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

Publications

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

Auteurs: 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
Publié dans: Bioinformatics, Numéro 10, 2022, ISSN 1367-4811
Éditeur: Oxford Press
DOI: 10.1093/bioinformatics/btac847

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

Auteurs: 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.
Publié dans: EMBO Journal, 2022, ISSN 0261-4189
Éditeur: 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

Auteurs: Maria Giovanna Garone, Vincenzo Alfano, Beatrice Salvatori, Clarissa Braccia, Giovanna Peruzzi, Alessio Colantoni, Irene Bozzoni, Andrea Armirotti, Alessandro Rosa
Publié dans: Scientific Reports, Numéro 10/1, 2020, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-68794-6

Phase separation drives X-chromosome inactivation.

Auteurs: Cerase, A.; Calabrese, J.M. ; Tartaglia, G.G.
Publié dans: Nature Structural and Molecular Biology, Numéro 29, 2022, Page(s) 183–185, ISSN 1545-9993
Éditeur: Nature Publishing Group
DOI: 10.1038/s41594-021-00697-0

Microglia reactivity entails microtubule remodeling from acentrosomal to centrosomal arrays

Auteurs: 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
Publié dans: Cell Reports, Numéro 2023 Feb 13;42(2):112104, 2023, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2023.112104

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

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

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

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

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

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

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

Auteurs: 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
Publié dans: Cell Reports, Numéro 4, 2020, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2020.108548

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

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

Deep learning for blind structured illumination microscopy

Auteurs: Emmanouil Xypakis, Giorgio Gosti, Taira Giordani, Raffaele Santagati, Giancarlo Ruocco & Marco Leonetti
Publié dans: Scientific Reports, Numéro 8623 (2022), 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-12571-0

Homage to Chris Dobson

Auteurs: 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
Publié dans: Frontiers in Molecular Biosciences, Numéro 6, 2019, ISSN 2296-889X
Éditeur: 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

Auteurs: Monti, Michele; Fiorentino, Jonathan; Milanetti, Edoardo; Gosti, Giorgio; Tartaglia, Gian Gaetano
Publié dans: Entropy, Numéro 1, 2022, ISSN 1099-4300
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e24020141

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

Auteurs: 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
Publié dans: Alzheimers Dement (Amst), Numéro 7, 2022, ISSN 2352-8729
Éditeur: Elsevier B.V.,
DOI: 10.1101/2021.08.30.21262815

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

Auteurs: 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
Publié dans: Scientific Reports, Numéro 12,Article number: 5257 (2022), 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-09016-z

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

Auteurs: 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.
Publié dans: MOLECULAR CELL, 2022, ISSN 1097-2765
Éditeur: Cell Press
DOI: 10.1016/j.molcel.2021.11.032

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

Auteurs: Natalia Pediconi, Ylenia Gigante, Silvia Cama, Martina Pitea, Lorenza Mautone, Giancarlo Ruocco, Silvia Ghirga and Silvia Di Angelantonio
Publié dans: Frontiers in Aging Neuroscience, Numéro Volume 15 - 2023, 2023, ISSN 1663-4365
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fnagi.2023.1110520

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

Auteurs: Crua Asensio N; Rizzieri S; Cuomo A; Tartaglia GG; Zacco E
Publié dans: Journal of Visualized Experiments : Jove, Numéro 193, 2023, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/64923

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

Auteurs: Giorgio Gosti; Edoardo Milanetti; Viola Folli; Francesco de Pasquale; Marco Leonetti; Maurizio Corbetta; Giancarlo Ruocco; Stefania Della Penna
Publié dans: Neural Networks, Numéro 1, 2024, ISSN 1879-2782
Éditeur: 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

Auteurs: Cecilia Battistelli, Sabrina Garbo, Veronica Riccioni, Claudia Montaldo, Laura Santangelo, Andrea Vandelli, Raffaele Strippoli, Gian Gaetano Tartaglia, Marco Tripodi, Carla Cicchini
Publié dans: Cancer Research, 2021, ISSN 2254-6081
Éditeur: 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

Auteurs: Alfredo De Lauro , Lorenzo Di Rienzo , Mattia Miotto , Pier Paolo Olimpieri , Edoardo Milanetti , Giancarlo Ruocco
Publié dans: Frontiers in Molecular Biosciences, Numéro Volume 9 - 2022, 2022, ISSN 2296-889X
Éditeur: Frontiers Media
DOI: 10.3389/fmolb.2022.874296

Aggregation is a Context-Dependent Constraint on Protein Evolution.

