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

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Publikacje

The PRALINE database: Protein and Rna humAn singLe nucleotIde variaNts in condEnsates

Autorzy: Andrea Vandelli; Magdalena Arnal Segura; Michele Monti; Jonathan Fiorentino; Laura Broglia; Alessio Colantoni; Natalia Sanchez de Groot; Marc Torrent Burgas; Alexandros Armaos; Gian Gaetano Tartaglia
Opublikowane w: Bioinformatics, Numer 10, 2022, ISSN 1367-4811
Wydawca: Oxford Press
DOI: 10.1093/bioinformatics/btac847

A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs

Autorzy: Carvelli A, Setti A, Desideri F, Galfrè SG, Biscarini S, Santini T, Colantoni A, Peruzzi G, Marzi MJ, Capauto D, Di Angelantonio S, Ballarino M, Nicassio F, Laneve P, Bozzoni I.
Opublikowane w: EMBO Journal, 2022, ISSN 0261-4189
Wydawca: Nature Publishing Group
DOI: 10.15252/embj.2021108918

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

Autorzy: Maria Giovanna Garone, Vincenzo Alfano, Beatrice Salvatori, Clarissa Braccia, Giovanna Peruzzi, Alessio Colantoni, Irene Bozzoni, Andrea Armirotti, Alessandro Rosa
Opublikowane w: Scientific Reports, Numer 10/1, 2020, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-020-68794-6

CyCoNP lncRNA establishes cis and trans RNA–RNA interactions to supervise neuron physiology

Autorzy: Fabio Desideri, Alessandro Grazzi, Michela Lisi, Adriano Setti, Tiziana Santini, Alessio Colantoni, Gabriele Proietti, Andrea Carvelli, Gian Gaetano Tartaglia, Monica Ballarino, Irene Bozzoni
Opublikowane w: Nucleic Acids Research, Numer 52, 2024, Strona(/y) 9936-9952, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkae590

M6A reduction relieves FUS-associated ALS granules

Autorzy: Di Timoteo G, Giuliani A, Setti A, Biagi MC, Lisi M, Santini T, Grandioso A, Mariani D, Castagnetti F, Perego E, Zappone S, Lattante S, Sabatelli M, Rotili D, Vicidomini G, Bozzoni I.
Opublikowane w: Nature Communication, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-024-49416-5

Phase separation drives X-chromosome inactivation.

Autorzy: Cerase, A.; Calabrese, J.M. ; Tartaglia, G.G.
Opublikowane w: Nature Structural and Molecular Biology, Numer 29, 2022, Strona(/y) 183–185, ISSN 1545-9993
Wydawca: Nature Publishing Group
DOI: 10.1038/s41594-021-00697-0

Microglia reactivity entails microtubule remodeling from acentrosomal to centrosomal arrays

Autorzy: Maria Rosito 1, Caterina Sanchini 1, Giorgio Gosti 2, Manuela Moreno 3, Simone De Panfilis 4, Maria Giubettini 5, Doriana Debellis 6, Federico Catalano 6, Giovanna Peruzzi 4, Roberto Marotta 6, Alessia Indrieri 7, Elvira De Leonibus 8, Maria Egle De Stefano 9, Davide Ragozzino 10, Giancarlo Ruocco 11, Silvia Di Angelantonio 12, Francesca Bartolini 13
Opublikowane w: Cell Reports, Numer 2023 Feb 13;42(2):112104, 2023, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2023.112104

Transmembrane Helices 7 and 8 Confer Aggregation Sensitivity to the Cystic Fibrosis Transmembrane Conductance Regulator

Autorzy: Bertrand Kleizen; Eduardo de Mattos; Olga Papaioannou; Michele Monti; Gian Gaetano Tartaglia; Peter van der Sluijs; Ineke Braakman
Opublikowane w: International Journal of Molecular Sciences, Vol 24, Iss 21, p 15741 (2023), Numer 2, 2023, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms242115741

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

Autorzy: Francesca Rossi; Alvaro Centrón-Broco; Dario Dattilo; Gaia Di Timoteo; Marco Guarnacci; Alessio Colantoni; Manuel Beltran Nebot; Irene Bozzoni; Irene Bozzoni
Opublikowane w: Numer 7, Numer 1, 2021, ISSN 2073-4425
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes12070985

