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

Publicaciones

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

Autores: 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
Publicado en: Bioinformatics, Edición 10, 2022, ISSN 1367-4811
Editor: Oxford Press
DOI: 10.1093/bioinformatics/btac847

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

Autores: 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.
Publicado en: EMBO Journal, 2022, ISSN 0261-4189
Editor: 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

Autores: Maria Giovanna Garone, Vincenzo Alfano, Beatrice Salvatori, Clarissa Braccia, Giovanna Peruzzi, Alessio Colantoni, Irene Bozzoni, Andrea Armirotti, Alessandro Rosa
Publicado en: Scientific Reports, Edición 10/1, 2020, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-020-68794-6

Phase separation drives X-chromosome inactivation.

Autores: Cerase, A.; Calabrese, J.M. ; Tartaglia, G.G.
Publicado en: Nature Structural and Molecular Biology, Edición 29, 2022, Página(s) 183–185, ISSN 1545-9993
Editor: Nature Publishing Group
DOI: 10.1038/s41594-021-00697-0

Microglia reactivity entails microtubule remodeling from acentrosomal to centrosomal arrays

Autores: 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
Publicado en: Cell Reports, Edición 2023 Feb 13;42(2):112104, 2023, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2023.112104

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

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

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

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

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

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

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

Autores: 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
Publicado en: Cell Reports, Edición 4, 2020, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2020.108548

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

Autores: Alessio Colantoni, Jakob Rupert, Andrea Vandelli, Gian Gaetano Tartaglia, Elsa Zacco
Publicado en: Biochemical Society Transactions, Edición 48/4, 2020, Página(s) 1529-1543, ISSN 0300-5127
Editor: Portland Press, Ltd.
DOI: 10.1042/bst20191059

Deep learning for blind structured illumination microscopy

Autores: Emmanouil Xypakis, Giorgio Gosti, Taira Giordani, Raffaele Santagati, Giancarlo Ruocco & Marco Leonetti
Publicado en: Scientific Reports, Edición 8623 (2022), 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-022-12571-0

Homage to Chris Dobson

Autores: 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
Publicado en: Frontiers in Molecular Biosciences, Edición 6, 2019, ISSN 2296-889X
Editor: 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

Autores: Monti, Michele; Fiorentino, Jonathan; Milanetti, Edoardo; Gosti, Giorgio; Tartaglia, Gian Gaetano
Publicado en: Entropy, Edición 1, 2022, ISSN 1099-4300
Editor: 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

Autores: 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
Publicado en: Alzheimers Dement (Amst), Edición 7, 2022, ISSN 2352-8729
Editor: 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

Autores: 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
Publicado en: Scientific Reports, Edición 12,Article number: 5257 (2022), 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-022-09016-z

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

Autores: 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.
Publicado en: MOLECULAR CELL, 2022, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1016/j.molcel.2021.11.032

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

Autores: Natalia Pediconi, Ylenia Gigante, Silvia Cama, Martina Pitea, Lorenza Mautone, Giancarlo Ruocco, Silvia Ghirga and Silvia Di Angelantonio
Publicado en: Frontiers in Aging Neuroscience, Edición Volume 15 - 2023, 2023, ISSN 1663-4365
Editor: Frontiers Research Foundation
DOI: 10.3389/fnagi.2023.1110520

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

Autores: Crua Asensio N; Rizzieri S; Cuomo A; Tartaglia GG; Zacco E
Publicado en: Journal of Visualized Experiments : Jove, Edición 193, 2023, ISSN 1940-087X
Editor: MYJoVE Corporation
DOI: 10.3791/64923

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

Autores: Giorgio Gosti; Edoardo Milanetti; Viola Folli; Francesco de Pasquale; Marco Leonetti; Maurizio Corbetta; Giancarlo Ruocco; Stefania Della Penna
Publicado en: Neural Networks, Edición 1, 2024, ISSN 1879-2782
Editor: 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

Autores: Cecilia Battistelli, Sabrina Garbo, Veronica Riccioni, Claudia Montaldo, Laura Santangelo, Andrea Vandelli, Raffaele Strippoli, Gian Gaetano Tartaglia, Marco Tripodi, Carla Cicchini
Publicado en: Cancer Research, 2021, ISSN 2254-6081
Editor: 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

Autores: Alfredo De Lauro , Lorenzo Di Rienzo , Mattia Miotto , Pier Paolo Olimpieri , Edoardo Milanetti , Giancarlo Ruocco
Publicado en: Frontiers in Molecular Biosciences, Edición Volume 9 - 2022, 2022, ISSN 2296-889X
Editor: Frontiers Media
DOI: 10.3389/fmolb.2022.874296

Aggregation is a Context-Dependent Constraint on Protein Evolution.