Auteurs: Michele Monti; Alexandros Armaos; Marco Fantini; Annalisa Pastore; Gian Gaetano Tartaglia
Publié dans: Frontiers in Molecular Biosciences, Numéro 4, 2021, ISSN 2296-889X
Éditeur: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2021.678115

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

Auteurs: Julie Martone, Davide Mariani, Tiziana Santini, Adriano Setti, Sama Shamloo, Alessio Colantoni, Francesca Capparelli, Alessandro Paiardini, Dacia Dimartino, Mariangela Morlando, Irene Bozzoni
Publié dans: EMBO reports, Numéro 21/6, 2020, ISSN 1469-221X
Éditeur: 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

Auteurs: Saif N. Haify, Teresa Botta-Orfila, Renate K. Hukema, Gian Gaetano Tartaglia
Publié dans: Frontiers in Molecular Biosciences, Numéro 7, 2020, ISSN 2296-889X
Éditeur: 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

Auteurs: Riccardo Reale , Giovanna Peruzzi , Maryamsadat Ghoreishi , Helena Stabile, Giancarlo Ruocco ORCID and Marco Leonetti
Publié dans: Lab on a Chip, Numéro Numéro 8, 2023, 2023, ISSN 1473-0197
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d2lc01179d

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 48/12, 2020, Page(s) 6889-6905, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa410

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

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

High-Throughput Interactome Determination via Sulfur Anomalous Scattering

Auteurs: Mattia Miotto; Edoardo Milanetti; Riccardo Mincigrucci; Claudio Masciovecchio; Giancarlo Ruocco
Publié dans: the journal of physical chemistry letters, Numéro 18, 2024, ISSN 1948-7185
Éditeur: American Chemical Society
DOI: 10.1021/acs.jpclett.3c03632

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 16, 2022, ISSN 1362-4962
Éditeur: Oxford Press
DOI: 10.1093/nar/gkac659

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

Auteurs: 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
Publié dans: Scientific Reports, Vol 14, Iss 1, Pp 1-16 (2024), Numéro 1, 2024, ISSN 2045-2322
Éditeur: 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

Auteurs: 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
Publié dans: Journal of Physical Chemistry B, Numéro 12, 2024, ISSN 1520-6106
Éditeur: American Chemical Society
DOI: 10.1021/acs.jpcb.3c06258

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

Auteurs: Claudia Cava, Alexandros Armaos, Benjamin Lang, Gian Gaetano Tartaglia, Isabella Castiglioni
Publié dans: Scientific Reports, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-021-04664-z

Long non-coding RNA-polycomb intimate rendezvous

Auteurs: Andrea Cerase, Gian Gaetano Tartaglia
Publié dans: Open Biology, Numéro 10/9, 2020, Page(s) 200126, ISSN 2046-2441
Éditeur: Royal Society Publishing
DOI: 10.1098/rsob.200126

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

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

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

Auteurs: Vandelli, Andrea; Vocino, Giovanni; Tartaglia, Gian Gaetano
Publié dans: Frontiers in Molecular Biosciences, Numéro 19, 2022, ISSN 2296-889X
Éditeur: 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

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

Probing TDP-43 condensation using an in silico designed aptamer

Auteurs: 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
Publié dans: Nature Communications, Numéro 7, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-30944-x

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

Auteurs: Jonathan Fiorentino; Alexandros Armaos; Alessio Colantoni; Gian Gaetano Tartaglia
Publié dans: Crossref, Numéro 52, 2024, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkae076

Circular RNAs in cell differentiation and development

Auteurs: Gaia Di Timoteo; Francesca Rossi; Irene Bozzoni; Irene Bozzoni
Publié dans: The Company of Biologists Ltd., Numéro 1, 2020, ISSN 0021-9533
Éditeur: 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