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

Autorzy: Nieves Lorenzo Gotor, Alexandros Armaos, Giulia Calloni, Marc Torrent Burgas, R Martin Vabulas, Natalia Sanchez De Groot, Gian Gaetano Tartaglia
Opublikowane w: Nucleic Acids Research, Numer 48/17, 2020, Strona(/y) 9491-9504, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkaa681

Intronic Determinants Coordinate Charme lncRNA Nuclear Activity through the Interaction with MATR3 and PTBP1

Autorzy: Fabio Desideri; Andrea Cipriano; Silvia Petrezsélyová; Giulia Buonaiuto; Tiziana Santini; Petr Kasparek; Jan Prochazka; Giacomo Janson; Alessandro Paiardini; Alessandro Calicchio; Alessio Colantoni; Radislav Sedlacek; Irene Bozzoni; Irene Bozzoni; Monica Ballarino
Opublikowane w: Cell Reports, Numer 4, 2020, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2020.108548

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

Autorzy: Alessio Colantoni, Jakob Rupert, Andrea Vandelli, Gian Gaetano Tartaglia, Elsa Zacco
Opublikowane w: Biochemical Society Transactions, Numer 48/4, 2020, Strona(/y) 1529-1543, ISSN 0300-5127
Wydawca: Portland Press, Ltd.
DOI: 10.1042/bst20191059

Deep learning for blind structured illumination microscopy

Autorzy: Emmanouil Xypakis, Giorgio Gosti, Taira Giordani, Raffaele Santagati, Giancarlo Ruocco & Marco Leonetti
Opublikowane w: Scientific Reports, Numer 8623 (2022), 2022, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-022-12571-0

Homage to Chris Dobson

Autorzy: 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
Opublikowane w: Frontiers in Molecular Biosciences, Numer 6, 2019, ISSN 2296-889X
Wydawca: Frontier in Molecular Biosciences
DOI: 10.3389/fmolb.2019.00137

Cell-mediated exon skipping normalizes dystrophin expression and muscle function in a new mouse model of Duchenne Muscular Dystrophy

Autorzy: Galli F, Bragg L, Rossi M, Proietti D, Perani L, Bagicaluppi M, Tonlorenzi R, Sibanda T, Caffarini M, Talapatra A, Santoleri S, Meregalli M, Bano-Otalora B, Bigot A, Bozzoni I, Bonini C, Mouly V, Torrente Y, Cossu G.
Opublikowane w: EMBO Molecular Medicine, 2024, ISSN 1757-4676
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1038/s44321-024-00031-3

Machine learning methods applied to genotyping data capture interactions between single nucleotide variants in late onset Alzheimer's disease

Autorzy: Magdalena Arnal Segura; Giorgio Bini; Dietmar Fernandez Orth; Eleftherios Samaras; Maya Kassis; Fotis Aisopos; Jordi Rambla De Argila; George Paliouras; Peter Garrard; Claudia Giambartolomei; Gian Gaetano Tartaglia
Opublikowane w: Alzheimers Dement (Amst), Numer 7, 2022, ISSN 2352-8729
Wydawca: Elsevier B.V.,
DOI: 10.1101/2021.08.30.21262815

RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding

Autorzy: Elsa Zacco; Laura Broglia;, Misuzu Kurihara; Michele Monti; Stefano Gustincich; Annalisa Pastore ; Kathrin Plath; Shinichi Nagakawa; Andrea Cerase ; Natalia Sanchez de Groot; Gian Gaetano Tartaglia
Opublikowane w: Chemical Reviews, 2024, ISSN 0009-2665
Wydawca: American Chemical Society
DOI: 10.1021/acs.chemrev.3c00575

Rational design and synthesis of a novel BODIPY-based probe for selective imaging of tau tangles in human iPSC-derived cortical neurons

Autorzy: Alessandro Soloperto 1, Deborah Quaglio 2, Paola Baiocco 1 3, Isabella Romeo 1 2, Mattia Mori 4, Matteo Ardini 5, Caterina Presutti 1 3, Ida Sannino 1, Silvia Ghirga 1, Antonia Iazzetti 6, Rodolfo Ippoliti 5, Giancarlo Ruocco 1, Bruno Botta 2, Francesca Ghirga 7, Silvia Di Angelantonio 8 9, Alberto Boffi 1 3
Opublikowane w: Scientific Reports, Numer 12,Article number: 5257 (2022), 2022, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-022-09016-z

