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About us
The RNA Systems Biology Lab
IIT
Gian
Stanford 2%
Academia Europaea
Previous Affiliations
ICREA
Sapienza
CRG
IRB
University of Cambridge
University of Zurich
Our articles
Biomedical publications
Citations metrics
General information
Protein solubility
Protein-RNA interactions
Our research in a nutshell (Italian)
Our recent papers (layman description)
Recent Press Releases
Our EMBO workshop on iCLIP (E. Bechara; 2025)
A new ERC PoC for ALS diagnostics (2025)
RAI interview on ALS (Italian; 2025)
ROBOT: A new tool to predict phase separation (2025)
On the Nobel prize for Medicine (2024, Italian)
Our great researcher L. Broglia (2024)
Our EMBO workshop on iCLIP (E. Bechara; 2024)
Identifying G quadruplex binding proteins - Nat Comm 2024
Our Pathfinder on Bruillouin Microscopy and Phase Transitions - April 2023
Aptamers against ALS - September 2022
Predire Alzheimer usando il machine learning - June 2022
Alzheimer's: a machine learning approach to identify genetic predisposition - June 2022
Unico compito di un virus è quello di riprodursi - January 2021
How does the replication of SARS-Cov2 work - November 2020
From ERC, ASTRA: a new study on neurodegenerative diseases - November 2019
Synergy Grant for the First all-Italian Project on the Diagnosis and Control of Neurodegenerative Diseases - November 2019
Messenger RNA Acts as a Chaperone to Protect Cells - August 2019
New Acquisitions on the Mechanism of Genetic Inheritance Associated with the X Chromosome - May 2019
Neurodegenerative diseases: Discovered the Role of RNAs in Toxic Protein Aggregates - February 2019
RNAs play key role in protein aggregation and in neurodegenerative disease - January 2019
Regulation of alpha-synuclein and link to Parkinson's disease - December 2017
Our section of Frontiers in Molecular Biosciences - August 2017
Special PhD award to Davide Cirillo, July 2017
Our H2020 grant on personalised medicine - La Vanguardia - June 2017
The Global Score algorithm [Italian] - Le Scienze April 2017
Our methods to predict protein interactions with non-coding RNAs - La Vanguardia - February 2017
Size matters and structure too - CRG News, February 2017
'Blobs' inside cells could be key to neurodegenerative diseases - CRG News, June 2016
How to know transcription factors by the company they keep - Atlas of Science, December 2015
By the company they keep - Life@CRG, October 2015
Cover of Molecular Biosystems - July 2014
Human cells, proteins and RNA - La Xarxa, April 2014
Collaboration with Hospitals - CRG News, December 2014
catRAPID, a guide to understanding the role of non-coding RNA - Elipse, July 2011
List of relevant publications
Recent Preprints
- Delli Ponti R, Vandelli A, Broglia L, Tartaglia GG Integrating RNA Structure and Protein Interactions to Uncover the Mechanisms of Viral and Cellular IRES Function
- BioRxiv 2025. Abstract PDF
- Milordini G, Zacco E, Armaos A, Di Palma F, Masi M, Gilodi M, Rupert J, Broglia L, Varignani G, Oneto M, Scotto M, Marotta R, Girotto S, Cavalli A, Tartaglia GG Computationally-designed aptamers targeting RAD51-BRCA2 interaction inhibit RAD51 nuclear recruitment
- BioRxiv 2025. Abstract PDF
- Zacco E, Gilodi M, Armaos A, Waldron FM, Rupert J, Shneider N, Gregory J, Tartaglia GG Computationally Designed RNA Aptamers Enable Selective Detection of FUS Pathology in ALS
- BioRxiv 2025. Abstract PDF
- Fiorentino J, Armaos A, Montrone C, Colantoni A, Tartaglia GG scRAPID-web: a web server for predicting protein-RNA interactions from single-cell transcriptomics
- BioRxiv 2025. Abstract PDF
- Dasti A, Antonelli M, Arnal M, Armaos A, Bonnin S, Graf T, Paronetto M, Tian T, Bechara E*, Tartaglia GG*. The RNA-Binding Protein SAM68 regulates cardiomyocyte differentiation by enhancing Gata4 translation