Auteurs: Greta Grassmann; Mattia Miotto; Lorenzo Di Rienzo; Federico Salaris; Beatrice Silvestri; Elsa Zacco; Alessandro Rosa; Gian Gaetano Tartaglia; Giancarlo Ruocco; Edoardo Milanetti
Publié dans: Biomolecules, Numéro 1, 2021, ISSN 2218-273X
Éditeur: 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

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

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

Auteurs: 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
Publié dans: Frontiers in Molecular Biosciences, Vol 10 (2023), Numéro 12, 2023, ISSN 2296-889X
Éditeur: Frontiers Media
DOI: 10.3389/fmolb.2023.1205919

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

Auteurs: Gian Gaetano Tartaglia; Alexandros Armaos; Johanna Luige; Ulf Ørom
Publié dans: Crossref, Numéro 15, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-46731-9

Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors

Auteurs: Lorenzo Di Rienzo 1, Luca De Flaviis 2, Giancarlo Ruocco 3 2, Viola Folli 3, Edoardo Milanetti 3 2
Publié dans: Journal of Computer-Aided Molecular Design 36, Numéro 11(2022), 2022, ISSN 1573-4951
Éditeur: Springer Nature
DOI: 10.1007/s10822-021-00434-1

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

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

FUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation

Auteurs: Alessio Colantoni; Davide Capauto; Vincenzo Alfano; Eleonora D’Ambra; Sara D’Uva; Gian Gaetano Tartaglia; Mariangela Morlando
Publié dans: International Journal of Molecular Sciences, Numéro 1, 2023, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24043181

Electrostatic complementarity at the interface drives transient protein-protein interactions

Auteurs: Greta Grassmann; Lorenzo Di Rienzo; Giorgio Gosti; Marco Leonetti; Giancarlo Ruocco; Mattia Miotto; Edoardo Milanetti
Publié dans: Scientific Reports, Vol 13, Iss 1, Pp 1-15 (2023), Numéro 18, 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-37130-z

A KO mouse model for the lncRNA Lhx1os produces motor neuron alterations and locomotor impairment

Auteurs: Pellegrini F, Padovano V, Biscarini S, Santini T, Setti A, Galfrè SG, Silenzi V, Vitiello E, Mariani D, Nicoletti C, Torromino G, De Leonibus E, Martone J, Bozzoni I.
Publié dans: iScience, 2022, ISSN 2589-0042
Éditeur: iScience
DOI: 10.1016/j.isci.2022.105891

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

Auteurs: Monti, Michele; Fiorentino, Jonathan; Milanetti, Edoardo; Gosti, Giorgio; Tartaglia, Gian Gaetano
Publié dans: Entropy, Numéro 24, 2022, ISSN 1099-4300
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)

Best practice standards for circular RNA research

Auteurs: Nielsen AF, Bindereif A, Bozzoni I, Hanan M, Hansen TB, Irimia M, Kadener S, Kristensen LS, Legnini I, Morlando M, Jarlstad Olesen MT, Pasterkamp RJ, Preibisch S, Rajewsky N, Suenkel C, Kjems J.
Publié dans: NATURE METHODS, 2022, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-022-01487-2

A novel computational strategy for defining the minimal protein molecular surface representation

Auteurs: Greta Grassmann,Mattia Miotto,Lorenzo Di Rienzo,Giorgio Gosti,Giancarlo Ruocco,Edoardo Milanetti
Publié dans: PLOS ONE, 2022, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0266004

Thermometer: a webserver to predict protein thermal stability

Auteurs: Mattia Miotto, Alexandros Armaos, Lorenzo Di Rienzo, Giancarlo Ruocco, Edoardo Milanetti, Gian Gaetano Tartaglia
Publié dans: Bioinformatics, 2022, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btab868

A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in noncoding RNAs.

