Toni Giorgino

Research staff

Research interests My research focuses on the application of computational models to biology and medicine, at various scales, to characterize genotype-phenotype and protein-drug interactions, making extensive use of molecular dynamics and statistical methods. My background includes statistical physics, software engineering, and high-performance computational architectures. Vitae summary I got tenured at the Italian National Research Council (IBF-CNR) in 2012. In 2009 I had been awarded a 3-year Beatriu de Pinós grant by the Generalitat de Catalunya for the in silico characterization of protein-protein and protein-drug interactions via large-scale all-atom simulations, which I developed in the Computational Biophysics Group at the University Pompeu Fabra in Barcelona (GRIB-IMIM-UPF). Before 2008 I was with the Laboratory for Biomedical Informatics ""Mario Stefanelli"" of the University of Pavia, conducting research on artificial intelligence for health-care. I have a PhD in Bioengineering and Bioinformatics (University of Pavia, 2005), and a degree in Physics (University of Pisa, 2001). I am an alumn of the Scuola Normale Superiore (Pisa, 1995).

orcid://0000-0001-6449-0596,

Contact:

- Email toni.giorgino@cnr.it
- Phone +39 02 503 14857
- Location Milano

Website:

https://www.giorginolab.it

Research interests:

- Applications of high-throughput molecular dynamics methods (Principal investigator)
- Development of statistical models in computational medicine (Principal investigator)
- Gelsolin physiopathology
- Widespread occurrence and novel functions of proteins binding Z-DNA/RNA, the left-handed helix of nucleic acids

Further collaborations:

- Prof. Jana Selent (Institut Municipal de Investigaciò Medica, Barcelona)
- Prof. Gianni De Fabritiis (Universitat Pompeu Fabra, Barcelona)
- Prof. Carlo Camilloni (Università di Milano, Milano)
- Prof. Giovanni Bussi (SISSA, Trieste)
- Dr. Andrea Mari (CNR-IN, Padova)

Financial support:

- Centro Nazionale HPC Spoke 7 - NextGenerationEU
- PROGETTO PRIN 2022 20225X2FS5
- Exscalate - Dompé Srl
- BOINC Support for High Throughput Molecular Simulations. DSB.AD003.036. Acellera Ltd.
- Analisi dati per la ricerca e caratterizzazione del rischio clinico in malattie oncoematologiche. DSB.AD003.040. Università degli Studi dell'Insubria.

Key publications:

Giorgino T, Mattioni D, Hassan A, Milani M, Mastrangelo E, Barbiroli A, et al. Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2019 Mar 1;1865(3):648–60.

Passamonti F, Giorgino T, Mora B, Guglielmelli P, Rumi E, Maffioli M, et al. A clinical-molecular prognostic model to predict survival in patients with post polycythemia vera and post essential thrombocythemia myelofibrosis. Leukemia. 2017 Dec;31(12):2726–31.

Cossu F, Sorrentino L, Fagnani E, Zaffaroni M, Milani M, Giorgino T*, Mastrangelo E*. Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly. J Chem Inf Model. 2020 Aug 21 doi:10.1021/acs.jcim.0c00518, [arXiv:2103.10915]. (* shared corresponding)

Giorgino T, (2019). PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python. Journal of Open Source Software, 4(42), 1773, doi:10.21105/joss.01773, OA

Giorgino T (2009) Computing and Visualizing Dynamic Time Warping Alignments in R: the dtw Package. Journal of Statistical Software 31(7)

Publications (24):

Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways
Aranda-García, David; Stepniewski, Tomasz Maciej; Torrens-Fontanals, Mariona; García-Recio, Adrian; Lopez-Balastegui, Marta; Medel-Lacruz, Brian; Morales-Pastor, Adrián; Peralta-García, Alejandro; Dieguez-Eceolaza, Miguel; Sotillo-Nuñez, David; Ding, Tianyi; Drabek, Matthäus; Jacquemard, Célien; Jakowiecki, Jakub; Jespers, Willem; Jiménez-Rosés, Mireia; Jun-Yu-Lim, Víctor; Nicoli, Alessandro; Orzel, Urszula; Shahraki, Aida; Tiemann, Johanna K. S.; Ledesma-Martin, Vicente; Nerín-Fonz, Francho; Suárez-Dou, Sergio; Canal, Oriol; Pándy-Szekeres, Gáspár; Mao, Jiafei; Gloriam, David E.; Kellenberger, Esther; Latek, Dorota; Guixà-González, Ramon; Gutiérrez-de-Terán, Hugo; Tikhonova, Irina G.; Hildebrand, Peter W.; Filizola, Marta; Babu, M. Madan; Di Pizio, Antonella; Filipek, Slawomir; Kolb, Peter; Cordomi, Arnau; Giorgino, Toni; Marti-Solano, Maria; Selent, Jana
NATURE COMMUNICATIONS, 16, 2025
DOI: 10.1038/s41467-025-57034-y

PLUMED Tutorials: A collaborative, community-driven learning ecosystem
Tribello, Gareth A.; Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Armstrong, Blake I.; Arsiccio, Andrea; Aureli, Simone; Ballabio, Federico; Bernetti, Mattia; Bonati, Luigi; Brookes, Samuel G. H.; Brotzakis, Z. Faidon; Capelli, Riccardo; Ceriotti, Michele; Chan, Kam-Tung; Cossio, Pilar; Dasetty, Siva; Donadio, Davide; Ensing, Bernd; Ferguson, Andrew L.; Fraux, Guillaume; Gale, Julian D.; Gervasio, Francesco Luigi; Giorgino, Toni; Herringer, Nicholas S. M.; Hocky, Glen M.; Hoff, Samuel E.; Invernizzi, Michele; Languin-Cattoën, Olivier; Leone, Vanessa; Limongelli, Vittorio; Lopez-Acevedo, Olga; Marinelli, Fabrizio; Febrer Martinez, Pedro; Masetti, Matteo; Mehdi, Shams; Michaelides, Angelos; Murtada, Mhd Hussein; Parrinello, Michele; Piaggi, Pablo M.; Pietropaolo, Adriana; Pietrucci, Fabio; Pipolo, Silvio; Pritchard, Claire; Raiteri, Paolo; Raniolo, Stefano; Rapetti, Daniele; Rizzi, Valerio; Rydzewski, Jakub; Salvalaglio, Matteo; Schran, Christoph; Seal, Aniruddha; Shayesteh Zadeh, Armin; Silva, Tomás F. D.; Spiwok, Vojtěch; Stirnemann, Guillaume; Sucerquia, Daniel; Tiwary, Pratyush; Valsson, Omar; Vendruscolo, Michele; Voth, Gregory A.; White, Andrew D.; Wu, Jiangbo
THE JOURNAL OF CHEMICAL PHYSICS, 162, 2025
DOI: 10.1063/5.0251501

A Prognostic Model to Predict Survival After 6 Months of Ruxolitinib in Patients with Myelofibrosis
Maffioli, Margherita and Mora, Barbara and Ball, Somedeb and Iurlo, Alessandra and Elli, Elena Maria and Finazzi, Maria Chiara and Polverelli, Nicola and Rumi, Elisa and Caramella, Marianna and Carraro, Maria Cristina and D'Adda, Mariella and Molteni, Alfredo and Sissa, Cinzia and Lunghi, Francesca and Vismara, Alessandro and Ubezio, Marta and Guidetti, Anna and Caberlon, Sabrina and Anghilieri, Michela and Komrokji, Rami S. and Cattaneo, Daniele and Della Porta, Matteo Giovanni and Giorgino, Toni and Bert?, Lorenza and Brociner, Marco and Kuykendall, Andrew T and Passamonti, Francesco
blood advances, 2022
DOI: 10.1182/bloodadvances.2021006889

Classification Model for the Second Extracellular Loop of Class A GPCRs
Nicoli, Alessandro and Dunkel, Andreas and Giorgino, Toni and de Graaf, Chris and Di Pizio, Antonella
journal of chemical information and modelingissn: 1549-9596american chemical society,, 2022
DOI: 10.1021/acs.jcim.1c01056