- bioRxiv. 2022. Abstract PDF
Methodology
- Fiorentino J#, Monti M#, Miltiadis-Vrachnos M, Bini G, Cutrufo T, Sanchez de Groot N, Armaos A, Tartaglia GG. catGRANULE 2.0: accurate predictions of liquid-liquid phase separating proteins at single amino acid resolution
- Genome Biology 2024. Abstract
- Fiorentino J , Armaos A, Colantoni A, Tartaglia GG, Prediction of protein-RNA interactions from single-cell transcriptomic data
- Nucleic Acids Research 2023. Abstract PDF
- Schwarzl T#, Sahadevan S# , Lang B#, Miladi M, Backofen R, Huber W, Hentze MW*, Tartaglia GG* Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq
- Nucleic Acids Research 2023. Abstract PDF
- Armaos A #, Serra F# , Nunez-Carpintero I, Seo JI, Baca SC, Gustincich S, Valencia A, Freedman ML, Cirillo D*, Giambartolomei C *, Tartaglia GG * The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer
- Nature Communications 2023. Abstract PDF
- Delli Ponti R, Broglia L*, Vandelli A, Armaos A, Torrent M, Sanchez N, Tartaglia GG. A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in non-coding RNAs
- IUBMB Life 2022. Abstract PDF
- Zacco E#, Kantelberg O#, Milanetti E, Armaos A, Panei FP, Gregory J, Jeacock K, Clarke DJ, Chandran S, Ruocco G, Gustincich S, Horrocks MH, Pastore A, Tartaglia GG. Probing TDP-43 condensation using an in silico designed aptamer
- Nature Communications. 2022. Abstract PDF
- Miotto M, Armaos A, Di Rienzo L, Ruocco G, Milanetti M, Tartaglia GG. Thermometer: a webserver to predict protein thermal stability
- Bioinformatics. 2022. Abstract PDF
- Monti M, Fiorentino J, Milanetti M, Gosti G, Tartaglia GG. Prediction of gene expression time series and structural analysis of gene regulatory networks using recurrent neural networks
- Entropy. 2022. Abstract PDF
- Armaos A#, Colantoni A.#, Prioetti G., Rupert J,, Tartaglia GG. catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions
- Nucleic Acids Res. 2021. Abstract PDF
- Delli Ponti R, Armaos A, Vandelli A, Tartaglia GG. CROSSalive: a web server for predicting the in vivo structure of RNA molecules
- Bioinformatics. 2019. Abstract PDF
- Delli Ponti R, Armaos A, Marti S, Tartaglia GG. A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs
- Frontiers Mol. Biosc. 2018. Abstract PDF
- Lang B, Armaos A, Tartaglia GG. RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data
- Nucleic Acids Res. 2018. Abstract PDF
- Armaos A, Cirillo D, Tartaglia GG. omiXcore: a web server for prediction of protein interactions with large RNA
- Bioinformatics. 2017. Abstract PDF
- Cirillo D, Blanco M, Armaos A, Buness A, Avner P, Guttman M, Cerase A, Tartaglia GG. Quantitative predictions of protein interactions with long noncoding RNAs
- Nat Methods. 2017. Abstract PDF
- Delli Ponti R, Marti S, Armaos A, Tartaglia GG. A high-throughput approach to profile RNA structure
- Nucleic Acids Res. 2017. Abstract PDF
- Bolognesi B, Lorenzo Gotor N, Dhar R, Cirillo D, Baldrighi M, Tartaglia GG*, Lehner B*. A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression
- Cell Reports. 2016. Abstract PDF
- Klus P, Delli Ponti R, Livi C, Tartaglia GG. Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets
- BMC Genomics. 2015. Abstract PDF
- Livi CM, Klus P, Delli Ponti R, Tartaglia GG. catRAPID signature: identification of ribonucleoproteins and RNA-binding regions
- Bioinformatics. 2015. Abstract PDF
- Cirillo D, Botta-Orfila T, Tartaglia GG. By the company they keep: interaction networks define the binding ability of transcription factors
- Nucleic Acids Res. 2015. Abstract PDF
- Agostini F, Cirillo D, Delli Ponti R, Tartaglia GG. SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences
- BMC Genomics. 2014. Abstract PDF
- Agostini F, Cirillo D, Livi CM, Delli Ponti R, Tartaglia GG. ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in E. coli.
