Publications

A Model Eye for fluorescent characterization of retinal cultures and tissues

Scientific Reports volume 13, Article number: 10983 (2023)

G. Ferraro, Y. Gigante, M. Pitea, L. Mautone, G. Ruocco, S. Di Angelantonio, and M. Leonetti.

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

Comput Struct Biotechnol J. 2023; 21: 3002–3009.

L. Di Rienzo, M. Miotto, E. Milanetti, and G. Ruocco.

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

Front Mol Biosci. 2023; 10: 1332359.

G. Parisi, R. Piacentini, A. Incocciati, A. Bonamore, A. Macone, J. Rupert, E. Zacco, M. Miotto, E. Milanetti, G. G. Tartaglia, G. Ruocco, A. Boffi, and L. Di Rienzo.

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

Front. Mol. Biosci., 27 June 2023

M. Miotto; L. Di Rienzo; G. Grassmann; F. Desantis; G. Cidonio; G. Gosti; M. Leonetti; G. Ruocco; E. Milanetti

Electrostatic complementarity at the interface drives transient protein-protein interactions

Scientific Reports volume 13, Article number: 10207 (2023)

G. Grassmann, L. Di Rienzo, G. Gosti, M. Leonetti, G. Ruocco, M. Miotto, and E. Milanetti.

Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression

Comput Struct Biotechnol J. 2023; 21: 5296–5308

M. Kalia, M. Miotto, ..., G. Ruocco, E. Milanetti, R. Dobson, A. Al Chalabi, and A. Iacoangeli.

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

Nucleic Acids Research, Volume 52, Issue 6, 12 April 2024, Page e31,

J. Fiorentino, A. Armaos, A. Colantoni, G. G. Tartaglia

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

Scientific Reports volume 14, Article number: 484 (2024)

L. Martinez-Vidal, C. Testi, E. Pontecorvo, F. Pederzoli, E. Alchera, I. Locatelli, C. Venegoni, A. Spinelli, R. Lucianò, A. Salonia, A. Podestà, G. Ruocco & M. Alfano

RNA sequestration driven by amyloid formation: the alpha synuclein case

Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11466–11478

J. Rupert, M. Monti, E. Zacco, G. G. Tartaglia

Reference-less wavefront shaping in an Hopfield-like rough intensity landscape

Optics Express Vol. 31, Issue 18, pp. 28987-28998 (2023)

M. Leonetti; L. Leuzzi; G. Ruocco

Retinal Fingerprints of ALS in Patients: Ganglion Cell Apoptosis and TDP-43/p62 Misplacement.

Front Aging Neurosci. 2023; 15: 1110520

Pediconi, N.; Gigante, Y.; Cama, S.; Pitea, M.; Mautone, L.; Ruocco, G.; Ghirga, S.; Di Angelantonio, S.

Two receptor binding strategy of SARS-CoV-2 is mediated by both the N-terminal and receptor-binding spike domain

J. Phys. Chem. B 2024, 128, 2, 451–464

M. Monti, E. Milanetti, M. T. Frans, M. Miotto, L. DiRienzo, M. V. Baranov, G. Gosti, A. K. Somavarapu, M. Nagaraj, T. W. Golbeck, E. Rossing, S. J. Moons, T. J. Boltje, G. van der Bogaart,..., G. G. Tartaglia, G.

Collective behavior and self-organization in neural rosette morphogenesis

Front Cell Dev Biol. 2023; 11: 1134091.

M. Miotto, M. Rosito, M. Paoluzi, V. de Turris, V. Folli, M. Leonetti, G. Ruocco, A. Rosa, and G. Gosti.

May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions

BioEssays 2023

Negri M. L., D'Annunzio S., Vitali G., Zippo A.

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

Proteins: Structure Function and Bioinformatics 2024

F. Desantis, M. Miotto, E. Milanetti, G. Ruocco, and L. Di Rienzo.

Exploring the NANOG-TET2 interaction interface. Effects of a selected mutation and hypothesis on the clinical correlation with anemias

Front. Chem. Biol., 06 January 2025

Testi C, Piacentini R, Perrone A, Bartoli C, Leso D, Pavia D, Pistolesi E, Scipione F, Cotronea I, Adinolfi Falcone M, Ierani M, Boffi A and Di Rienzo L.

Rationalizing the effects of RNA modifications on protein interactions

Mol Ther Nucleic Acids. 2024 Nov 15;35(4):102391.

Vandelli A, Broglia L, Armaos A, Delli Ponti R, Tartaglia GG.

Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation

Nat Commun . 2024 Mar 22;15(1):2585

Luige J, Armaos A, Tartaglia GG, Ørom UAV.

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

Chem Rev . 2024 Apr 10;124(7):3932-3977

Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E.

High throughput interactome determination via sulfur anomalous scattering

J Phys Chem Lett . 2024 Apr 4;15(13):3478-3485

Miotto M, Milanetti E, Mincigrucci R, Masciovecchio C, Ruocco G.

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

Sci Rep . 2024 May 21;14(1):11533

Barolo L, Gigante Y, Mautone L, Ghirga S, Soloperto A, Giorgi A, Ghirga F, Pitea M, Incocciati A, Mura F, Ruocco G, Boffi A, Baiocco P, Di Angelantonio S.

A size-dependent division strategy accounts for leukemia cell size heterogeneity

Commun Phys 7, 248 (2024)

Miotto, M., Scalise, S., Leonetti, M. et al.

Synchronized motion of interface residues for evaluating protein–RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates

Protein Sci. 2024 Dec;33(12):e5201

Panei FP, Di Rienzo L, Zacco E, Armaos A, Tartaglia GG, Ruocco G, Milanetti E.

Jingle Cell Rock: Steering Cellular Activity With Low-Intensity Pulsed Ultrasound (LIPUS) to Engineer Functional Tissues in Regenerative Medicine

Ultrasound Med Biol. 2024 Dec;50(12):1973-1986

Marcotulli M, Barbetta A, Scarpa E, Bini F, Marinozzi F, Ruocco G, Casciola CM, Scognamiglio C, Carugo D, Cidonio G.

Stochastically Structured Illumination Microscopy: a scan-less super resolution imaging methodology

Npj Imaging. 2024;2(1):45

Fusco D, Xypakis E, Gigante Y, Mautone L, Di Angelantonio S, Ponsi G, Ruocco G, Leonetti M.

Osmolyte-Induced Protein Stability Changes Explained by Graph Theory

Comput Struct Biotechnol J. 2024 Oct 28;23:4077-4087

Miotto M, Warner N, Ruocco G, Tartaglia GG, Scherman OA, Milanetti E.

Localised therapies using 3D-printed collagen-based micro-implant for ocular indications

Macromol. Mater. Eng. 2024, 2400236

H. H. Kashkooli, A. Farokh, S. Mohammadi, M. Marcotulli,
S. Franco, R. Angelini, G. Ruocco, H. Khalili and G. Cidonio

The RNA-Binding Properties of Annexins

J Mol Biol. 2025 Feb 15;437(4):168933

Tartaglia GG, Hollås H, Håvik B, Vedeler A, Pastore A.