4706-4716. DOI: 10.1016/j.csbj.2023.09.041 ISSN: 20010370
JIF 6.3
9.Desideri, F., D’Ambra, E., Laneve, P., Ballarino, M. Advances in endogenous RNA pull-down: A straightforward dextran sulfate-based method enhancing RNA recovery (2022) Frontiers in Molecular Biosciences, 9, art. no. 1004746. DOI: 10.3389/fmolb.2022.1004746 ISSN: 2296889X* JIF 5.2
10.Carvelli, A., Setti, A., Desideri, F., Galfrè, S.G., Biscarini, S., Santini, T., Colantoni, A., Peruzzi, G., Marzi, M.J., Capauto, D., Di Angelantonio, S., Ballarino, M., Nicassio, F., Laneve, P., Bozzoni, I. A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs. (2022) EMBO Journal, 41 (13), art. no. e108918. DOI: 10.15252/embj.2021108918 ISSN: 02614189
JIF 12
11.Macino, M., Biferali, B., Cipriano, A., Ballarino, M., Mozzetta, C. Targeting the expression of long noncoding rnas in murine satellite cells from single myofibers (2021) Bio-protocol, 11 (21), art. no. e4209. DOI: 10.21769/BioProtoc.4209 ISSN: 23318325
JIF 1.3
12.Buonaiuto, G., Desideri, F., Taliani, V., Ballarino, M. Muscle Regeneration and RNA: New Perspectives for Ancient Molecules (2021) Cells, 10 (10), art. no. 2512. DOI: 10.3390/cells10102512 ISSN: 20734409
JIF 6.7
13.Cipriano, A., Macino, M., Buonaiuto, G., Santini, T., Biferali, B., Peruzzi, G., Colantoni, A., Mozzetta, C., Ballarino, M. Epigenetic regulation of wnt7b expression by the cis-acting long noncoding rna lnc-rewind in muscle stem cells. (2021) eLife, 10, art. no. e54782, pp. 1-25. DOI: 10.7554/ELIFE.54782 ISSN: 2050084X
JIF 8.3
14.Santini, T., Martone, J., Ballarino, M. Visualization of nuclear and cytoplasmic long noncoding rnas at single-cell level by rna-fish (2021) Methods in Molecular Biology, 2157, pp. 251-280. DOI: 10.1007/978-1-0716-0664-3_15 ISSN: 10643745
Book Chapter
15.Desideri, F., Cipriano, A., Petrezselyova, S., Buonaiuto, G., Santini, T., Kasparek, P., Prochazka, J., Janson, G., Paiardini, A., Calicchio, A., Colantoni, A., Sedlacek, R., Bozzoni, I., Ballarino, M. Intronic Determinants Coordinate Charme lncRNA Nuclear Activity through the Interaction with MATR3 and PTBP1 (2020) Cell Reports, 33 (12), art. no. 108548. DOI: 10.1016/j.celrep.2020.108548 ISSN: 22111247
JIF 9.9
16.Rea, J., Menci, V., Tollis, P., Santini, T., Armaos, A., Garone, M.G., Iberite, F., Cipriano, A., Tartaglia, G.G., Rosa, A., Ballarino, M., Laneve, P., Caffarelli, E. HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade. (2020) Cell Death and Disease, 11 (7), art. no. 527. DOI: 10.1038/s41419-020-02738-w ISSN: 20414889
JIF 9.2
17.Martone, J., Mariani, D., Desideri, F., Ballarino, M. Non-coding RNAs Shaping Muscle (2020) Frontiers in Cell and Developmental Biology, 7, art. no. 394. DOI: 10.3389/fcell.2019.00394 ISSN: 2296634X
JIF 5.8
18.Pagano, F., Calicchio, A., Picchio, V., Ballarino, M. The noncoding side of cardiac differentiation and regeneration (2020) Current Stem Cell Research and Therapy, 15 (8), pp. 723-738. DOI: 10.2174/1574888X15666200123120249 ISSN: 1574888X
JIF 3.3
19.Ballarino, M., Cipriano, A., Tita, R., Santini, T., Desideri, F., Morlando, M., Colantoni, A., Carrieri, C., Nicoletti, C., Musarò, A., Carroll, D.O., Bozzoni, I. Deficiency in the nuclear long noncoding RNA Charme causes myogenic defects and heart remodeling in mice. (2018) EMBO Journal, 37 (18), art. no. e99697. DOI: 10.15252/embj.20189969 ISSN: 02614189