Evidence of Covid-19 lockdown effects on riverine dissolved organic matter dynamics provides a proof-of-concept for needed regulations of anthropogenic emissions
Retelletti Brogi, S.; Cossarini, G.; Bachi, G.; Balestra, C.; Camatti, E.; Casotti, R.; Checcucci, G.; Colella, S.; Evangelista, V.; Falcini, F.; Francocci, F.; Giorgino, T.; Margiotta, F.; Ribera d'Alcalà, M.; Sprovieri, M.; Vestri, S.; Santinelli, C.
SCIENCE OF THE TOTAL ENVIRONMENT, 812, 2022
DOI: 10.1016/j.scitotenv.2021.152412

SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions
Mariona Torrens-Fontanals, Alejandro Peralta-García, Carmine Talarico, Ramon Guixà-González, Toni Giorgino, Jana Selent
nucleic acids researchissn: 0305-1048oxford university press, 50, 2022
DOI: 10.1093/nar/gkab977

A novel hotspot of gelsolin instability triggers an alternative mechanism of amyloid aggregation
Bollati, Michela; Diomede, Luisa; Giorgino, Toni; Natale, Carmina; Fagnani, Elisa; Boniardi, Irene; Barbiroli, Alberto; Alemani, Rebecca; Beeg, Marten; Gobbi, Marco; Fakin, Ana; Mastrangelo, Eloise; Milani, Mario; Presciuttini, Gianluca; Gabellieri, Edi; Cioni, Patrizia; de Rosa, Matteo
computational and structural biotechnology journalissn: 2001-0370chalmers university of technology,, 19, 2021
DOI: 10.1016/j.csbj.2021.11.025

TorchMD: A Deep Learning Framework for Molecular Simulations
Doerr, Stefan and Majewski, Maciej and Pérez, Adrià and Krämer, Andreas and Clementi, Cecilia and Noe, Frank and Giorgino, Toni and De Fabritiis, Gianni
journal of chemical theory and computationissn: 1549-9618american chemical society,, 2021
DOI: 10.1021/acs.jctc.0c01343

Computational and Experimental Characterization of NF023, A Candidate Anticancer Compound Inhibiting cIAP2/TRAF2 Assembly
Federica Cossu, Luca Sorrentino, Elisa Fagnani, Mattia Zaffaroni, Mario Milani, Toni Giorgino, Eloise Mastrangelo
Journal of chemical information and modeling, 60, 2020
DOI: 10.1021/acs.jcim.0c00518

GPCRmd uncovers the dynamics of the 3D-GPCRome
Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J.K.S., Aranda-García, D., Ramírez-Anguita, J.M., Stepniewski, T.M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Medel-Lacruz, B., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J.,..
Nature Methods, 17, 2020
DOI: 10.1038/s41592-020-0884-y

The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties
Matteo de Rosa, Alberto Barbiroli, Francesco Bonì, Emanuele Scalone, Davide Mattioni, Maria A Vanoni, Marco Patrone, Michela Bollati, Eloise Mastrangelo, Toni Giorgino, Mario Milani
European biophysics journal, 49, 2020
DOI: 10.1007/s00249-019-01409-9

Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD
Giorgino T.
Journal of Open Source software, 4, 2019
DOI: 10.21105/joss.01698

Exploring the role of interdisciplinarity in physics: Success, talent and luck
Pluchino A, Burgio G, Rapisarda A, Biondo AE, Pulvirenti A, Ferro A, Giorgino T
PLoS One, 14, 2019
DOI: 10.1371/journal.pone.0218793

Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration
Wilman HR, Parisinos CA, Atabaki-Pasdar N, Kelly M, Thomas EL, Neubauer S, IMI DIRECT Consortium (Giorgino T. et al.), Mahajan A, Hingorani AD, Patel RS, Hemingway H, Franks PW, Bell JD, Banerjee R, Yaghootkar H
Journal of hepatology, 71, 2019
DOI: 10.1016/j.jhep.2019.05.032

