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

Author(s): 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
Published in: Bioinformatics, Issue 10, 2022, ISSN 1367-4811
Publisher: Oxford Press
DOI: 10.1093/bioinformatics/btac847

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

Author(s): 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.
Published in: EMBO Journal, 2022, ISSN 0261-4189
Publisher: 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

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, Issue 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-68794-6

Phase separation drives X-chromosome inactivation.

Author(s): Cerase, A.; Calabrese, J.M. ; Tartaglia, G.G.
Published in: Nature Structural and Molecular Biology, Issue 29, 2022, Page(s) 183–185, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-021-00697-0

Microglia reactivity entails microtubule remodeling from acentrosomal to centrosomal arrays

Author(s): 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
Published in: Cell Reports, Issue 2023 Feb 13;42(2):112104, 2023, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.112104

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

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

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, Issue 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, Issue 48/17, 2020, Page(s) 9491-9504, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa681

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

Author(s): 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
Published in: Cell Reports, Issue 4, 2020, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.108548

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, Issue 48/4, 2020, Page(s) 1529-1543, ISSN 0300-5127
Publisher: Portland Press, Ltd.
DOI: 10.1042/bst20191059

Deep learning for blind structured illumination microscopy

Author(s): Emmanouil Xypakis, Giorgio Gosti, Taira Giordani, Raffaele Santagati, Giancarlo Ruocco & Marco Leonetti
Published in: Scientific Reports, Issue 8623 (2022), 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-12571-0

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, Issue 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, Issue 1, 2022, ISSN 1099-4300
Publisher: 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

Author(s): 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
Published in: Alzheimers Dement (Amst), Issue 7, 2022, ISSN 2352-8729
Publisher: 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

Author(s): 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
Published in: Scientific Reports, Issue 12,Article number: 5257 (2022), 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-09016-z

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

Author(s): 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.
Published in: MOLECULAR CELL, 2022, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2021.11.032

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

Author(s): Natalia Pediconi, Ylenia Gigante, Silvia Cama, Martina Pitea, Lorenza Mautone, Giancarlo Ruocco, Silvia Ghirga and Silvia Di Angelantonio
Published in: Frontiers in Aging Neuroscience, Issue Volume 15 - 2023, 2023, ISSN 1663-4365
Publisher: Frontiers Research Foundation
DOI: 10.3389/fnagi.2023.1110520

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

Author(s): Crua Asensio N; Rizzieri S; Cuomo A; Tartaglia GG; Zacco E
Published in: Journal of Visualized Experiments : Jove, Issue 193, 2023, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/64923

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

Author(s): Giorgio Gosti; Edoardo Milanetti; Viola Folli; Francesco de Pasquale; Marco Leonetti; Maurizio Corbetta; Giancarlo Ruocco; Stefania Della Penna
Published in: Neural Networks, Issue 1, 2024, ISSN 1879-2782
Publisher: 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

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

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

Author(s): Alfredo De Lauro , Lorenzo Di Rienzo , Mattia Miotto , Pier Paolo Olimpieri , Edoardo Milanetti , Giancarlo Ruocco
Published in: Frontiers in Molecular Biosciences, Issue Volume 9 - 2022, 2022, ISSN 2296-889X
Publisher: Frontiers Media
DOI: 10.3389/fmolb.2022.874296

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, Issue 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, Issue 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, Issue 7, 2020, ISSN 2296-889X
Publisher: 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

Author(s): Riccardo Reale , Giovanna Peruzzi , Maryamsadat Ghoreishi , Helena Stabile, Giancarlo Ruocco ORCID and Marco Leonetti
Published in: Lab on a Chip, Issue Issue 8, 2023, 2023, ISSN 1473-0197
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2lc01179d

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, Issue 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, Issue 43/2, 2021, Page(s) 2000118, ISSN 0265-9247
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/bies.202000118

High-Throughput Interactome Determination via Sulfur Anomalous Scattering

Author(s): Mattia Miotto; Edoardo Milanetti; Riccardo Mincigrucci; Claudio Masciovecchio; Giancarlo Ruocco
Published in: the journal of physical chemistry letters, Issue 18, 2024, ISSN 1948-7185
Publisher: 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