JIF 12
20.Dimartino, D., Colantoni, A., Ballarino, M., Martone, J., Mariani, D., Danner, J., Bruckmann, A., Meister, G., Morlando, M., Bozzoni, I. The Long Non-coding RNA lnc-31 Interacts with Rock1 mRNA and Mediates Its YB-1-Dependent Translation. (2018) Cell Reports, 23 (3), pp. 733-740. DOI: 10.1016/j.celrep.2018.03.101 ISSN: 22111247
JIF 9.9
21.Cipriano, A., Ballarino, M. The ever-evolving concept of the gene: The use of RNA/Protein experimental techniques to understand genome functions. (2018) Frontiers in Molecular Biosciences, 5 (MAR), art. no. 20. DOI: 10.3389/fmolb.2018.00020 ISSN: 2296889X
JIF 5.2
22.Ribeiro, D.M., Zanzoni, A., Cipriano, A., Ponti, R.D., Spinelli, L., Ballarino, M., Bozzoni, I., Tartaglia, G.G., Brun, C. Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs. (2018) Nucleic Acids Research, 46 (2), pp. 917-928. DOI: 10.1093/nar/gkx1169 ISSN: 03051048
JIF 16.4
23.Rosa, A., Ballarino, M. Divergent lncRNAs take the lead on pluripotent cell differentiation (2016) Stem Cell Investigation, 2016 (SEP), art. no. 47. DOI: 10.21037/sci.2016.09.02 ISSN: 23069759
Commentary
24.Ballarino, M., Morlando, M., Fatica, A., Bozzoni, I. Non-coding RNAs in muscle differentiation and musculoskeletal disease (2016) Journal of Clinical Investigation, 126 (6), pp. 2021-2030. DOI: 10.1172/JCI84419 ISSN: 00219738 3
JIF 16.7
25.Rosa, A., Ballarino, M. Long Noncoding RNA Regulation of Pluripotency (2016) Stem Cells International, 2016, art. no. 1797692. DOI: 10.1155/2016/1797692 ISSN: 16879678
JIF 4.9
26.Morlando, M., Ballarino, M., Fatica, A. Long non-coding RNAs: New players in hematopoiesis and leukemia, (2015) Frontiers in Medicine, 2 (APR), art. no. 23. DOI: 10.3389/fmed.2015.00023 ISSN: 2296858X
JIF 4.2
27.Ballarino, M., Cazzella, V., D'Andrea, D., Grassi, L., Bisceglie, L., Cipriano, A., Santini, T., Pinnarò, C., Morlando, M., Tramontano, A., Bozzoni, I. Novel long noncoding RNAs (lncRNAs) in Myogenesis: A miR-31 overlapping lncRNA transcript controls myoblast differentiation (2015) Molecular and Cellular Biology, 35 (4), pp. 728-736. DOI: 10.1128/MCB.01394-14 ISSN: 02707306
JIF 4.4
Articles in revision
1.Protocol for the simultaneous detection of nuclear long non-coding RNAs and proteins in human iPSC-derived cardiomyocytes. STAR-PROTOCOLS-D-25-00638, under review
2.Zouhair M, Cosentino M,...Ballarino M, Musarò A “A 3D skeletal muscle system for Disease Modelling and Secretome Profiling of Duchenne Muscular Dystrophy” Skeletal Muscle ID f1975296-6b5a-435e-9a0a-571313849ccf, under review
3.Matarrese M… Ballarino M, Chiodo L, Tesei L. “Decoding RNA Triple Helices: Identification from Sequence and Secondary StructureI” https://doi.org/10.1101/2025.10.01.679706; Briefings in Bioinformatics - BIB-25-1647, under review
4.Floris E, Cozzolino C, Buonaiuto G, Taliani T, Bordin A, Palma A, Picchio V , Dhori X, Nutile F, Nicoletti C, Frati G, 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" CDDIS-25-2877-T, under review
5.Palma A and Ballarino M, “Transcriptional profiling of human brain cortices identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis” HELIYON-D-24-71208 under review
Patents
Patent for industrial invention " A n t i s e n s e o l i g o n u c l e o t i d e s t a r g e t i n g o n c o g e n i c.