Auteurs: Riccardo Delli Ponti; Laura Broglia; Andrea Vandelli; Alexandros Armaos; Marc Torrent Burgas; Natalia Sanchez de Groot; Gian Gaetano Tartaglia
Publié dans: IUBMB Life ., 2022, ISSN 1521-6551
Éditeur: John Wiley & Sons
DOI: 10.1002/iub.2673

The protective role of m1A during stress-induced granulation

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

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

Auteurs: Shashaank N1, Somayaji M2, Miotto M3, Mosharov EV2, Makowicz EA2, Knowles DA1, Ruocco G3, Sulzer DL2
Publié dans: PNAS Nexus, Numéro Volume 2, Numéro 3, March 2023, 2023, ISSN 2752-6542
Éditeur: Oxford University Press
DOI: 10.1093/pnasnexus/pgad044

Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity

Auteurs: Fausta Desantis, Mattia Miotto, Lorenzo Di Rienzo, Edoardo Milanetti & Giancarlo Ruocco
Publié dans: Scientific Reports, Numéro Article number: 12087 (2022), 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-16338-5

ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins

Auteurs: Aina Maria Mas; Enrique Goñi; Igor Ruiz de los Mozos; Aida Arcas; Luisa Statello; Jovanna González; Lorea Blázquez; Wei Ting Chelsea Lee; Dipika Gupta; Álvaro Sejas; Shoko Hoshina; Alexandros Armaos; Gian Gaetano Tartaglia; Shou Waga; Jernej Ule; Eli Rothenberg; María Gómez; Maite Huarte
Publié dans: Nature Communications, Numéro 20, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-40105-3

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

Auteurs: Thomas Schwarzl; Sudeep Sahadevan; Benjamin Lang; Milad Miladi; Rolf Backofen; Wolfgang Huber; Matthias W Hentze; Gian Gaetano Tartaglia
Publié dans: Crossref, Numéro 3, 2024, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad998

Direct Visualization and Identification of Membrane Voltage-Gated Sodium Channels from Human iPSC-Derived Neurons by Multiple Imaging and Light Enhanced Spectroscopy

Auteurs: Manola Moretti 1, Tania Limongi 2, Claudia Testi 3, Edoardo Milanetti 3 4, Maria Teresa De Angelis 5, Elvira I Parrotta 5, Stefania Scalise 5, Gianluca Santamaria 5, Marco Allione 1, Sergei Lopatin 6, Bruno Torre 1, Peng Zhang 1, Monica Marini 2, Gerardo Perozziello 7, Patrizio Candeloro 7, Candido Fabrizio Pirri 2, Giancarlo Ruocco 4, Giovanni Cuda 5, Enzo Di Fabrizio 2
Publié dans: small methods, Numéro 2022 Jul;6(7), 2022, ISSN 2366-9608
Éditeur: Wiley
DOI: 10.1002/smtd.202200402

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

Auteurs: Alexandra Louka, Sara Bagnoli, Jakob Rupert, Benjamin Esapa, Gian Gaetano Tartaglia, Alessandro Cellerino, Annalisa Pastore, Eva Terzibasi Tozzini
Publié dans: Aging Cell, 2021, ISSN 1474-9726
Éditeur: John Wiley & Sons
DOI: 10.1111/acel.13517

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

Auteurs: 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
Publié dans: Cell Death & Disease, Numéro 11/7, 2020, ISSN 2041-4889
Éditeur: Nature Publishing Group
DOI: 10.1038/s41419-020-02738-w

A longitudinal study defined circulating microRNAs as reliable biomarkers for disease prognosis and progression in ALS human patients

Auteurs: Dobrowolny G, Martone J, Lepore E, Casola I, Petrucci A, Inghilleri M, Morlando M, Colantoni A, Scicchitano BM, Calvo A, Bisogni G, Chiò A, Sabatelli M, Bozzoni I, Musarò A.
Publié dans: Cell Death Discovery, 2021, ISSN 2058-7716
Éditeur: Cell Death Discovery
DOI: 10.1038/s41420-020-00397-6

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

Auteurs: Lorenzo Di Rienzo, Mattia Miotto, Fausta Desantis, Greta Grassmann, Giancarlo Ruocco, Edoardo Milanetti
Publié dans: Proteins, Numéro April, 2023, 2023, ISSN 0887-3585
Éditeur: Wiley-Liss Inc
DOI: 10.1002/prot.26497