Author(s): 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
Published in: Nucleic Acids Research, Issue 16, 2022, ISSN 1362-4962
Publisher: Oxford Press
DOI: 10.1093/nar/gkac659

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

Author(s): 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
Published in: Scientific Reports, Vol 14, Iss 1, Pp 1-16 (2024), Issue 1, 2024, ISSN 2045-2322
Publisher: 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

Author(s): 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
Published in: Journal of Physical Chemistry B, Issue 12, 2024, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.3c06258

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, Issue 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, Issue 19, 2021, Page(s) 3034-3041, ISSN 2001-0370
Publisher: Computational and Structural Biotechnology Journal
DOI: 10.1016/j.csbj.2021.05.019

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

Author(s): Vandelli, Andrea; Vocino, Giovanni; Tartaglia, Gian Gaetano
Published in: Frontiers in Molecular Biosciences, Issue 19, 2022, ISSN 2296-889X
Publisher: 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

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

Probing TDP-43 condensation using an in silico designed aptamer

Author(s): 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
Published in: Nature Communications, Issue 7, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-30944-x

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

Author(s): Jonathan Fiorentino; Alexandros Armaos; Alessio Colantoni; Gian Gaetano Tartaglia
Published in: Crossref, Issue 52, 2024, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae076

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., Issue 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, Issue 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

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

Author(s): 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
Published in: Frontiers in Molecular Biosciences, Vol 10 (2023), Issue 12, 2023, ISSN 2296-889X
Publisher: Frontiers Media
DOI: 10.3389/fmolb.2023.1205919

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

Author(s): Gian Gaetano Tartaglia; Alexandros Armaos; Johanna Luige; Ulf Ørom
Published in: Crossref, Issue 15, 2024, ISSN 2041-1723
Publisher: 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

Author(s): Lorenzo Di Rienzo 1, Luca De Flaviis 2, Giancarlo Ruocco 3 2, Viola Folli 3, Edoardo Milanetti 3 2
Published in: Journal of Computer-Aided Molecular Design 36, Issue 11(2022), 2022, ISSN 1573-4951
Publisher: 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

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

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

Author(s): Alessio Colantoni; Davide Capauto; Vincenzo Alfano; Eleonora D’Ambra; Sara D’Uva; Gian Gaetano Tartaglia; Mariangela Morlando
Published in: International Journal of Molecular Sciences, Issue 1, 2023, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24043181

Electrostatic complementarity at the interface drives transient protein-protein interactions

Author(s): Greta Grassmann; Lorenzo Di Rienzo; Giorgio Gosti; Marco Leonetti; Giancarlo Ruocco; Mattia Miotto; Edoardo Milanetti
Published in: Scientific Reports, Vol 13, Iss 1, Pp 1-15 (2023), Issue 18, 2023, ISSN 2045-2322
Publisher: 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

Author(s): 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.
Published in: iScience, 2022, ISSN 2589-0042
Publisher: 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

Author(s): Monti, Michele; Fiorentino, Jonathan; Milanetti, Edoardo; Gosti, Giorgio; Tartaglia, Gian Gaetano
Published in: Entropy, Issue 24, 2022, ISSN 1099-4300
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)

Best practice standards for circular RNA research

Author(s): 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.
Published in: NATURE METHODS, 2022, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01487-2

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

Author(s): Greta Grassmann,Mattia Miotto,Lorenzo Di Rienzo,Giorgio Gosti,Giancarlo Ruocco,Edoardo Milanetti
Published in: PLOS ONE, 2022, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0266004

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

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

Author(s): Riccardo Delli Ponti; Laura Broglia; Andrea Vandelli; Alexandros Armaos; Marc Torrent Burgas; Natalia Sanchez de Groot; Gian Gaetano Tartaglia
Published in: IUBMB Life ., 2022, ISSN 1521-6551
Publisher: John Wiley & Sons
DOI: 10.1002/iub.2673

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, Issue 12/11, 2020, Page(s) 870-880, ISSN 1674-2788
Publisher: Oxford University Press
DOI: 10.1093/jmcb/mjaa023