Autores: Michele Monti; Alexandros Armaos; Marco Fantini; Annalisa Pastore; Gian Gaetano Tartaglia
Publicado en: Frontiers in Molecular Biosciences, Edición 4, 2021, ISSN 2296-889X
Editor: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2021.678115

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

Autores: Julie Martone, Davide Mariani, Tiziana Santini, Adriano Setti, Sama Shamloo, Alessio Colantoni, Francesca Capparelli, Alessandro Paiardini, Dacia Dimartino, Mariangela Morlando, Irene Bozzoni
Publicado en: EMBO reports, Edición 21/6, 2020, ISSN 1469-221X
Editor: 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

Autores: Saif N. Haify, Teresa Botta-Orfila, Renate K. Hukema, Gian Gaetano Tartaglia
Publicado en: Frontiers in Molecular Biosciences, Edición 7, 2020, ISSN 2296-889X
Editor: 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

Autores: Riccardo Reale , Giovanna Peruzzi , Maryamsadat Ghoreishi , Helena Stabile, Giancarlo Ruocco ORCID and Marco Leonetti
Publicado en: Lab on a Chip, Edición Edición 8, 2023, 2023, ISSN 1473-0197
Editor: Royal Society of Chemistry
DOI: 10.1039/d2lc01179d

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

Autores: 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
Publicado en: Nucleic Acids Research, Edición 48/12, 2020, Página(s) 6889-6905, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkaa410

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

Autores: Alexandros Armaos, Elsa Zacco, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Publicado en: BioEssays, Edición 43/2, 2021, Página(s) 2000118, ISSN 0265-9247
Editor: John Wiley & Sons Inc.
DOI: 10.1002/bies.202000118

High-Throughput Interactome Determination via Sulfur Anomalous Scattering

Autores: Mattia Miotto; Edoardo Milanetti; Riccardo Mincigrucci; Claudio Masciovecchio; Giancarlo Ruocco
Publicado en: the journal of physical chemistry letters, Edición 18, 2024, ISSN 1948-7185
Editor: 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

Autores: 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
Publicado en: Nucleic Acids Research, Edición 16, 2022, ISSN 1362-4962
Editor: Oxford Press
DOI: 10.1093/nar/gkac659

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

Autores: 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
Publicado en: Scientific Reports, Vol 14, Iss 1, Pp 1-16 (2024), Edición 1, 2024, ISSN 2045-2322
Editor: 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

Autores: 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
Publicado en: Journal of Physical Chemistry B, Edición 12, 2024, ISSN 1520-6106
Editor: American Chemical Society
DOI: 10.1021/acs.jpcb.3c06258

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

Autores: Claudia Cava, Alexandros Armaos, Benjamin Lang, Gian Gaetano Tartaglia, Isabella Castiglioni
Publicado en: Scientific Reports, 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-021-04664-z

Long non-coding RNA-polycomb intimate rendezvous

Autores: Andrea Cerase, Gian Gaetano Tartaglia
Publicado en: Open Biology, Edición 10/9, 2020, Página(s) 200126, ISSN 2046-2441
Editor: Royal Society Publishing
DOI: 10.1098/rsob.200126

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

Autores: Michele Monti, Giulia Guiducci, Alessio Paone, Serena Rinaldo, Giorgio Giardina, Francesca Romana Liberati, Francesca Cutruzzolá, Gian Gaetano Tartaglia
Publicado en: Computational and Structural Biotechnology Journal, Edición 19, 2021, Página(s) 3034-3041, ISSN 2001-0370
Editor: Computational and Structural Biotechnology Journal
DOI: 10.1016/j.csbj.2021.05.019

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

Autores: Vandelli, Andrea; Vocino, Giovanni; Tartaglia, Gian Gaetano
Publicado en: Frontiers in Molecular Biosciences, Edición 19, 2022, ISSN 2296-889X
Editor: 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