Circular RNA ZNF609/CKAP5 mRNA interaction regulates microtubule dynamics and tumorigenicity

Autorzy: Rossi F, Beltran M, Damizia M, Grelloni C, Colantoni A, Setti A, Di Timoteo G, Dattilo D, Centrón-Broco A, Nicoletti C, Fanciulli M, Lavia P, Bozzoni I.
Opublikowane w: MOLECULAR CELL, 2022, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2021.11.032

Retinal fingerprints of ALS in patients: Ganglion cell apoptosis and TDP-43/p62 misplacement

Autorzy: Natalia Pediconi, Ylenia Gigante, Silvia Cama, Martina Pitea, Lorenza Mautone, Giancarlo Ruocco, Silvia Ghirga and Silvia Di Angelantonio
Opublikowane w: Frontiers in Aging Neuroscience, Numer Volume 15 - 2023, 2023, ISSN 1663-4365
Wydawca: Frontiers Research Foundation
DOI: 10.3389/fnagi.2023.1110520

Single-photon microscopy to studybiomolecular condensates

Autorzy: Perego E, Zappone S, Castagnetti F, Mariani D, Vitiello E, Rupert J, Zacco E, Tartaglia GG, Bozzoni I, Slenders E, Vicidomini G.
Opublikowane w: Nature Communication, 2023, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-023-43969-7

Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and ACE2-derived peptides

Autorzy: G. Parisi, R. Piacentini, A. Incocciati, A. Bonamore, A. Macone, J. Rupert, E. Zacco, M. Miotto, E. Milanetti, G. G. Tartaglia, G. Ruocco, A. Boffi, and L. Di Rienzo.
Opublikowane w: Frontiers in Molecular Biosciences, 2024, ISSN 2296-889X
Wydawca: Frontiers Media
DOI: 10.3389/fmolb.2023.1332359

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Autorzy: Crua Asensio N; Rizzieri S; Cuomo A; Tartaglia GG; Zacco E
Opublikowane w: Journal of Visualized Experiments : Jove, Numer 193, 2023, ISSN 1940-087X
Wydawca: MYJoVE Corporation
DOI: 10.3791/64923

A recurrent Hopfield network for estimating meso-scale effective connectivity in MEG

Autorzy: Giorgio Gosti; Edoardo Milanetti; Viola Folli; Francesco de Pasquale; Marco Leonetti; Maurizio Corbetta; Giancarlo Ruocco; Stefania Della Penna
Opublikowane w: Neural Networks, Numer 1, 2024, ISSN 1879-2782
Wydawca: Elsevier
DOI: 10.1016/j.neunet.2023.11.027

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

Autorzy: Cecilia Battistelli, Sabrina Garbo, Veronica Riccioni, Claudia Montaldo, Laura Santangelo, Andrea Vandelli, Raffaele Strippoli, Gian Gaetano Tartaglia, Marco Tripodi, Carla Cicchini
Opublikowane w: Cancer Research, 2021, ISSN 2254-6081
Wydawca: Cancer Research
DOI: 10.1158/0008-5472.can-20-1764

Shape Complementarity Optimization of Antibody-Antigen Interfaces: The Application to SARS-CoV-2 Spike Protein

Autorzy: Alfredo De Lauro , Lorenzo Di Rienzo , Mattia Miotto , Pier Paolo Olimpieri , Edoardo Milanetti , Giancarlo Ruocco
Opublikowane w: Frontiers in Molecular Biosciences, Numer Volume 9 - 2022, 2022, ISSN 2296-889X
Wydawca: Frontiers Media
DOI: 10.3389/fmolb.2022.874296

Aggregation is a Context-Dependent Constraint on Protein Evolution.

Autorzy: Michele Monti; Alexandros Armaos; Marco Fantini; Annalisa Pastore; Gian Gaetano Tartaglia
Opublikowane w: Frontiers in Molecular Biosciences, Numer 4, 2021, ISSN 2296-889X
Wydawca: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2021.678115

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

Autorzy: Julie Martone, Davide Mariani, Tiziana Santini, Adriano Setti, Sama Shamloo, Alessio Colantoni, Francesca Capparelli, Alessandro Paiardini, Dacia Dimartino, Mariangela Morlando, Irene Bozzoni
Opublikowane w: EMBO reports, Numer 21/6, 2020, ISSN 1469-221X
Wydawca: 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