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

Auteurs: Leonardo Bo , Edoardo Milanetti 1 2, Cheng Giuseppe Chen 3, Giancarlo Ruocco 2 1, Andrea Amadei 4, Marco D'Abramo 3
Publié dans: ACS Omega, Numéro 2022, 7, 16, 2022, Page(s) 13448–13454, ISSN 2470-1343
Éditeur: American Chemical Society
DOI: 10.1021/acsomega.1c06206

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

Auteurs: Alexandra Louka; Sara Bagnoli; Jakob Rupert; Esapa B; Gian Gaetano Tartaglia; Alessandro Cellerino; Annalisa Pastore; Eva Terzibasi Tozzini
Publié dans: Aging Cell ., Numéro 22, 2022, ISSN 1474-9718
Éditeur: Blackwell Publishing Inc.
DOI: 10.1101/2021.02.04.429704

Mitochondria inter-organelle relationships in cancer protein aggregation

Auteurs: Ilaria Genoves, Ersilia Fornetti, Giancarlo Ruocco
Publié dans: Frontiers in Cell and Developmental Biology, Numéro 2022 Dec 19;10:1062993, 2022, ISSN 2296-634X
Éditeur: Frontiers Media
DOI: 10.3389/fcell.2022.1062993

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

Auteurs: 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
Publié dans: EMBO Molecular Medicine, Numéro 12/8, 2020, ISSN 1757-4676
Éditeur: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202012063

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

Auteurs: Lorenzo Di Rienzo; Mattia Miotto; Edoardo Milanetti; Giancarlo Ruocco
Publié dans: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 3002-3009 (2023), Numéro 8, 2023, ISSN 2001-0370
Éditeur: Science Direct
DOI: 10.1016/j.csbj.2023.05.004

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

Auteurs: Roberta Piacentini ,Laura Centi ,Mattia Miotto ,Edoardo Milanetti ,Lorenzo Di Rienzo ,Martina Pitea Paolo Piazza ,Giancarlo Ruocco ,Alberto Boffi andGiacomo Parisi
Publié dans: International Journal of Molecular Science, Numéro 2022, 23(10), 5436, 2022, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23105436

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

Auteurs: Emmanouil Xypakis; Valeria De Turis; Fabrizio Gala; Giancarlo Ruocco; Marco Leonetti
Publié dans: Optic Express, Numéro 9, 2023, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.21203/rs.3.rs-2049014/v1

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

Auteurs: Dattilo D, Di Timoteo G, Setti A, Giuliani A, Peruzzi G, Beltran Nebot M, Centrón-Broco A, Mariani D, Mozzetta C, Bozzoni I.
Publié dans: Nature Comunication, Numéro 2023 Apr 5, 2023, Page(s) 14(1):1898, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-37578-7

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

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

Modulation of circRNA Metabolism by m6A Modification

Auteurs: i Timoteo G, Dattilo D, Centrón-Broco A, Colantoni A, Guarnacci M, Rossi F, Incarnato D, Oliviero S, Fatica A, Morlando M, Bozzoni I.
Publié dans: Cell Reports, 2020, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2020.107641

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

Auteurs: Greta Grassmann; Mattia Miotto; Fausta Desantis; Lorenzo Di Rienzo; Gian Gaetano Tartaglia; Annalisa Pastore; Giancarlo Ruocco; Michele Monti; Edoardo Milanetti
Publié dans: Chemical Reviews, Numéro 3, 2024, ISSN 0009-2665
Éditeur: American Chemical Society
DOI: 10.1021/acs.chemrev.3c00550

Circ-Hdgfrp3 shuttles along neurites and is trapped in aggregates formed by ALS-associated mutant FUS

Auteurs: D'Ambra E, Santini T, Vitiello E, D'Uva S, Silenzi V, Morlando M, Bozzoni I.
Publié dans: ISCIENCE, 2021, ISSN 2589-0042
Éditeur: ISCIENCE
DOI: 10.1016/j.isci.2021.103504

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

Auteurs: Reinoso-Sánchez JF, Baroli G, Duranti G, Scaricamazza S, Sabatini S, Valle C, Morlando M, Casero RA Jr, Bozzoni I, Mariottini P, Ceci R, Cervelli M.
Publié dans: International Journal of Molecular Sciences, 2020, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21218227

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