RNA complexes and their application in antitumor therapy", n. 102025000012682, 30/05/2025
Last 10-years publications in the Proceedings of Meetings and Courses
Abstract
"Noncoding RNA vulnerabilities and ferritin-based targeting in high-risk medulloblastoma"
P. Laneve, A. Grandioso, P. Tollis, E. Falvo, G. Tisci, A. Belvedere, M. Ballarino, and P. Ceci
Spoke 6 - National Center for Gene Therapy and Drugs based on RNA, Final Meeting.
Naples, 14-15 January 2026
1.2025 Durante D., Luchetti N., Matarrese M.A.G., Quadrini M., Di Petta F., Simula M., Chiodo L., Tesei L., Ballarino M. Bridging between in silico prediction and in vitro functional characterisation of RNA secondary structures, BBCC2025 Conference, Naples
2.2025 Matarrese M.A.G., Luchetti N., Quadrini M., F. Di Petta, Durante D, Ballarino M, Tesei L. and Chiodo L. Computational Identification and Characterization of RNA Triple Helices, 15th EBSA Congress, Rome
3.2024 Buonaiuto, Simula, Durante, Storari, Palma, Laneve, Ballarino. The lncRNA Charme, an evolutionary conserved regulator of muscle differentiation and pathology. Non-coding RNA World 2024: Exploring Mechanisms, Designing Medicines, Poster Presentation 7-9 Oct 2024, Basel, Switzerland
4.2024 Grandioso, Tollis, Pellegrini, Rea, Migliaccio, Carissimo, Trisciuoglio, Palma, Ballarino, Tisci, Falvo, Ceci, Laneve. Targeting the MYC-dependent long non-coding RNA MB3 regulates the TGF-β and OTX2 pathways in Group 3 Medulloblastoma. Non-coding RNA World 2024: Exploring Mechanisms, Designing Medicines, Oral Presentation 7-9 Oct 2024, Basel, Switzerland
5.2024 Floris, Cozzolino, Taliani, Buonaiuto, Bordin, Palma, Picchio, Nicoletti, Ballarino, Chimenti, Pagano. The role of the long non-coding RNA Charme in the phenotype and function of resident cardiac mesenchymal stromal cell" Non-coding RNA World 2024: Exploring Mechanisms, Designing Medicines, Poster Presentation 7-9 Oct 2024, Basel, Switzerland
6.2024 Matarrese, Quadrini, Buonaiuto, Ballarino, Chiodo, Tesei. Complex ncRNAs structures: the case of MALAT1 triple helix, proc. of 19th conference on Computational Intelligence methods for Bioinformatics and Biostatistics
7.2024 Buonaiuto, Simula, Durante, Storari, Palma, Laneve, Ballarino. The lncRNA Charme, an evolutionary conserved regulator of muscle differentiation and pathology. Non-coding RNA World 2024: Exploring Mechanisms, Designing Medicines, Poster Presentation 7-9 Oct 2024, Basel, Switzerland
8.2024 Grandioso, Tollis, Pellegrini, Rea, Migliaccio, Carissimo, Trisciuoglio, Palma, Ballarino, Tisci, Falvo, Ceci, Laneve. Targeting the MYC-dependent long non-coding RNA MB3 regulates the TGFb and OTX2 pathways in Group 3 Medulloblastoma. Non-coding RNA World 2024: Exploring Mechanisms, Designing Medicines, Oral Presentation 7-9 Oct 2024, Basel, Switzerland
9.2024 Floris, Cozzolino, Taliani, Buonaiuto, Bordin, Palma, Picchio, Nicoletti, Ballarino, Chimenti, Pagano. The role of the long non-coding RNA Charme in the phenotype and function of resident cardiac mesenchymal stromal cells Non-coding RNA World 2024: Exploring Mechanisms, Designing Medicines, Poster Presentation 7-9 Oct 2024, Basel, Switzerland
10.2024 Simula, Tollis, Buonaiuto, Palma, Durante, Storari, Laneve, Ballarino. Neuromuscular interplay and lncRNAs: a synaptic liason. Regulatory & Non-Coding RNAs, CSHL, NY