Autorzy: Saif N. Haify, Teresa Botta-Orfila, Renate K. Hukema, Gian Gaetano Tartaglia
Opublikowane w: Frontiers in Molecular Biosciences, Numer 7, 2020, ISSN 2296-889X
Wydawca: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2020.00031

A low-cost, label-free microfluidic scanning flow cytometer for high-accuracy quantification of size and refractive index of particles

Autorzy: Riccardo Reale , Giovanna Peruzzi , Maryamsadat Ghoreishi , Helena Stabile, Giancarlo Ruocco ORCID and Marco Leonetti
Opublikowane w: Lab on a Chip, Numer Numer 8, 2023, 2023, ISSN 1473-0197
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d2lc01179d

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 48/12, 2020, Strona(/y) 6889-6905, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkaa410

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

Autorzy: Alexandros Armaos, Elsa Zacco, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Opublikowane w: BioEssays, Numer 43/2, 2021, Strona(/y) 2000118, ISSN 0265-9247
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/bies.202000118

High-Throughput Interactome Determination via Sulfur Anomalous Scattering

Autorzy: Mattia Miotto; Edoardo Milanetti; Riccardo Mincigrucci; Claudio Masciovecchio; Giancarlo Ruocco
Opublikowane w: the journal of physical chemistry letters, Numer 18, 2024, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.3c03632

RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides withSTMN-2cryptic splicing and precedes clinical manifestation in ALS

Autorzy: Holly Spence, Fergal M. Waldron, Rebecca S. Saleeb, Anna-Leigh Brown, Olivia M. Rifai, Martina Gilodi, Fiona Read, Kristine Roberts, Gillian Milne, Debbie Wilkinson, Judi O’Shaughnessy, Annalisa Pastore, Pietro Fratta, Neil Shneider, Gian Gaetano Tartaglia, Elsa Zacco, Mathew H. Horrocks, Jenna M. Gregory
Opublikowane w: Acta Neuropathol, Numer 2024 Mar, 2023, Strona(/y) 5;147, ISSN 1432-0533
Wydawca: Springer
DOI: 10.1101/2023.10.24.563701

TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron-dependent neurological phenotypes in vivo and prevents neurodegeneration

Autorzy: Chen; Lu; Roake; Caitlin M; Maccallini; Paolo; Bavasso; Francesca; Dehghannasiri; Roozbeh; Santonicola; Pamela; Mendoza-Ferreira; Natalia; Scatolini; Livia; Rizzuti; Ludovico; Esposito; Alessandro; Gallotta; Ivan; Francia; Sofia; Cacchione; Stefano; Galati; Alessandra; Palumbo; Valeria; Kobin; Marie A; Tartaglia; Gian Gaetano; Colantoni; Alessio; Proietti; Gabriele; Wu; Yunming; Hammerschmidt; Mat
Opublikowane w: Nucleic Acids Research, Numer 16, 2022, ISSN 1362-4962
Wydawca: Oxford Press
DOI: 10.1093/nar/gkac659

In Situ Hybridization of circRNAs in Cells and Tissues through BaseScope™ Strategy

Autorzy: D'Ambra E, Vitiello E, Santini T, Bozzoni I.
Opublikowane w: Methods in Molecular Biology, 2024, ISSN 1064-3745
Wydawca: Humana Press, Inc.
DOI: 10.1007/978-1-0716-3678-7_4

Progressive alteration of murine bladder elasticity in actinic cystitis detected by Brillouin microscopy

Autorzy: Laura Martinez-Vidal; Claudia Testi; Emanuele Pontecorvo; Filippo Pederzoli; Elisa Alchera; Irene Locatelli; Chiara Venegoni; Antonello Spinelli; Roberta Lucianò; Andrea Salonia; Alessandro Podestà; Giancarlo Ruocco; Massimo Alfano
Opublikowane w: Scientific Reports, Vol 14, Iss 1, Pp 1-16 (2024), Numer 1, 2024, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-023-51006-2

Two Receptor Binding Strategy of SARS-CoV-2 Is Mediated by Both the N-Terminal and Receptor-Binding Spike Domain