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

Probing TDP-43 condensation using an in silico designed aptamer

Autores: 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
Publicado en: Nature Communications, Edición 7, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-30944-x

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

Autores: Jonathan Fiorentino; Alexandros Armaos; Alessio Colantoni; Gian Gaetano Tartaglia
Publicado en: Crossref, Edición 52, 2024, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkae076

Circular RNAs in cell differentiation and development

Autores: Gaia Di Timoteo; Francesca Rossi; Irene Bozzoni; Irene Bozzoni
Publicado en: The Company of Biologists Ltd., Edición 1, 2020, ISSN 0021-9533
Editor: 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

Autores: Greta Grassmann; Mattia Miotto; Lorenzo Di Rienzo; Federico Salaris; Beatrice Silvestri; Elsa Zacco; Alessandro Rosa; Gian Gaetano Tartaglia; Giancarlo Ruocco; Edoardo Milanetti
Publicado en: Biomolecules, Edición 1, 2021, ISSN 2218-273X
Editor: 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

Autores: Andrea Vandelli, Fernando Cid Samper, Marc Torrent Burgas, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Publicado en: Journal of Molecular Biology, 2021, ISSN 0022-2836
Editor: 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

Autores: 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
Publicado en: Frontiers in Molecular Biosciences, Vol 10 (2023), Edición 12, 2023, ISSN 2296-889X
Editor: Frontiers Media
DOI: 10.3389/fmolb.2023.1205919

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

Autores: Gian Gaetano Tartaglia; Alexandros Armaos; Johanna Luige; Ulf Ørom
Publicado en: Crossref, Edición 15, 2024, ISSN 2041-1723
Editor: 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

Autores: Lorenzo Di Rienzo 1, Luca De Flaviis 2, Giancarlo Ruocco 3 2, Viola Folli 3, Edoardo Milanetti 3 2
Publicado en: Journal of Computer-Aided Molecular Design 36, Edición 11(2022), 2022, ISSN 1573-4951
Editor: 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

Autores: Alexandros Armaos, Alessio Colantoni, Gabriele Proietti, Jakob Rupert, Gian Gaetano Tartaglia
Publicado en: Nucleic Acids Research, Edición 49/W1, 2021, Página(s) W72-W79, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkab393

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

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

Electrostatic complementarity at the interface drives transient protein-protein interactions

Autores: Greta Grassmann; Lorenzo Di Rienzo; Giorgio Gosti; Marco Leonetti; Giancarlo Ruocco; Mattia Miotto; Edoardo Milanetti
Publicado en: Scientific Reports, Vol 13, Iss 1, Pp 1-15 (2023), Edición 18, 2023, ISSN 2045-2322
Editor: 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

Autores: 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.
Publicado en: iScience, 2022, ISSN 2589-0042
Editor: 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

Autores: Monti, Michele; Fiorentino, Jonathan; Milanetti, Edoardo; Gosti, Giorgio; Tartaglia, Gian Gaetano
Publicado en: Entropy, Edición 24, 2022, ISSN 1099-4300
Editor: Multidisciplinary Digital Publishing Institute (MDPI)

Best practice standards for circular RNA research

Autores: 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.
Publicado en: NATURE METHODS, 2022, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-022-01487-2

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

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

Thermometer: a webserver to predict protein thermal stability

Autores: Mattia Miotto, Alexandros Armaos, Lorenzo Di Rienzo, Giancarlo Ruocco, Edoardo Milanetti, Gian Gaetano Tartaglia
Publicado en: Bioinformatics, 2022, ISSN 1367-4803
Editor: 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.

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

The protective role of m1A during stress-induced granulation

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

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

Autores: Shashaank N1, Somayaji M2, Miotto M3, Mosharov EV2, Makowicz EA2, Knowles DA1, Ruocco G3, Sulzer DL2
Publicado en: PNAS Nexus, Edición Volume 2, Edición 3, March 2023, 2023, ISSN 2752-6542
Editor: Oxford University Press
DOI: 10.1093/pnasnexus/pgad044

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

Autores: Fausta Desantis, Mattia Miotto, Lorenzo Di Rienzo, Edoardo Milanetti & Giancarlo Ruocco
Publicado en: Scientific Reports, Edición Article number: 12087 (2022), 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-022-16338-5