11.2024 Buonaiuto, Palma, Simula, Desideri, Santini, Musarò, Ballarino. From mouse to human: how RNA epigenetic influences cardiomyocytes maturation to prevent cardiac hyperplasia - The new cardiobiology, EMBO Workshop 2024, Heidelberg, Germany
12.2023 Palma, Buonaiuto, Montrone, Ballarino. Integration of transcriptomic data to dissect the role of long noncoding RNAs in amyotrophic lateral sclerosis - BITS 2023, Bari, Italy
13.2023 Buonaiuto, Palma, Simula, Desideri, Ballarino. From mouse to human: how RNA epigenetic influences cardiomyocytes maturation - SIBBM 2023 Beyond Genomics: Next Generation Molecular Biology, Bari, Italy
14.2023 Palma, Buonaiuto, Montrone, Ballarino. Integration of transcriptomic data to dissect the role of long noncoding RNAs in amyotrophic lateral sclerosis - SIBBM 2023, Beyond Genomics: Next Generation Molecular Biology, Bari, Italy
15.2023 Floris, Picchio, Cozzolino, Taliani, Buonaiuto, Nicoletti, Ballarino, Pagano, Chimenti. The role of Charme in the phenotype and function of resident cardiac mesenchymal stromal cells. ESC European Society of Cardiology congress Amsterdam - Netherlands
16.2022 Buonaiuto, Taliani, D’Onghia, Desideri, Ballarino. Non-coding RNA-mediated regulation of cardiac development: how RNA epigenetics influences cardiomyocytes maturation, EMBL symposium: The complex life of RNA, Heidelberg, Germany
17.2022 Buonaiuto, Taliani, Desideri, D’Onghia, Bozzoni, Ballarino. LncRNAs in heart development: how RNA epigenetics influences cardiomyocytes maturation to prevent cardiac hyperplasia SIBBM2022: The RNA world 3.0, Rome, Italy
18.2022 Buonaiuto, Taliani, Desideri, Ballarino. From mouse to human: how RNA epigenetic influences cardiac and neuromuscular physiology and disease, National PhD Meeting, Salerno, Italy
19.2022 Desideri, Buonaiuto, Taliani, Bozzoni, Ballarino. Noncoding RNA shaping gene expression: implications in neuromuscular physiopathology, Regulatory & Non-coding RNAs, CSHL, NY
20.2022 Desideri et al, Noncoding RNA shaping gene expression: implications in motor neurons specification, Regulatory & Non-coding RNAs, CSHL, NY
21.2021 Buonaiuto, Taliani, Desideri, Bozzoni, Nicoletti, Musarò, Ballarino. From mouse to human: the nuclear lncRNA Charme as a putative candidate for clinical application? Noncoding RNA World: From Mechanism to Therapy, ncRNA2021
22.2020 Desideri, Buonaiuto, Taliani, Santini, Kasparek, Petrezselyova, Sedlacek, Bozzoni, Ballarino. A comprehensive glimpse on Charme long noncoding RNA, CCP Phenogenomics, Conference2020 Vestec, Prague
23.2020 Ballarino. FISHing for Charme, a long noncoding solution to cell differentiation issues, EMBO Practical Course: FISHing for RNAs: Classical to Single Molecule Approaches EMBL Heidelberg, Germany
24.2020 Desideri, Cipriano, Buonaiuto, Santini, Taliani, Petrezselyova, Colantoni, Nicoletti, Musarò, Bozzoni, Ballarino. On the impact of nuclear long noncoding RNAs in myogenesis: Charme interacts with the chromatin to fine-tune muscle specification, 17th Meeting of IIM, Virtual
25.2020 Macino, Cipriano, Buonaiuto, Santini, Biferali, Peruzzi, Colantoni, Mozzetta, Ballarino. Epigenetic regulation of Wnt7b expression by the cis-acting lncRNA lncRewind in muscle stem cells, 17th Meeting of IIM, the Interuniversity Institute of Myology Virtual meeting