Autorzy: Michele Monti; Edoardo Milanetti; Myrthe T. Frans; Mattia Miotto; Lorenzo Di Rienzo; Maksim V. Baranov; Giorgio Gosti; Arun Kumar Somavarapu; Madhu Nagaraj; Thaddeus W. Golbek; Emiel Rossing; Sam J. Moons; Thomas J. Boltje; Geert van den Bogaart; Tobias Weidner; Daniel E. Otzen; Gian Gaetano Tartaglia; Giancarlo Ruocco; Steven J. Roeters
Opublikowane w: Journal of Physical Chemistry B, Numer 12, 2024, ISSN 1520-6106
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpcb.3c06258

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

Autorzy: Claudia Cava, Alexandros Armaos, Benjamin Lang, Gian Gaetano Tartaglia, Isabella Castiglioni
Opublikowane w: Scientific Reports, 2022, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-021-04664-z

CircAFF1 Is a Circular RNA with a Role in Alveolar Rhabdomyosarcoma Cell Migration

Autorzy: Centrón-Broco A, Rossi F, Grelloni C, Garraffo R, Dattilo D, Giuliani A, Di Timoteo G, Colantoni A, Bozzoni I, Beltran Nebot M.
Opublikowane w: Biomedicines, 2023, ISSN 2078-2489
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/biomedicines11071893

Long non-coding RNA-polycomb intimate rendezvous

Autorzy: Andrea Cerase, Gian Gaetano Tartaglia
Opublikowane w: Open Biology, Numer 10/9, 2020, Strona(/y) 200126, ISSN 2046-2441
Wydawca: Royal Society Publishing
DOI: 10.1098/rsob.200126

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

Autorzy: Michele Monti, Giulia Guiducci, Alessio Paone, Serena Rinaldo, Giorgio Giardina, Francesca Romana Liberati, Francesca Cutruzzolá, Gian Gaetano Tartaglia
Opublikowane w: Computational and Structural Biotechnology Journal, Numer 19, 2021, Strona(/y) 3034-3041, ISSN 2001-0370
Wydawca: Computational and Structural Biotechnology Journal
DOI: 10.1016/j.csbj.2021.05.019

Phase Separation Drives SARS-CoV-2 Replication: A Hypothesis

Autorzy: Vandelli, Andrea; Vocino, Giovanni; Tartaglia, Gian Gaetano
Opublikowane w: Frontiers in Molecular Biosciences, Numer 19, 2022, ISSN 2296-889X
Wydawca: Lausanne: Frontiers Media S.A., 2014-
DOI: 10.3389/fmolb.2022.893067

Inferring the stabilization effects of SARS-CoV-2 variants on the binding with ACE2 receptor

Autorzy: Mattia Miotto, Lorenzo Di Rienzo, Giorgio Gosti, Leonardo Bo’, Giacomo Parisi, Roberta Piacentini, Alberto Boffi, Giancarlo Ruocco & Edoardo Milanetti
Opublikowane w: Communications Biology, Numer 5,20221(2022), 2022, ISSN 2399-3642
Wydawca: Springer Nature
DOI: 10.1038/s42003-021-02946-w

Probing TDP-43 condensation using an in silico designed aptamer

Autorzy: Elsa Zacco; Owen Kantelberg; Edoardo Milanetti; Alexandros Armaos; Francesco Paolo Panei; Jenna Gregory; Kiani Jeacock; David J. Clarke; Siddharthan Chandran; Giancarlo Ruocco; Stefano Gustincich; Mathew H. Horrocks; Annalisa Pastore; Gian Gaetano Tartaglia
Opublikowane w: Nature Communications, Numer 7, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-30944-x

Prediction of protein-RNA interactions from single-cell transcriptomic data

Autorzy: Jonathan Fiorentino; Alexandros Armaos; Alessio Colantoni; Gian Gaetano Tartaglia
Opublikowane w: Crossref, Numer 52, 2024, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkae076

Circular RNAs in cell differentiation and development

Autorzy: Gaia Di Timoteo; Francesca Rossi; Irene Bozzoni; Irene Bozzoni
Opublikowane w: The Company of Biologists Ltd., Numer 1, 2020, ISSN 0021-9533
Wydawca: The Company of Biologists Ltd.
DOI: 10.1242/dev.182725

Photonic Stochastic Emergent Storage for deep classification by scattering-intrinsic patterns

Autorzy: Marco Leonetti, Giorgio Gosti, Giancarlo Ruocco
Opublikowane w: Nature Communications, Numer 15, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-023-44498-z