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

Autores: 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
Publicado en: Nature Communications, Edición 20, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-40105-3

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

Autores: Thomas Schwarzl; Sudeep Sahadevan; Benjamin Lang; Milad Miladi; Rolf Backofen; Wolfgang Huber; Matthias W Hentze; Gian Gaetano Tartaglia
Publicado en: Crossref, Edición 3, 2024, ISSN 0305-1048
Editor: 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

Autores: 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
Publicado en: small methods, Edición 2022 Jul;6(7), 2022, ISSN 2366-9608
Editor: Wiley
DOI: 10.1002/smtd.202200402

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

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

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

Autores: 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
Publicado en: Cell Death & Disease, Edición 11/7, 2020, ISSN 2041-4889
Editor: 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

Autores: 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.
Publicado en: Cell Death Discovery, 2021, ISSN 2058-7716
Editor: 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

Autores: Lorenzo Di Rienzo, Mattia Miotto, Fausta Desantis, Greta Grassmann, Giancarlo Ruocco, Edoardo Milanetti
Publicado en: Proteins, Edición April, 2023, 2023, ISSN 0887-3585
Editor: Wiley-Liss Inc
DOI: 10.1002/prot.26497

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

Autores: Leonardo Bo , Edoardo Milanetti 1 2, Cheng Giuseppe Chen 3, Giancarlo Ruocco 2 1, Andrea Amadei 4, Marco D'Abramo 3
Publicado en: ACS Omega, Edición 2022, 7, 16, 2022, Página(s) 13448–13454, ISSN 2470-1343
Editor: American Chemical Society
DOI: 10.1021/acsomega.1c06206

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

Autores: Alexandra Louka; Sara Bagnoli; Jakob Rupert; Esapa B; Gian Gaetano Tartaglia; Alessandro Cellerino; Annalisa Pastore; Eva Terzibasi Tozzini
Publicado en: Aging Cell ., Edición 22, 2022, ISSN 1474-9718
Editor: Blackwell Publishing Inc.
DOI: 10.1101/2021.02.04.429704

Mitochondria inter-organelle relationships in cancer protein aggregation

Autores: Ilaria Genoves, Ersilia Fornetti, Giancarlo Ruocco
Publicado en: Frontiers in Cell and Developmental Biology, Edición 2022 Dec 19;10:1062993, 2022, ISSN 2296-634X
Editor: Frontiers Media
DOI: 10.3389/fcell.2022.1062993

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

Autores: 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
Publicado en: EMBO Molecular Medicine, Edición 12/8, 2020, ISSN 1757-4676
Editor: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202012063

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

Autores: Lorenzo Di Rienzo; Mattia Miotto; Edoardo Milanetti; Giancarlo Ruocco
Publicado en: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 3002-3009 (2023), Edición 8, 2023, ISSN 2001-0370
Editor: 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

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

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

Autores: Emmanouil Xypakis; Valeria De Turis; Fabrizio Gala; Giancarlo Ruocco; Marco Leonetti
Publicado en: Optic Express, Edición 9, 2023, ISSN 1094-4087
Editor: 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

Autores: Dattilo D, Di Timoteo G, Setti A, Giuliani A, Peruzzi G, Beltran Nebot M, Centrón-Broco A, Mariani D, Mozzetta C, Bozzoni I.
Publicado en: Nature Comunication, Edición 2023 Apr 5, 2023, Página(s) 14(1):1898, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-37578-7

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

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

Modulation of circRNA Metabolism by m6A Modification

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

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

Autores: Greta Grassmann; Mattia Miotto; Fausta Desantis; Lorenzo Di Rienzo; Gian Gaetano Tartaglia; Annalisa Pastore; Giancarlo Ruocco; Michele Monti; Edoardo Milanetti
Publicado en: Chemical Reviews, Edición 3, 2024, ISSN 0009-2665
Editor: 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

Autores: D'Ambra E, Santini T, Vitiello E, D'Uva S, Silenzi V, Morlando M, Bozzoni I.
Publicado en: ISCIENCE, 2021, ISSN 2589-0042
Editor: ISCIENCE
DOI: 10.1016/j.isci.2021.103504

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

Autores: 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.
Publicado en: International Journal of Molecular Sciences, 2020, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21218227

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