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

Author(s): Shashaank N1, Somayaji M2, Miotto M3, Mosharov EV2, Makowicz EA2, Knowles DA1, Ruocco G3, Sulzer DL2
Published in: PNAS Nexus, Issue Volume 2, Issue 3, March 2023, 2023, ISSN 2752-6542
Publisher: Oxford University Press
DOI: 10.1093/pnasnexus/pgad044

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

Author(s): Fausta Desantis, Mattia Miotto, Lorenzo Di Rienzo, Edoardo Milanetti & Giancarlo Ruocco
Published in: Scientific Reports, Issue Article number: 12087 (2022), 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-16338-5

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

Author(s): 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
Published in: Nature Communications, Issue 20, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-40105-3

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

Author(s): Thomas Schwarzl; Sudeep Sahadevan; Benjamin Lang; Milad Miladi; Rolf Backofen; Wolfgang Huber; Matthias W Hentze; Gian Gaetano Tartaglia
Published in: Crossref, Issue 3, 2024, ISSN 0305-1048
Publisher: 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

Author(s): 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
Published in: small methods, Issue 2022 Jul;6(7), 2022, ISSN 2366-9608
Publisher: Wiley
DOI: 10.1002/smtd.202200402

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, Issue 11/7, 2020, ISSN 2041-4889
Publisher: 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

Author(s): 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.
Published in: Cell Death Discovery, 2021, ISSN 2058-7716
Publisher: 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

Author(s): Lorenzo Di Rienzo, Mattia Miotto, Fausta Desantis, Greta Grassmann, Giancarlo Ruocco, Edoardo Milanetti
Published in: Proteins, Issue April, 2023, 2023, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.26497

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

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

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

Author(s): Alexandra Louka; Sara Bagnoli; Jakob Rupert; Esapa B; Gian Gaetano Tartaglia; Alessandro Cellerino; Annalisa Pastore; Eva Terzibasi Tozzini
Published in: Aging Cell ., Issue 22, 2022, ISSN 1474-9718
Publisher: Blackwell Publishing Inc.
DOI: 10.1101/2021.02.04.429704

Mitochondria inter-organelle relationships in cancer protein aggregation

Author(s): Ilaria Genoves, Ersilia Fornetti, Giancarlo Ruocco
Published in: Frontiers in Cell and Developmental Biology, Issue 2022 Dec 19;10:1062993, 2022, ISSN 2296-634X
Publisher: Frontiers Media
DOI: 10.3389/fcell.2022.1062993

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, Issue 12/8, 2020, ISSN 1757-4676
Publisher: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202012063

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

Author(s): Lorenzo Di Rienzo; Mattia Miotto; Edoardo Milanetti; Giancarlo Ruocco
Published in: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 3002-3009 (2023), Issue 8, 2023, ISSN 2001-0370
Publisher: 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

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

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

Author(s): Emmanouil Xypakis; Valeria De Turis; Fabrizio Gala; Giancarlo Ruocco; Marco Leonetti
Published in: Optic Express, Issue 9, 2023, ISSN 1094-4087
Publisher: 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

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

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, Issue 48/20, 2020, Page(s) 11270-11283, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa864

Modulation of circRNA Metabolism by m6A Modification

Author(s): i Timoteo G, Dattilo D, Centrón-Broco A, Colantoni A, Guarnacci M, Rossi F, Incarnato D, Oliviero S, Fatica A, Morlando M, Bozzoni I.
Published in: Cell Reports, 2020, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.107641

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

Author(s): Greta Grassmann; Mattia Miotto; Fausta Desantis; Lorenzo Di Rienzo; Gian Gaetano Tartaglia; Annalisa Pastore; Giancarlo Ruocco; Michele Monti; Edoardo Milanetti
Published in: Chemical Reviews, Issue 3, 2024, ISSN 0009-2665
Publisher: 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

Author(s): D'Ambra E, Santini T, Vitiello E, D'Uva S, Silenzi V, Morlando M, Bozzoni I.
Published in: ISCIENCE, 2021, ISSN 2589-0042
Publisher: ISCIENCE
DOI: 10.1016/j.isci.2021.103504

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

Author(s): 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.
Published in: International Journal of Molecular Sciences, 2020, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21218227

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