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ASsembly and phase Transitions of Ribonucleoprotein Aggregates in neurons: from physiology to pathology.

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Publications

Proteomics analysis of FUS mutant human motoneurons reveals altered regulation of cytoskeleton and other ALS-linked proteins via 3′UTR binding

Author(s): Maria Giovanna Garone, Vincenzo Alfano, Beatrice Salvatori, Clarissa Braccia, Giovanna Peruzzi, Alessio Colantoni, Irene Bozzoni, Andrea Armirotti, Alessandro Rosa
Published in: Scientific Reports, 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-68794-6

CircVAMP3: A circRNA with a Role in Alveolar Rhabdomyosarcoma Cell Cycle Progression

Author(s): Francesca Rossi; Alvaro Centrón-Broco; Dario Dattilo; Gaia Di Timoteo; Marco Guarnacci; Alessio Colantoni; Manuel Beltran Nebot; Irene Bozzoni; Irene Bozzoni
Published in: Issue 7, 1, 2021, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes12070985

RNA-binding and prion domains: the Yin and Yang of phase separation

Author(s): Nieves Lorenzo Gotor, Alexandros Armaos, Giulia Calloni, Marc Torrent Burgas, R Martin Vabulas, Natalia Sanchez De Groot, Gian Gaetano Tartaglia
Published in: Nucleic Acids Research, 48/17, 2020, Page(s) 9491-9504, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa681

Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners

Author(s): Alessio Colantoni, Jakob Rupert, Andrea Vandelli, Gian Gaetano Tartaglia, Elsa Zacco
Published in: Biochemical Society Transactions, 48/4, 2020, Page(s) 1529-1543, ISSN 0300-5127
Publisher: Portland Press, Ltd.
DOI: 10.1042/bst20191059

Homage to Chris Dobson

Author(s): Jean Baum, Fabrizio Chiti, Alfonso De Simone, Tuomas P. J. Knowles, Janet R. Kumita, Sheena E. Radford, Carol V. Robinson, Xavier Salvatella, Karen Valelli, Michele Vendruscolo, Annalisa Pastore, Gian Gaetano Tartaglia
Published in: Frontiers in Molecular Biosciences, 6, 2019, ISSN 2296-889X
Publisher: Frontier in Molecular Biosciences
DOI: 10.3389/fmolb.2019.00137

Prediction of gene expression time series and structural analysis of gene regulatory networks using recurrent neural networks

Author(s): Monti, Michele; Fiorentino, Jonathan; Milanetti, Edoardo; Gosti, Giorgio; Tartaglia, Gian Gaetano
Published in: Entropy, 1, 2022, ISSN 1099-4300
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e24020141

Design and Functional Validation of a Mutant Variant of the LncRNA HOTAIR to Counteract Snail Function in Epithelial-to-Mesenchymal Transition

Author(s): Cecilia Battistelli, Sabrina Garbo, Veronica Riccioni, Claudia Montaldo, Laura Santangelo, Andrea Vandelli, Raffaele Strippoli, Gian Gaetano Tartaglia, Marco Tripodi, Carla Cicchini
Published in: Cancer Research, 2021, ISSN 2254-6081
Publisher: Cancer Research
DOI: 10.1158/0008-5472.can-20-1764

Aggregation is a Context-Dependent Constraint on Protein Evolution.

Author(s): Michele Monti; Alexandros Armaos; Marco Fantini; Annalisa Pastore; Gian Gaetano Tartaglia
Published in: Frontiers in Molecular Biosciences, 4, 2021, ISSN 2296-889X
Publisher: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2021.678115

SMaRT lncRNA controls translation of a G‐quadruplex‐containing mRNA antagonizing the DHX36 helicase

Author(s): Julie Martone, Davide Mariani, Tiziana Santini, Adriano Setti, Sama Shamloo, Alessio Colantoni, Francesca Capparelli, Alessandro Paiardini, Dacia Dimartino, Mariangela Morlando, Irene Bozzoni
Published in: EMBO reports, 21/6, 2020, ISSN 1469-221X
Publisher: Nature Publishing Group
DOI: 10.15252/embr.201949942

In silico, in vitro, and in vivo Approaches to Identify Molecular Players in Fragile X Tremor and Ataxia Syndrome

Author(s): Saif N. Haify, Teresa Botta-Orfila, Renate K. Hukema, Gian Gaetano Tartaglia
Published in: Frontiers in Molecular Biosciences, 7, 2020, ISSN 2296-889X
Publisher: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2020.00031

FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention

Author(s): Jack Humphrey, Nicol Birsa, Carmelo Milioto, Martha McLaughlin, Agnieszka M Ule, David Robaldo, Andrea B Eberle, Rahel Kräuchi, Matthew Bentham, Anna-Leigh Brown, Seth Jarvis, Cristian Bodo, Maria G Garone, Anny Devoy, Gianni Soraru, Alessandro Rosa, Irene Bozzoni, Elizabeth M C Fisher, Oliver Mühlemann, Giampietro Schiavo, Marc-David Ruepp, Adrian M Isaacs, Vincent Plagnol, Pietro Fratta
Published in: Nucleic Acids Research, 48/12, 2020, Page(s) 6889-6905, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa410