- Bioinformatics. 2014. Abstract PDF
- Klus P, Bolognesi B, Agostini F, Marchese D, Zanzoni A, Tartaglia GG. The cleverSuite Approach for Protein Characterization: Predictions of Structural Properties, Solubility, Chaperone Requirements and RNA-Binding Abilities.
- Bioinformatics. 2014; Abstract
PDF
- Agostini F, Zanzoni A, Klus P, Marchese M, Cirillo D, Tartaglia GG. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions.
- Bioinformatics. 2013; Abstract PDF
- Agostini F, Vendruscolo M, Tartaglia GG. Sequence-based prediction of protein solubility. [CCSOL]
- J Mol Biol. 2012;421(2-3):237-41. Abstract PDF
- Bellucci M, Agostini F, Masin M, Tartaglia GG. Predicting protein associations with long noncoding RNAs.
- Nat Methods. 2011; 8(6):444-5. Abstract PDF Supplementary
Applications
- Cipriano A#, Colantoni A#, Gomes D, Moqri M, Parker A, Caldwell M, Briganti F, Fiorentino J, Roncarolo MG, Baldini A, Weinacht KG, Tartaglia GG *, Sebastiano V *. Multi-omics analysis reveals a crucial role for Retinoic Acid in promoting epigenetic and transcriptional competence of an in vitro model of human Pharyngeal Endoderm
- Genome Biology 2024. Abstract PDF
- Luige J#, Armaos A S#, Tartaglia GG*, Orom UA* Identification and prediction of G-quadruplex RNA-binding proteins with roles in transcription and phase separation
- Nucleic Acids Research 2024. Abstract PDF
- Rupert J, Monti M, Zacco E, Tartaglia GG. ARNA sequestration driven by amyloid formation: the alpha synuclein case
- Nucleic Acids Reseearch 2023. Abstract PDF
- Giambruno R #, Zacco E #, Ugolini C, Vandelli A, Mulroney L, D'Onghia M, Criscuolo E, Castelli M, Clementi N, Clementi M, Mancini N, Bonaldi T, Gustincich S, Leonardi T, Tartaglia GG *, Nicassio F *. Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome
- Mol Ther Nucleic Acids 2023 Abstract PDF
- Vandelli A, Vocino G, Tartaglia GG. Phase Separation Drives SARS-CoV-2 Replication: A Hypothesis
- Front Mol Biosci. 2022. Abstract PDF
- Arnal M, Bini G, Fernandez D, Samaras E, Kassis M, Aisopos F, Rambla De Argila J, Paliouras G, Garrard P, Giambartolomei C, Tartaglia GG. Machine learning methods applied to genotyping data capture interactions between single nucleotide variants in late onset Alzheimer’s disease
- Alzheimers Dement (Amst). 2022. Abstract PDF
- Vandelli A, Cid-Samper F, Burgas M. T., Sanchez de Groot N., Tartaglia G.G. The Interplay Between DisorderedRegions in RNAs and ProteinsModulates Interactions Within StressGranules and Processing Bodies
- JMB. 2021. Abstract PDF
- Avolio R., Bechara E., Tartaglia GG The quest for long non-coding RNAs involved in aging
- Nature Aging, 2021, Abstract
- Monti M, Armaos A., Fantini M., Pastore A., Tartaglia GG. Aggregation is a context-dependent constraint on protein evolution
- Front. Mol. Biosci. 2021. Abstract
- Monti M, Guiducci G., Paone A., Rinaldo S., Giardina G., Liberati R., Cutruzzola F., Tartaglia GG. Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments
- CSBJ. 2021. Abstract PDF
- Armaos A, Zacco E, Sanchez de Groot N., Tartaglia GG RNA-protein interactions: Central players in coordinationof regulatory networks
- BioEssays 2020, bies. 2020. PDF
- Vandelli A, Monti M, Milanetti E, Armaos A, Rupert J, Zacco E, Bechara E, Delli Ponti R, Tartaglia GG Structural analysis of SARS-CoV-2 and prediction of the human interactome
- Nucleic Acid Res. 2020, PDF. bioarXiv. 2020. PDF
- Lorenzo Gotor N, Armaos A, Calloni G., Burgas M. T., Vabulas M.R., Sanchez de Groot N., Tartaglia G.G. RNA-Binding and Prion Domains: The Yin and Yang of Phase Separation
- Nucleic Acid Res. 2020. PDF
- Alriquet M., Calloni G., Martínez-Limón A., Delli Ponti R, Hanspach G., Hengesbach M., Tartaglia GG, Vabulas M.R. The Protective Role of m1A During Stress-Induced Granulation
- J Mol Cell Biol. 2020. Abstract
- Sanchez de Groot N*, Armaos A*, Grana-Montes R, Alriquet M, Calloni G, Vabulas M, Tartaglia GG. RNA structure drives interaction with proteins
- Nature Communications. 2019. Abstract PDF
- Cerase A*, Armaos A*, Neumayer C, Avner P, Guttman M, Tartaglia GG. Phase separation drives X-chromosome inactivation: a hypothesis
- Nature Structural & Molecular Biology. 2019. Abstract PDF
- Zacco E, Grana Montes R, Martin S, Sanchez de Groot N, Alfano C, Tartaglia GG, Pastore A. RNA as a key factor in driving or preventing self-assembly of the TAR DNA-binding protein 43
- JMB 2019. Abstract PDF
- Cid-Samper F, Gelabert Baldrich M, Lang B, Lorenzo Gotor N, Delli Ponti R, Severijnen L, Bolognesi B, Gelpi E, Hukema T, Botta-Orfila T, Tartaglia GG. An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome
- Cell Reports. 2018. Abstract PDF
- Ribeiro D, Zanzoni A, Cipriano A, Delli Ponti R, Spinelli L, Ballarino M, Bozzoni I, Tartaglia GG, Brun C. Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs
- Nucleic Acids Res. 2017. Abstract PDF
- Marchese D, Botta Orfila T, Cirillo D, Rodriguez JA, Livi C, Fernández-Santiago R, Ezquerra M, Martí M, Bechara E, Tartaglia GG. Discovering the 3′ UTR-mediated regulation of alpha-synuclein
- Nucleic Acids Res. 2017. Abstract PDF
- Botta Orfila T, Bodi L, Marti S, Kovacs G, Grau-Rivera O, Lozano M, Sánchez-Valle R, Muñoz E, Valldeoriola F, Pagonabarraga J, Tartaglia GG, Milà. Neuronal intranuclear (hyaline) inclusion disease and fragile X-associated tremor/ataxia syndrome: a morphological and molecular dilemma.
- Brain 2017. Abstract PDF
- Lobanov MY, Klus P, Sokolovsky IV, Tartaglia GG, Galzitskaya OV. Non-random distribution of homo-repeats: links with biological functions and human diseases.
- Scientifc Reports 2016. Abstract PDF
- Klus P, Cirillo D, Botta Orfila T, Tartaglia GG. Neurodegeneration and Cancer: Where the Disorder Prevails.
- Scientifc Reports 2015. Abstract PDF
- Cirillo D, Marchese D, Agostini F, Livi CM, Botta-Orfila MT, Tartaglia GG. Constitutive patterns of gene expression regulated by RNA-binding proteins.