26.2020 Taliani, Buonaiuto, Desideri, Cipriano, Santini, Perlas, Nicoletti, Musaro, Bozzoni, Ballarino. Figuring out the role of nuclear lncRNA Charme in muscle development” 9TH international course on non-coding genome, Institut Curie, Paris
27.2019 Desideri, Buonaiuto, Taliani, Cipriano, Calicchio, Bozzoni, Kasparek, Petrezselyova, Sedlacek, Ballarino. LncRNAs fine tune myogenesis: a comprehensive glimpse on Charme, EMBO Symposium: Non-Coding Genome, Heidelberg, Germany
28.2019 Buonaiuto, Desideri, Taliani, Santini, Bozzoni, Ballarino. Deciphering the lncRNAs language in myogenesis: a comprehensive glimpse on Charme, Dip. BBCD, Sapienza, Roma, Italy
29.2019 Desideri, Buonaiuto, Taliani, Cipriano, Calicchio, Bozzoni, Kasparek, Petrezselyova, Sedlacek, Ballarino. Sequence determinants regulating Charme long noncoding RNA epigenetic activities, CCP Phenogenomics Conference2019, Vestec, Prague
30.2019 Buonaiuto, Desideri, Taliani, Santini, Colantoni, Perlas, Nicoletti, Musarò, Bozzoni, Ballarino. Deciphering the lncRNAs language in myogenesis: a comprehensive glimpse on Charme, ShareScience 2019 Sapienza, Roma, Italy
31.2018 Ballarino. Non-coding regulation of myogenic chromatin, EPIGEN Final Meeting, San Servolo, Venice, Italy
32.2018 Cipriano, Desideri, Tita, Santini, Nicoletti, Calicchio, Carrieri, Musaro, O’Carroll, Bozzoni, Ballarino. The “Charming” regulation of muscle development and heart remodelling by Charme lncRNA, - SIBBM2018, Rome, Italy
33.2018 Ballarino et al. Non-coding regulation of myogenic chromatin, SIBBM2018, Rome, Italy
34.2018 Desideri, Cipriano, Calicchio, Buonaiuto, Santini, Tita, Musarò, O’Carroll, Bozzoni, Ballarino. Charme Shapes the 3D Nuclear Structure by its Close Cooperation with Chromatin, Keystone Simposia, Canada
35.2018 Cipriano, Desideri, Tita, Santini, Nicoletti, Calicchio, Buonaiuto, Musarò, O’Carroll, Bozzoni, Ballarino. The lncRNA Charme regulates skeletal muscle differentiation and heart development, Muscle Meeting Berlin, Germany
36.2018 Cipriano, Desideri, Tita, Santini, Nicoletti, Calicchio, Musaro’, O’Carroll, Bozzoni, Ballarino. The charming regulation of muscle development and heart remodeling by Charme EMBO Symposium: Non-coding Genome, Heidelberg, Germany
37.2017 Desideri, Cipriano, Calicchio, Tita, Musarò, Bozzoni, Ballarino. Analysis of 3D chromatin conformation structures mediated by the lncRNA Charme, ABCD Meeting, Bologna, Italy
38.2017 Ballarino et al. Charme lncRNA controls the chromosomal architecture of pro-myogenic genomic loci and regulates heart remodelling, Ponzano Meeting, Ponzano Romano, Italy
39.2017 Ballarino et al. Charme lncRNA controls the chromosomal architecture of pro-myogenic genomic loci and regulates heart remodelling, EMBO Conference: Nuclear structure and Dynamics, L’IIsle sur la Sorgue, France
40.2016 Ballarino et al. Lnc-405 interacts with Purα/β to regulate myogenic differentiation, SIBBM2016, Napoli, Italy
41.2015 Ballarino et al. The lncRNA lnc-405 is a nuclear transcript which promotes myoblasts differentiation, EMBO Conference: Chromatin and Epigenetics, Heidelberg, Germany
Credits
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Vincenti S, “The position of yeast snoRNA-coding regions within host introns is essential for their biosynthesis and for efficient splicing of the host pre-mRNA” RNA 2007