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

Autorzy: Greta Grassmann; Mattia Miotto; Lorenzo Di Rienzo; Federico Salaris; Beatrice Silvestri; Elsa Zacco; Alessandro Rosa; Gian Gaetano Tartaglia; Giancarlo Ruocco; Edoardo Milanetti
Opublikowane w: Biomolecules, Numer 1, 2021, ISSN 2218-273X
Wydawca: 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

Autorzy: Andrea Vandelli, Fernando Cid Samper, Marc Torrent Burgas, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Opublikowane w: Journal of Molecular Biology, 2021, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2021.167159

4D Single-particle tracking with asynchronous read-out single-photon avalanche diode array detector

Autorzy: Andrea Bucci, Giorgio Tortarolo, Marcus Oliver Held, Luca Bega, Eleonora Perego, Francesco Castagnetti, Irene Bozzoni, Eli Slenders, Giuseppe Vicidomini
Opublikowane w: Nature Communications, Numer 15, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-024-50512-9

Differences in the organization of interface residues tunes the stability of the SARS-CoV-2 spike-ACE2 complex

Autorzy: Mattia Miotto; Lorenzo Di Rienzo; Greta Grassmann; Greta Grassmann; Fausta Desantis; Fausta Desantis; Gianluca Cidonio; Giorgio Gosti; Giorgio Gosti; Marco Leonetti; Marco Leonetti; Giancarlo Ruocco; Giancarlo Ruocco; Edoardo Milanetti; Edoardo Milanetti
Opublikowane w: Frontiers in Molecular Biosciences, Vol 10 (2023), Numer 12, 2023, ISSN 2296-889X
Wydawca: Frontiers Media
DOI: 10.3389/fmolb.2023.1205919

A tripartite circRNA/mRNA/miRNA interaction regulates glutamatergic signaling in the mouse brain

Autorzy: Valentina Silenzi, Eleonora D’Ambra, Tiziana Santini, Sara D’Uva, Adriano Setti, Nicolò Salvi, Carmine Nicoletti, Rebecca Scarfò, Federica Cordella, Brunella Mongiardi, Diletta Cavezza, Nara Liessi, Laura Ferrucci, Davide Ragozzino, Andrea Armirotti, Silvia Di Angelantonio, Elvira De Leonibus, Irene Bozzoni, Mariangela Morlando
Opublikowane w: Cell Reports, Numer 43, 2024, Strona(/y) 114766, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2024.114766

Identification and prediction of G-quadruplex RNA-binding proteins with roles in transcription and phase separation

Autorzy: Gian Gaetano Tartaglia; Alexandros Armaos; Johanna Luige; Ulf Ørom
Opublikowane w: Crossref, Numer 15, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-024-46731-9

The long noncoding RNA nHOTAIRM1 is necessary for differentiation and activity of iPSC-derived spinal motor neurons

Autorzy: Tollis P, Vitiello E, Migliaccio F, D'Ambra E, Rocchegiani A, Garone MG, Bozzoni I, Rosa A, Carissimo A, Laneve P, Caffarelli E.
Opublikowane w: Cell Death Dis, 2023, ISSN 1350-9047
Wydawca: Nature Publishing Group
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The protective role of m1A during stress-induced granulation

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Computational evidences of a misfolding event in an aggregation-prone light chain preceding the formation of the non-native pathogenic dimer

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Computational models of dopamine release measured by fast scan cyclic voltammetry in vivo

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Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq

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Dynamical changes of SARS-CoV-2 spike variants in the highly immunogenic regions impact the viral antibodies escaping

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Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein

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Collective Behavior and Self-Organization in Neural Rosette Morphogenesis

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Mitochondria inter-organelle relationships in cancer protein aggregation

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

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Computational structural-based GPCR optimization for user-defined ligand: Implications for the development of biosensors

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Lactoferrin Inhibition of the Complex Formation between ACE2 Receptor and SARS CoV-2 Recognition Binding Domain

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Physics-informed loss function for a deep neural network for Poissonian noise reduction

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Ferritin nanocage-enabled detection of pathological tau in living human retinal cells

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The m6A reader YTHDC1 and the RNA helicase DDX5 control the production of rhabdomyosarcoma-enriched circRNAs

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

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A Model Eye for fluorescent characterization of retinal cultures and tissues

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Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments

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Emerging Role for Linear and Circular Spermine Oxidase RNAs in Skeletal Muscle Physiopathology

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