High-resolution crystal structure of gelsolin domain 2 in complex with the physiological calcium ion
Bollati M, Scalone E, Bonì F, Mastrangelo E, Giorgino T, Milani M, de Rosa M
Biochemical and biophysical research communications, 518, 2019
DOI: 10.1016/j.bbrc.2019.08.013

Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant
Giorgino T, Mattioni D, Hassan A, Milani M, Mastrangelo E, Barbiroli A, Verhelle A, Gettemans J, Barzago MM, Diomede L, de Rosa M
Biochimica et biophysica acta. Molecular basis of disease, 1865, 2019
DOI: 10.1016/j.bbadis.2019.01.010

Promoting transparency and reproducibility in enhanced molecular simulations
Bonomi M, Bussi G, Camilloni C, Tribello GA, Banas P, Barducci A, Bernetti M, Bolhuis PG, Bottaro S, Branduardi D, Capelli R, Carloni P, Ceriotti M, Cesari A, Chen HC, Chen W, Colizzi F, De S, De La Pierre M, Donadio D, Drobot V, Ensing B, Ferguson AL
Nature methods, 16, 2019
DOI: 10.1038/s41592-019-0506-8

PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python
Giorgino T.
Journal of Open Source software, 4, 2019
DOI: 10.21105/joss.01773

Second primary malignancies in postpolycythemia vera and postessential thrombocythemia myelofibrosis: A study on 2233 patients
Mora B, Rumi E, Guglielmelli P, Barraco D, Maffioli M, Rambaldi A, Caramella M, Komrokji R, Gotlib J, Kiladjian JJ, Cervantes F, Devos T, Palandri F, De Stefano V, Ruggeri M, Silver RT, Benevolo G, Albano F, Cavalloni C, Pietra D, Barbui T, Rotunno G
Cancer Medicine, 8, 2019
DOI: 10.1002/cam4.2107

Second primary malignancies in ruxolitinib-treated myelofibrosis: real-world evidence from 219 consecutive patients
Maffioli M, Giorgino T, Mora B, Iurlo A, Elli E, Finazzi MC, Caramella M, Rumi E, Carraro MC, Polverelli N, D'Adda M, Malato S
Blood advances, 3, 2019
DOI: 10.1182/bloodadvances.2019000646

The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties
de Rosa M, Barbiroli A, Bonì F, Scalone E, Mattioni D, Vanoni MA, Patrone M, Bollati M, Mastrangelo E, Giorgino T, Milani M
European biophysics journal, 49, 2019
DOI: 10.1007/s00249-019-01409-9

How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation
Giorgino T
Computer physics communications, 228, 2018
DOI: 10.1016/j.cpc.2018.02.017

Phenotype variability of patients with post polycythemia vera and post essential thrombocythemia myelofibrosis is associated with the time to progression from polycythemia vera and essential thrombocythemia
Mora B, Giorgino T, Guglielmelli P, Rumi E, Maffioli M, Rambaldi A, Caramella M, Komrokji R, Gotlib J, Kiladjian JJ, Cervantes F, Devos T, Palandri F, De Stefano V, Ruggeri M, Silver RT, Benevolo G, Albano F, Cavalloni C, Barraco D, Pietra D, Barbui T, Ro
Leukemia research, 69, 2018
DOI: 10.1016/j.leukres.2018.04.012

Value of cytogenetic abnormalities in post-polycythemia vera and post-essential thrombocythemia myelofibrosis: a study of the MYSEC project
Mora B, Giorgino T, Guglielmelli P, Rumi E, Maffioli M, Rambaldi A, Caramella M, Komrokji R, Gotlib J, Kiladjian JJ, Cervantes F, Devos T, Palandri F, De Stefano V, Ruggeri M, Silver RT, Benevolo G, Albano F, Cavalloni C, Barraco D, Merli M, Pietra D, Cas
Haematologica, 103, 2018
DOI: 10.3324/haematol.2017.185751