- Genome Biology. 2014. Abstract PDF
- Zanzoni A, Marchese D, Agostini F, Bolognesi B, Cirillo D, Botta-Orfila MT, Livi CM Rodriguez-Mulero S, Tartaglia GG. Principles of Self-Organization in Biological Pathways: A Hypothesis on the Autogenous Association of Alpha-Synuclein.
- Nucleic Acids Res. 2013. Abstract PDF
- Cirillo D, Agostini F, Klus P, Marchese D, Rodriguez S, Bolognesi B, Tartaglia GG. Neurodegenerative Diseases: Quantitative Predictions of Protein-RNA Interactions.
- RNA 2013. Abstract PDF
- Agostini F, Cirillo D, Bolognesi B, Tartaglia GG. X-inactivation: quantitative predictions of protein interactions in the Xist network. [catRAPID]
- Nucleic Acids Res. 2013. Abstract PDF
- Iglesias-Platas I, Martin-Trujillo A, Cirillo D, Court F, Guillaumet-Adkins A, Camprubi C, Bourc'his D, Hata K, Feil R, Tartaglia GG, Arnaud P, Monk D. Characterization of novel paternal ncRNAs at the Plagl1 locus, including Hymai, predicted to interact with regulators of active chromatin. [catRAPID]
- PLoS One. 2012;7(6):e38907. Abstract PDF
Reviews / general information
- Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding
- Chemical Reviews 2024 PDF
- Cerase A., Calabrese JM, Tartaglia GG. Phase separation drives X-chromosome inactivation.
- Nat Struct Mol Biol. 2022 PDF
- Haify SN, Botta-Orfila T, Hukema RK, Tartaglia GG. In silico, in vitro, and in vivo Approaches to Identify Molecular Players in Fragile X Tremor and Ataxia Syndrome.
- Front Mol Biosci. 2020 PDF
- Cerase A., Tartaglia GG. Long non-coding RNA-polycomb intimate rendezvous.
- Open Biol. 2020 PDF
- Colantoni A, Rupert J, Vandelli A, Tartaglia GG, Zacco E. Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners.
- Biochem Soc Trans. 2020 PDF
- Dast A, Cid-Samper F, Bechara E, Tartaglia GG. RNA-centric approaches to study RNA-protein interactions in vitro and in silico.
- Methods. 2020 PDF
- Marchese D, Sanchez de Groot N, Lorenzo Gotor N, Livi CM, Tartaglia GG. Advances in the characterization of RNA-binding proteins.
- WIREs. 2016. Abstract PDF
- Tartaglia GG. The Grand Challenge of Characterizing Ribonucleoprotein Networks.
- Front. Mol. Biosci. 2016. Abstract PDF
- Botta-Orfila T, Tartaglia GG, Michalon A. Molecular Pathophysiology of Fragile X-Associated Tremor/Ataxia Syndrome and Perspectives for Drug Development.
- Cerebellum. 2016. Abstract PDF
- Cirillo D, Livi CM, Agostini F, Tartaglia GG. Discovery of Protein-RNA Networks.
- Molecular BioSystems. 2014. Abstract PDF
- Johnson R, Noble W, Tartaglia GG, Buckley NJ. Neurodegeneration as an RNA disorder.
- Prog Neurobiol. 2012 Dec;99(3):293-315. Abstract PDF
- Cirillo D, Agostini F, Tartaglia GG. Predictions of protein-RNA interactions.
- WIREs Comput Mol Sci 2012. Abstract PDF
Book Chapters
- Marchese D, Livi CM, Tartaglia GG. A Computational Approach for the Discovery of Protein-RNA Networks.
- Methods Mol Biol. 2016;1358:29-39. doi: 10.1007/978-1-4939-3067-8_2. Abstract PDF
- Bolognesi B, Tartaglia GG. Physicochemical principles of protein aggregation.
- Prog Mol Biol Transl Sci 2013. Abstract PDF