RNA‐protein interactions: Central players in coordination of regulatory networks

Author(s): Alexandros Armaos, Elsa Zacco, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Published in: BioEssays, 43/2, 2021, Page(s) 2000118, ISSN 0265-9247
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/bies.202000118

Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes

Author(s): Claudia Cava, Alexandros Armaos, Benjamin Lang, Gian Gaetano Tartaglia, Isabella Castiglioni
Published in: Scientific Reports, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-04664-z

Long non-coding RNA-polycomb intimate rendezvous

Author(s): Andrea Cerase, Gian Gaetano Tartaglia
Published in: Open Biology, 10/9, 2020, Page(s) 200126, ISSN 2046-2441
Publisher: Royal Society Publishing
DOI: 10.1098/rsob.200126

Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments

Author(s): Michele Monti, Giulia Guiducci, Alessio Paone, Serena Rinaldo, Giorgio Giardina, Francesca Romana Liberati, Francesca Cutruzzolá, Gian Gaetano Tartaglia
Published in: Computational and Structural Biotechnology Journal, 19, 2021, Page(s) 3034-3041, ISSN 2001-0370
Publisher: Computational and Structural Biotechnology Journal
DOI: 10.1016/j.csbj.2021.05.019

Circular RNAs in cell differentiation and development

Author(s): Gaia Di Timoteo; Francesca Rossi; Irene Bozzoni; Irene Bozzoni
Published in: The Company of Biologists Ltd., 1, 2020, ISSN 0021-9533
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/dev.182725

A Computational Approach to Investigate TDP-43 RNA-Recognition Motif 2 C-Terminal Fragments Aggregation in Amyotrophic Lateral Sclerosis

Author(s): Greta Grassmann; Mattia Miotto; Lorenzo Di Rienzo; Federico Salaris; Beatrice Silvestri; Elsa Zacco; Alessandro Rosa; Gian Gaetano Tartaglia; Giancarlo Ruocco; Edoardo Milanetti
Published in: Biomolecules, 1, 2021, ISSN 2218-273X
Publisher: Multidisciplinary Digital Publishing Institute
DOI: 10.3390/biom11121905

The Interplay Between Disordered Regions in RNAs and Proteins Modulates Interactions Within Stress Granules and Processing Bodies

Author(s): Andrea Vandelli, Fernando Cid Samper, Marc Torrent Burgas, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Published in: Journal of Molecular Biology, 2021, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2021.167159

cat RAPID omics v2.0 : going deeper and wider in the prediction of protein–RNA interactions

Author(s): Alexandros Armaos, Alessio Colantoni, Gabriele Proietti, Jakob Rupert, Gian Gaetano Tartaglia
Published in: Nucleic Acids Research, 49/W1, 2021, Page(s) W72-W79, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab393

Thermometer: a webserver to predict protein thermal stability

Author(s): Mattia Miotto, Alexandros Armaos, Lorenzo Di Rienzo, Giancarlo Ruocco, Edoardo Milanetti, Gian Gaetano Tartaglia
Published in: Bioinformatics, 2022, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab868

The protective role of m1A during stress-induced granulation

Author(s): Marion Alriquet, Giulia Calloni, Adrían Martínez-Limón, Riccardo Delli Ponti, Gerd Hanspach, Martin Hengesbach, Gian G. Tartaglia, R. Martin Vabulas
Published in: Journal of Molecular Cell Biology, 12/11, 2020, Page(s) 870-880, ISSN 1674-2788
Publisher: Oxford University Press
DOI: 10.1093/jmcb/mjaa023

New lessons on TDP-43 from old N. furzeri killifish

Author(s): Alexandra Louka, Sara Bagnoli, Jakob Rupert, Benjamin Esapa, Gian Gaetano Tartaglia, Alessandro Cellerino, Annalisa Pastore, Eva Terzibasi Tozzini
Published in: Aging Cell, 2021, ISSN 1474-9726
Publisher: John Wiley & Sons
DOI: 10.1111/acel.13517

HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade

Author(s): Jessica Rea, Valentina Menci, Paolo Tollis, Tiziana Santini, Alexandros Armaos, Maria Giovanna Garone, Federica Iberite, Andrea Cipriano, Gian Gaetano Tartaglia, Alessandro Rosa, Monica Ballarino, Pietro Laneve, Elisa Caffarelli
Published in: Cell Death & Disease, 11/7, 2020, ISSN 2041-4889
Publisher: Nature Publishing Group
DOI: 10.1038/s41419-020-02738-w

Trans‐generational epigenetic regulation associated with the amelioration of Duchenne Muscular Dystrophy

Author(s): Julie Martone, Michela Lisi, Francesco Castagnetti, Alessandro Rosa, Valerio Di Carlo, Enrique Blanco, Adriano Setti, Davide Mariani, Alessio Colantoni, Tiziana Santini, Lucia Perone, Luciano Di Croce, Irene Bozzoni
Published in: EMBO Molecular Medicine, 12/8, 2020, ISSN 1757-4676
Publisher: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202012063

Structural analysis of SARS-CoV-2 genome and predictions of the human interactome

Author(s): Andrea Vandelli, Michele Monti, Edoardo Milanetti, Alexandros Armaos, Jakob Rupert, Elsa Zacco, Elias Bechara, Riccardo Delli Ponti, Gian Gaetano Tartaglia
Published in: Nucleic Acids Research, 48/20, 2020, Page(s) 11270-11283, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa864