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Nature biotechnology (Print), 2023
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Pharmacogenomics of GLP-1 receptor agonists: a genome-wide analysis of observational data and large randomised controlled trials
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The Lancet Diabetes and Endocrinology, 2023
DOI: 10.1016/S2213-8587(22)00340-0
Machine learning coarse-grained potentials of protein thermodynamics
Majewski, Maciej and Pérez, Adrià and Thölke, Philipp and Doerr, Stefan and Charron, Nicholas E. and Giorgino, Toni and Husic, Brooke E. and Clementi, Cecilia and Noe, Frank and De Fabritiis, Gianni
Nature communications, 2023
DOI: 10.1038/s41467-023-41343-1
Maternal immune activation leads to defective brain-blood vessels and intracerebral hemorrhages in male offspring
Rasile, Marco; Lauranzano, Eliana; Faggiani, Elisa; Ravanelli, Margherita M.; Colombo, Federico S.; Mirabella, Filippo; Corradini, Irene; Malosio, Maria L.; Borreca, Antonella; Focchi, Elisa; Pozzi, Davide; Giorgino, Toni; Barajon, Isabella; Matteoli, Michela
EMBO journal (Print), 2022
DOI: 10.15252/embj.2022111192
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 modeling, 2022
DOI: 10.1021/acs.jcim.1c01056
A Prognostic Model to Predict Survival After 6 Months of Ruxolitinib in Patients with Myelofibrosis
Maffioli Margherita, Mora Barbara, Ball Somedeb, Iurlo Alessandra, Elli Elena Maria, Finazzi Maria Chiara, Polverelli Nicola, Rumi Elisa, Caramella Marianna, Carraro Maria Cristina, D'Adda Mariella, Molteni Alfredo, Sissa Cinzia, Lunghi Francesca, Vismara Alessandro, Ubezio Marta, Guidetti Anna, Caberlon Sabrina, Anghilieri Michela, Komrokji Rami S., Cattaneo Daniele, Della Porta Matteo Giovanni, Giorgino Toni, Bertù Lorenza, Brociner Marco, Kuykendall Andrew T and Passamonti Francesco
Blood advances, 2022
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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 research, 2022
DOI: 10.1093/nar/gkab977
Evidence of Covid-19 lockdown effects on riverine dissolved organic matter dynamics provides a proof-of-concept for needed regulations of anthropogenic emissions
Brogi S. Retelletti, Cossarini G., Bachi G., Balestra C., Camatti E., Casotti R., Checcucci G., Colella S., Evangelista V., Falcini F., Francocci F., Giorgino T., Margiotta F., D'Alcala M. Ribera, Sprovieri M., Vestri S. and Santinelli C.
Science of the total environment, 2022
DOI: 10.1016/j.scitotenv.2021.152412
TorchMD: A Deep Learning Framework for Molecular Simulations
Doerr Stefan; Majewski Maciej; Pérez Adrià; Krämer Andreas; Clementi Cecilia; Noe Frank; Giorgino Toni; De Fabritiis Gianni.
Journal of chemical theory and computation, 2021
DOI: 10.1021/acs.jctc.0c01343
Evidence of Covid-19 lockdown effects on riverine dissolved organic matter dynamics provides a proof-of-concept for needed regulations of anthropogenic emissions
Brogi, S. Retelletti; Cossarini, G.; Bachi, G.; Balestra, C.; Camatti, E.; Casotti, R.; Checcucci, G.; Colella, S.; Evangelista, V.; Falcini, F.; Francocci, F.; Giorgino, T.; Margiotta, F.; d'Alcala, M. Ribera; Sprovieri, M.; Vestri, S.; Santinelli, C.
Science of the total environment, 2021
DOI: 10.1016/j.scitotenv.2021.152412
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 Journal, 2021
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GPCRmd uncovers the dynamics of the 3D-GPCRome
Rodríguez-Espigares Ismael; Torrens-Fontanals Mariona; Tiemann Johanna K.S.; Aranda-García David; Ramírez-Anguita Juan Manuel; Stepniewski Tomasz Maciej; Worp Nathalie; Varela-Rial Alejandro; Morales-Pastor Adrián; Medel-Lacruz Brian; Pándy-Szekeres Gáspár; Mayol Eduardo; Giorgino Toni; Carlsson Jens; Deupi Xavier; Filipek Slawomir; Filizola Marta; Gómez-Tamayo José Carlos; Gonzalez Angel; Gutiérrez-de-Terán Hugo; Jiménez-Rosés Mireia; Jespers Willem; Kapla Jon; Khelashvili George; Kolb Peter; Latek Dorota; Marti-Solano Maria; Matricon Pierre; Matsoukas Minos Timotheos; Miszta Przemyslaw; Olivella Mireia; Perez-Benito Laura; Provasi Davide; Ríos Santiago; R. Torrecillas Iván; Sallander Jessica; Sztyler Agnieszka; Vasile Silvana; Weinstein Harel; Zachariae Ulrich; Hildebrand Peter W.; De Fabritiis Gianni; Sanz Ferran; Gloriam David E.; Cordomi Arnau; Guixà-González Ramon; Selent Jana
Nature methods (Online), 2020
DOI: 10.1038/s41592-020-0884-y
A reference map of potential determinants for the human serum metabolome
Bar, Noam; Korem, Tal; Weissbrod, Omer; Zeevi, David; Rothschild, Daphna; Leviatan, Sigal; Kosower, Noa; Lotan-Pompan, Maya; Weinberger, Adina; Le Roy, Caroline I.; Menni, Cristina; Visconti, Alessia; Falchi, Mario; Spector, Tim D.; The IMI DIRECT consortium: Henrik Vestergaard, Manimozhiyan Arumugam, Torben Hansen, Kristine Allin, Tue Hansen, Mun-Gwan Hong, Jochen Schwenk, Ragna Haussler, Matilda Dale, Toni Giorgino, Marianne Rodriquez, Mandy Perry, Rachel Nice, Timothy McDonald, Andrew Hattersley, Angus Jones, Ulrike Graefe-Mody, Patrick Baum, Rolf Grempler, Cecilia Engel Thomas, Federico De Masi, Caroline Anna Brorsson, Gianluca Mazzoni, Rosa Allesøe, Simon Rasmussen, Valborg Gudmundsdóttir, Agnes Martine Nielsen, Karina Banasik, Konstantinos Tsirigos, Birgitte Nilsson, Helle Pedersen, Søren Brunak, Tugce Karaderi, Agnete Troen Lundgaard, Joachim Johansen, Ramneek Gupta, Peter Wad Sackett, Joachim Tillner, Thorsten Lehr, Nina Scherer, Christiane Dings, Iryna Sihinevich, Heather Loftus, Louise Cabrelli, Donna McEvoy, Andrea Mari, Roberto Bizzotto, Andrea Tura, Leen 't Hart, Koen Dekkers, Nienke van Leeuwen, Roderick Slieker, Femke Rutters, Joline Beulens, Giel Nijpels, Anitra Koopman, Sabine van Oort, Lenka Groeneveld, Leif Groop, Petra Elders, Ana Viñuela, Anna Ramisch, Emmanouil Dermitzakis, Beate Ehrhardt, Christopher Jennison, Philippe Froguel, Mickaël Canouil, Amélie Boneford, Ian McVittie, Dianne Wake, Francesca Frau, Hans-Henrik Staerfeldt, Kofi Adragni, Melissa Thomas, Han Wu, Imre Pavo, Birgit Steckel-Hamann, Henrik Thomsen, Giuseppe Nicola Giordano, Hugo Fitipaldi, Martin Ridderstråle, Azra Kurbasic, Naeimeh Atabaki Pasdar, Hugo Pomares-Millan, Pascal Mutie, Robert Koivula, Nicky McRobert, Mark McCarthy, Agata Wesolowska-Andersen, Anubha Mahajan, Moustafa Abdalla, Juan Fernandez, Reinhard Holl, Alison Heggie, Harshal Deshmukh, Anita Hennige, Susanna Bianzano, Barbara Thorand, Sapna Sharma, Harald Grallert, Jonathan Adam, Martina Troll, Andreas Fritsche, Anita Hill, Claire Thorne, Michelle Hudson, Teemu Kuulasmaa, Jagadish Vangipurapu, Markku Laakso, Henna Cederberg, Tarja Kokkola, Yunlong Jiao, Stephen Gough, Neil Robertson, Helene Verkindt, Violeta Raverdi, Robert Caiazzo, Francois Pattou, Margaret White, Louise Donnelly, Andrew Brown, Colin Palmer, David Davtian, Adem Dawed, Ian Forgie, Ewan Pearson, Hartmut Ruetten, Petra Musholt, Jimmy Bell, Elizabeth Louise Thomas, Brandon Whitcher, Mark Haid, Claudia Nicolay, Miranda Mourby, Jane Kaye, Nisha Shah, Harriet Teare, Gary Frost, Bernd Jablonka, Mathias Uhlen, Rebeca Eriksen, Josef Vogt, Avirup Dutta, Anna Jonsson, Line Engelbrechtsen, Annemette Forman, Nadja Sondertoft, Nathalie de Preville, Tania Baltauss, Mark Walker, Johann Gassenhuber, Maria Klintenberg, Margit Bergstrom, Jorge Ferrer; Adamski, Jerzy; Franks, Paul W.; Pedersen, Oluf; Segal, Eran
Nature (Lond.), 2020
DOI: 10.1038/s41586-020-2896-2
The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties
De Rosa Matteo; Barbiroli Alberto; Bonì Francesco; Scalone Emanuele; Mattioni Davide; Vanoni Maria A.; Patrone Marco; Bollati Michela; Mastrangelo Eloise; Giorgino Toni; Milani Mario
European biophysics journal, 2020
DOI: 10.1007/s00249-019-01409-9
Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly
Cossu Federica; Sorrentino Luca; Fagnani Elisa; Zaffaroni Mattia; Milani Mario; Giorgino Toni; Mastrangelo Eloise
Journal of chemical information and modeling (Online), 2020
DOI: 10.1021/acs.jcim.0c00518
Different mechanisms of GIP and GLP-1 action explain their different therapeutic efficacy in type 2 diabetes
Grespan, Eleonora ; Giorgino, Toni; Natali, Andrea; Ferrannini, Ele; Mari, Andrea
Metabolism, clinical and experimental (Print), 2020
DOI: 10.1016/j.metabol.2020.154415
Exploring the role of interdisciplinarity in physics: Success, talent and luck
Pluchino Alessandro; Burgio Giulio; Rapisarda Andrea; Biondo Alessio Emanuele; Pulvirenti Alfredo; Ferro Alfredo; Giorgino Toni
PloS one, 2019
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Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration
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Journal of hepatology (Print), 2019
DOI: 10.1016/j.jhep.2019.05.032
Second primary malignancies in postpolycythemia vera and postessential thrombocythemia myelofibrosis: A study on 2233 patients
Mora Barbara; Rumi Elisa; Guglielmelli Paola; Barraco Daniela; Maffioli Margherita; Rambaldi Alessandro; Caramella Marianna; Komrokji Rami; Gotlib Jason; Kiladjian Jean Jacques; Cervantes Francisco; Devos Timothy; Palandri Francesca; De Stefano Valerio; Ruggeri Marco; Silver Richard T.; Benevolo Giulia; Albano Francesco; Cavalloni Chiara; Pietra Daniela; Barbui Tiziano; Rotunno Giada; Cazzola Mario; Vannucchi Alessandro Maria; Giorgino Toni and Passamonti Francesco
Cancer Medicine, 2019
DOI: 10.1002/cam4.2107
Promoting transparency and reproducibility in enhanced molecular simulations
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Nature methods (Online), 2019
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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, 2019
DOI: 10.1016/j.bbadis.2019.01.010
Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD
Toni Giorgino
Journal of open source software On line, 2019
DOI: 10.21105/joss.01698
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 (Print), 2019
DOI: 10.1016/j.bbrc.2019.08.013
PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python
Toni Giorgino
Journal of open source software On line, 2019
DOI: 10.21105/joss.01773
Second primary malignancies in ruxolitinib-treated myelofibrosis: real-world evidence from 219 consecutive patients
Margherita Maffioli; Toni Giorgino; Barbara Mora; Alessandra Iurlo; Elena Elli; Maria Chiara Finazzi; Marianna Caramella; Elisa Rumi; Maria Cristina Carraro; Nicola Polverelli; Mariella D'Adda; Simona Malato; Marianna Rossi; Alfredo Molteni; Alessandro Vismara; Cinzia Sissa; Francesco Spina; Michela Anghilieri; Daniele Cattaneo; Rossella Renso; Marta Bellini; Maria Luisa Pioltelli; Chiara Cavalloni; Daniela Barraco; Raffaella Accetta; Lorenza Bert`u; Matteo Giovanni Della Porta and Francesco Passamonti
Blood advances, 2019
DOI: 10.1182/bloodadvances.2019000646
Synthesis, molecular modelling studies and biological evaluation of new oxoeoicosanoid receptor 1 agonists
Tomasz Maciej Stepniewski and Mariona Torrens-Fontanals and Ismael Rodriguez-Espigares and Toni Giorgino and Karoline G. Primdahl and Anders Vik and Yngve Stenstrom and Jana Selent and Trond Vidar Hansen
Bioorganic & medicinal chemistry (Print), 2018
DOI: 10.1016/j.bmc.2018.05.036
How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation
Giorgino T
Computer physics communications, 2018
DOI: 10.1016/j.cpc.2018.02.017
Defective amplifying pathway of ?-cell secretory response to glucose in type 2 diabetes: Integrated modeling of in vitro and in vivo evidence
Grespan, Eleonora; Giorgino, Toni; Arslanian, Silva; Arslanian, Silva; Natali, Andrea; Ferrannini, Ele; Mari, Andrea
Diabetes (N.Y.N.Y.), 2018
DOI: 10.2337/db17-1039
High-throughput automated preparation and simulation of membrane proteins with HTMD
Doerr, S.; Giorgino, T.; Martinez-Rosell, G.; Damas, JM.; De Fabritiis, G.
Journal of chemical theory and computation, 2017
DOI: 10.1021/acs.jctc.7b00480
Driver mutations' effect in secondary myelofibrosis: An international multicenter study based on 781 patients
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Leukemia, 2017
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Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale.
Martinez-Rosell, Gerard; Giorgino, Toni; Harvey, Matt J; de Fabritiis, Gianni
Current topics in medicinal chemistry (Print), 2017
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METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations
Giorgino, T.; Laio, A.; Rodriguez, A.
Computer physics communications, 2017
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A clinical-molecular prognostic model to predict survival in patients with post polycythemia vera and post essential thrombocythemia myelofibrosis
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Leukemia (Basingstoke, Online), 2017
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PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations
Gerard Martinez-Rosell, Toni Giorgino, and Gianni De Fabritiis
Journal of chemical information and modeling, 2017
DOI: 10.1021/acs.jcim.7b00190
Amyloid-beta 1-24 C-terminal truncated fragment promotes amyloid-beta 1-42 aggregate formation in the healthy brain
Mazzitelli S.; Filipello F.; Rasile M.; Lauranzano E.; Starvaggi-Cucuzza C.; Tamborini M.; Pozzi D.; Barajon I.; Giorgino T.; Natalello A.; Matteoli M.
Acta Neuropathologica Communications, 2016
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Pharmacometrics Markup Language (PharmML): Opening new perspectives for model exchange in drug development
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CPT: Pharmacometrics & Systems Pharmacology, 2015
DOI: 10.1002/psp4.57
Impact of allogeneic stem cell transplantation on survival of patients less than 65 years of age with primary myelofibrosis
Kroger, N.; Giorgino, T.; Scott, B.L.; Ditschkowski, M.; Alchalby, H.; Cervantes, F.; Vannucchi, A.; Cazzola, M.; Morra, E.; Zabelina, T.; Maffioli, M.; Pereira, A.; Beelen, D.; Deeg, H.J.; Passamonti, F.
Blood, 2015
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PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts
Giorgino, T.
Computer physics communications, 2014
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MEMBPLUGIN: studying membrane complexity in VMD
Guixà-González, R.;Rodriguez-Espigares, I.;Ramírez-Anguita, J.M.;Carrió-Gaspar, P.;Martinez-Seara, H.;Giorgino, T.;Selent, J.
Bioinformatics (Oxf., Print), 2014
DOI: 10.1093/bioinformatics/btu037
Looking for CALR mutations in familial myeloproliferative neoplasms
Maffioli, M.;Genoni, A.;Caramazza, D.;Mora, B.;Bussini, A.;Merli, M.;Giorgino, T.;Casalone, R.;Passamonti, F.,
Leukemia, 2014
DOI: 10.1038/leu.2014.33
Computing 1-D atomic densities in macromolecular simulations: the Density Profile tool for VMD
Giorgino, T.
Computer physics communications, 2014
DOI: 10.1016/j.cpc.2013.08.022
Membrane lipids are key-modulators of the endocannabinoid-hydrolase FAAH
Dainese, E.;De Fabritiis, G.;Sabatucci, A.;Oddi, S.;Angelucci, C.A.;Di Pancrazio, C.;Giorgino, T.;Stanley, N.;Del Carlo, M.;Cravatt, B.;Maccarrone, M.
Biochemical journal (Online), 2013
DOI: 10.1042/BJ20130960
Identification of slow molecular order parameters for Markov model construction
Pérez-Hernández, G.; Paul, F.; Giorgino, T.; De Fabritiis, G.; Noe, F.
The Journal of chemical physics, 2013
DOI: 10.1063/1.4811489
Visualizing the Induced Binding of SH2-Phosphopeptide
Giorgino, T.;Buch, I.;de Fabritiis, G.
Journal of chemical theory and computation, 2012
DOI: 10.1021/ct300003f
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Buch, I.; Giorgino, T.; De Fabritiis, G.
Proceedings of the National Academy of Sciences of the United States of America, 2011
DOI: 10.1073/pnas.1103547108
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
Giorgino, T,: De Fabritiis, G.
Journal of chemical theory and computation, 2011
DOI: 10.1021/ct100707s
The Virtual Physiological Human TOOLKIT
Cooper, J.; Cervenansky, F.; De Fabritiis, G.; Fenner, J.; Friboulet, D.; Giorgino, T.; Manos, S.; Martelli, Y.; Villà-Freixa, J.; Zasada, S.; Lloyd, S.; McCormack, K.; Coveney, P. V.
Philosophical transactions - Royal Society. Mathematical, Physical and engineering sciences (Print), 2010
DOI: 10.1098/rsta.2010.0144
Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations
Giorgino, T.; Harvey, M.J.; De Fabritiis, G.
Computer physics communications, 2010
DOI: 10.1016/j.cpc.2010.04.007
High-throughput all-atom molecular dynamics simulations using distributed computing
Buch, I.; Harvey, MJ.; Giorgino, T.; Anderson, DP.; De Fabritiis, G.
Journal of chemical information and modeling, 2010
DOI: 10.1021/ci900455r
Wireless Support to Post-Stroke Rehabilitation: MyHeart's Neurological Rehabilitation Concept
Giorgino, T.; Tormene, P.; Maggioni, G.; Pistarini, C.; Quaglini, S.
IEEE transactions on information technology in biomedicine, 2009
DOI: 10.1109/TITB.2009.2028020
Computing and Visualizing Dynamic Time Warping Alignments in R: the dtw Package
Giorgino, T.
Journal of statistical software, 2009
Matching incomplete time series with dynamic time warping: an algorithm and an application to post-stroke rehabilitation
Tormene, P.; Giorgino, T.; Quaglini, S.; Stefanelli, M.
Artificial intelligence in medicine (Print), 2009
DOI: 10.1016/j.artmed.2008.11.007
Assessment of sensorized garments as a flexible support to self-administered post-stroke physical rehabilitation
Giorgino, T.; Tormene, P.; Maggioni, G.; Capozzi, D.; Quaglini, S.; Pistarini, C.
European Journal of Physical and Rehabilitation Medicine (Testo stamp.), 2009
Adaptable dialog architecture and runtime engine (AdaRTE): a framework for rapid prototyping of health dialog systems.
Rojas-Barahona, LM.; Giorgino, T.
International journal of medical informatics, 2009
DOI: 10.1016/j.ijmedinf.2008.07.017
Sensor evaluation for wearable strain gauges in neurological rehabilitation
Giorgino, T.; Tormene, P.; Lorussi, F.; Rossi, DD.; Quaglini, S.
IEEE transactions on neural systems and rehabilitation engineering, 2009
DOI: 10.1109/TNSRE.2009.2019584
An automated voice response system for anticoagulant therapy management
Quaglini, S.; Giorgino, T.; Rojas-Barahona, L.M.; Caff, E.; Vito, M.D.E.;Persico, A.;Cavallini, A.
Studies in health technology and informatics (Print), 2009
DOI: 10.3233/978-1-60750-044-5-453
Health dialog systems for patients and consumers
Bickmore, T.; Giorgino, T.
Journal of biomedical informatics, 2006
DOI: 10.1016/j.jbi.2005.12.004
Special issue on dialog systems for health communication (guest editorial).
Bickmore, T.; Giorgino, T.; Green, N.; Picard, R.
Journal of biomedical informatics, 2006
DOI: 10.1016/j.jbi.2006.02.002
Automated spoken dialogue system for hypertensive patient home management
Giorgino, T.; Azzini, I.; Rognoni, C.; Quaglini, S.; Stefanelli, M.; Gretter, R.; Falavigna, D.
International journal of medical informatics, 2005
DOI: 10.1016/j.ijmedinf.2004.04.026
New frontiers of telemedicine systems for chronic patients monitoring: Adaptive systems and multi-access service
Bellazzi, R.; Giorgino, T.; Azzini, I.; Larizza, C.; Quaglini, S.; Hernando, E.
Measurement and control (Lond., 1968), 2004
DOI: 10.1177/002029400403700502
APE computers--past, present and future
Bodin, F.; Boucaud, Ph.; Cabibbo, N. Cascino, G.; Calvayrac, F.; Della Morte, M.; Del Re, A.; De Pietri, R.; Deriso, P.; Di Carlo, F.; Di Renzo, F.; Errico, W.; Frezzotti, R.; Gensch, U.; Giorgino, T.; Guagnelli, M.; Hervé, N.; Jansen, K.; Kaldass, H.; Lonardo, A.; Lukyanov, M.; Magazzú, G.; Micheli, J.; Morénas, V.; Mori, L.; Palombi, F.; Paschedag, N.; Pech, J.; Péne, O.; Petronzio, R.; Pleiter, D.; Rapuano, F.; Rossetti, D.; Roiesnel, C.; Sartori, L.; Simma, H.; Schifano, F.; Tripiccione, R.; Vicini, P.; Wegner, W.
Computer physics communications, 2002
DOI: 10.1016/S0010-4655(02)00314-4
Status of APEmille
Bartoloni, A.; Boucaud, P.; Cabibbo, N.; Calvayrac, C.; Della Morte, A.; Del Pietri, R.; De Riso, P.; Di Carlo, F.; Di Renzo, F.; Errico, W.; Frezzotti, R.; Giorgino, T.; Heitger, J.; Lonardo, A.; Loukianov, M.; Magazzú, G.; Micheli, J.; Morenas, V.; Paschedag, N.; Péne, O.; Petronzio, R.; Pleiter, D.; Rapuano, F.; Rolf, J.; Rossetti, D.; Sartori, L.; Simma, H.; Schifano, F.; Torelli, M.; Tripiccione, R.; Vicini, P.; Wegner, P.
Nuclear physics. B, Proceedings supplement (Print), 2002
DOI: 10.1016/S0920-5632(01)01922-3
The apeNEXT project
Bodin, F.; Boucaud, P.; Cabibbo, N.; Calvayrac, F.; Della Morte, M.;De Pietri, R.; De Riso, P.; Di Carlo, F.; Di Renzo, F.; Errico, W.; Frezzotti, R.; Gensch, U.; Giorgino, T.; Guagnelli, M.; Hervé, N.; Kaldass, H.; Lonardo, A.; Lukyanov, M.; Magazzú, G.; Micheli, J.; Morénas, V.; Mori, L.; Palombi, F.; Paschedag, N.; Péne, O.; Petronzio, R.; Pleiter, D.; Rapuano, F.; Rossetti, D.; Sartori, L.; Simma, H.; Schifano, F.; Tripiccione, R.; Vicini, P.
Nuclear physics. B, Proceedings supplement (Print), 2002
DOI: 10.1016/S0920-5632(01)01656-5
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:
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 (63):
Discovery of drug-omics associations in type 2 diabetes with generative deep-learning modelsAllesøe, Rosa Lundbye; Lundgaard, Agnete Troen; Hernández Medina, Ricardo; Aguayo-Orozco, Alejandro; Johansen, Joachim; Nissen, Jakob Nybo; Brorsson, Caroline; Mazzoni, Gianluca; Niu, Lili; Biel, Jorge Hernansanz; Brasas, Valentas; Webel, Henry; Benros, Michael Eriksen; Pedersen, Anders Gorm; Chmura, Piotr Jaroslaw; Jacobsen, Ulrik Plesner; Mari, Andrea; Koivula, Robert; Mahajan, Anubha; Vinuela, Ana; Tajes, Juan Fernandez; Sharma, Sapna; Haid, Mark; Hong, Mun Gwan; Musholt, Petra B.; De Masi, Federico; Vogt, Josef; Pedersen, Helle Krogh; Gudmundsdottir, Valborg; Jones, Angus; Kennedy, Gwen; Bell, Jimmy; Thomas, E. Louise; Frost, Gary; Thomsen, Henrik; Hansen, Elizaveta; Hansen, Tue Haldor; Vestergaard, Henrik; Muilwijk, Mirthe; Blom, Marieke T.; 't Hart, Leen M.; Pattou, Francois; Raverdy, Violeta; Brage, Soren; Kokkola, Tarja; Heggie, Alison; McEvoy, Donna; Mourby, Miranda; Kaye, Jane; Hattersley, Andrew; McDonald, Timothy; Ridderstråle, Martin; Walker, Mark; Forgie, Ian; Giordano, Giuseppe N.; Pavo, Imre; Ruetten, Hartmut; Pedersen, Oluf; Hansen, Torben; Dermitzakis, Emmanouil; Franks, Paul W.; Schwenk, Jochen M.; Adamski, Jerzy; McCarthy, Mark I.; Pearson, Ewan; Banasik, Karina; Rasmussen, Simon; Brunak, Søren; Froguel, Philippe; Thomas, Cecilia Engel; Haussler, Ragna; Beulens, Joline; Rutters, Femke; Nijpels, Giel; van Oort, Sabine; Groeneveld, Lenka; Elders, Petra; Giorgino, Toni; Rodriquez, Marianne; Nice, Rachel; Perry, Mandy; Bianzano, Susanna; Graefe-Mody, Ulrike; Hennige, Anita; Grempler, Rolf; Baum, Patrick; Stærfeldt, Hans Henrik; Shah, Nisha; Teare, Harriet; Ehrhardt, Beate; Tillner, Joachim; Dings, Christiane; Lehr, Thorsten; Scherer, Nina; Sihinevich, Iryna; Cabrelli, Louise; Loftus, Heather; Bizzotto, Roberto; Tura, Andrea; Dekkers, Koen
Nature biotechnology (Print), 2023
DOI: 10.1038/s41587-022-01520-x
Pharmacogenomics of GLP-1 receptor agonists: a genome-wide analysis of observational data and large randomised controlled trials
Dawed, Adem Y.; Mari, Andrea; Brown, Andrew; McDonald, Timothy J.; Li, Lin; Wang, Shuaicheng; Hong, Mun Gwan; Sharma, Sapna; Robertson, Neil R.; Mahajan, Anubha; Wang, Xuan; Walker, Mark; Gough, Stephen; Hart, Leen M.'t; Zhou, Kaixin; Forgie, Ian; Ruetten, Hartmut; Pavo, Imre; Bhatnagar, Pallav; Jones, Angus G.; Pearson, Ewan R.; 't Hart, L. M.; Abdalla, M.; Adam, J.; Adamski, J.; Adragni, K.; Allin, K. H.; Arumugam, M.; Atabaki Pasdar, N.; Baltauss, T.; Banasik, K. B.; Baum, P.; Bell, J. D.; Bergstrom, M.; Beulens, J. W.; Bianzano, S.; Bizzotto, R.; Bonneford, A.; Brorsson, C. A.B.; Brown, A. A.; Brunak, S. B.; Cabrelli, L.; Caiazzo, R.; Canouil, M.; Dale, M.; Davtian, D.; Dawed, Adem Y.; De Masi, F. M.; de Preville, N.; Dekkers, K. F.; Dermitzakis, E. T.; Deshmukh, H. A.; Dings, C.; Donnelly, L.; Dutta, A.; Ehrhardt, B.; Elders, P. J.M.; Engel Thomas, C. E.T.; Engelbrechtsen, L.; Eriksen, R. G.; Eriksen, R. E.; Fan, Y.; Fernandez, J.; Ferrer, J.; Fitipaldi, H.; Forgie, Ian; Forman, A.; Franks, P. W.; Frau, F.; Fritsche, A.; Froguel, P.; Frost, G.; Gassenhuber, J.; Giordano, G. N.; Giorgino, T.; Gough, S.; Graefe-Mody, U.; Grallert, H.; Grempler, R.; Groeneveld, L.; Groop, L.; Gudmundsdóttir, V. G.; Gupta, R. G.; Haid, M.; Hansen, T.; Hansen, T. H.; Hattersley, A. T.; Haussler, R. S.; Heggie, A. J.; Hennige, A. M.; Hill, A. V.; Holl, R. W.; Hong, M. G.; Hudson, M.; Jablonka, B.; Jennison, C.; Jiao, J.; Johansen, J. J.; Jones, A. G.; Jonsson, A.
The Lancet Diabetes and Endocrinology, 2023
DOI: 10.1016/S2213-8587(22)00340-0
Machine learning coarse-grained potentials of protein thermodynamics
Majewski, Maciej and Pérez, Adrià and Thölke, Philipp and Doerr, Stefan and Charron, Nicholas E. and Giorgino, Toni and Husic, Brooke E. and Clementi, Cecilia and Noe, Frank and De Fabritiis, Gianni
Nature communications, 2023
DOI: 10.1038/s41467-023-41343-1
Maternal immune activation leads to defective brain-blood vessels and intracerebral hemorrhages in male offspring
Rasile, Marco; Lauranzano, Eliana; Faggiani, Elisa; Ravanelli, Margherita M.; Colombo, Federico S.; Mirabella, Filippo; Corradini, Irene; Malosio, Maria L.; Borreca, Antonella; Focchi, Elisa; Pozzi, Davide; Giorgino, Toni; Barajon, Isabella; Matteoli, Michela
EMBO journal (Print), 2022
DOI: 10.15252/embj.2022111192
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 modeling, 2022
DOI: 10.1021/acs.jcim.1c01056
A Prognostic Model to Predict Survival After 6 Months of Ruxolitinib in Patients with Myelofibrosis
Maffioli Margherita, Mora Barbara, Ball Somedeb, Iurlo Alessandra, Elli Elena Maria, Finazzi Maria Chiara, Polverelli Nicola, Rumi Elisa, Caramella Marianna, Carraro Maria Cristina, D'Adda Mariella, Molteni Alfredo, Sissa Cinzia, Lunghi Francesca, Vismara Alessandro, Ubezio Marta, Guidetti Anna, Caberlon Sabrina, Anghilieri Michela, Komrokji Rami S., Cattaneo Daniele, Della Porta Matteo Giovanni, Giorgino Toni, Bertù Lorenza, Brociner Marco, Kuykendall Andrew T and Passamonti Francesco
Blood advances, 2022
DOI: 10.1182/bloodadvances.2021006889
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 research, 2022
DOI: 10.1093/nar/gkab977
Evidence of Covid-19 lockdown effects on riverine dissolved organic matter dynamics provides a proof-of-concept for needed regulations of anthropogenic emissions
Brogi S. Retelletti, Cossarini G., Bachi G., Balestra C., Camatti E., Casotti R., Checcucci G., Colella S., Evangelista V., Falcini F., Francocci F., Giorgino T., Margiotta F., D'Alcala M. Ribera, Sprovieri M., Vestri S. and Santinelli C.
Science of the total environment, 2022
DOI: 10.1016/j.scitotenv.2021.152412
TorchMD: A Deep Learning Framework for Molecular Simulations
Doerr Stefan; Majewski Maciej; Pérez Adrià; Krämer Andreas; Clementi Cecilia; Noe Frank; Giorgino Toni; De Fabritiis Gianni.
Journal of chemical theory and computation, 2021
DOI: 10.1021/acs.jctc.0c01343
Evidence of Covid-19 lockdown effects on riverine dissolved organic matter dynamics provides a proof-of-concept for needed regulations of anthropogenic emissions
Brogi, S. Retelletti; Cossarini, G.; Bachi, G.; Balestra, C.; Camatti, E.; Casotti, R.; Checcucci, G.; Colella, S.; Evangelista, V.; Falcini, F.; Francocci, F.; Giorgino, T.; Margiotta, F.; d'Alcala, M. Ribera; Sprovieri, M.; Vestri, S.; Santinelli, C.
Science of the total environment, 2021
DOI: 10.1016/j.scitotenv.2021.152412
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 Journal, 2021
DOI: 10.1016/j.csbj.2021.11.025
GPCRmd uncovers the dynamics of the 3D-GPCRome
Rodríguez-Espigares Ismael; Torrens-Fontanals Mariona; Tiemann Johanna K.S.; Aranda-García David; Ramírez-Anguita Juan Manuel; Stepniewski Tomasz Maciej; Worp Nathalie; Varela-Rial Alejandro; Morales-Pastor Adrián; Medel-Lacruz Brian; Pándy-Szekeres Gáspár; Mayol Eduardo; Giorgino Toni; Carlsson Jens; Deupi Xavier; Filipek Slawomir; Filizola Marta; Gómez-Tamayo José Carlos; Gonzalez Angel; Gutiérrez-de-Terán Hugo; Jiménez-Rosés Mireia; Jespers Willem; Kapla Jon; Khelashvili George; Kolb Peter; Latek Dorota; Marti-Solano Maria; Matricon Pierre; Matsoukas Minos Timotheos; Miszta Przemyslaw; Olivella Mireia; Perez-Benito Laura; Provasi Davide; Ríos Santiago; R. Torrecillas Iván; Sallander Jessica; Sztyler Agnieszka; Vasile Silvana; Weinstein Harel; Zachariae Ulrich; Hildebrand Peter W.; De Fabritiis Gianni; Sanz Ferran; Gloriam David E.; Cordomi Arnau; Guixà-González Ramon; Selent Jana
Nature methods (Online), 2020
DOI: 10.1038/s41592-020-0884-y
A reference map of potential determinants for the human serum metabolome
Bar, Noam; Korem, Tal; Weissbrod, Omer; Zeevi, David; Rothschild, Daphna; Leviatan, Sigal; Kosower, Noa; Lotan-Pompan, Maya; Weinberger, Adina; Le Roy, Caroline I.; Menni, Cristina; Visconti, Alessia; Falchi, Mario; Spector, Tim D.; The IMI DIRECT consortium: Henrik Vestergaard, Manimozhiyan Arumugam, Torben Hansen, Kristine Allin, Tue Hansen, Mun-Gwan Hong, Jochen Schwenk, Ragna Haussler, Matilda Dale, Toni Giorgino, Marianne Rodriquez, Mandy Perry, Rachel Nice, Timothy McDonald, Andrew Hattersley, Angus Jones, Ulrike Graefe-Mody, Patrick Baum, Rolf Grempler, Cecilia Engel Thomas, Federico De Masi, Caroline Anna Brorsson, Gianluca Mazzoni, Rosa Allesøe, Simon Rasmussen, Valborg Gudmundsdóttir, Agnes Martine Nielsen, Karina Banasik, Konstantinos Tsirigos, Birgitte Nilsson, Helle Pedersen, Søren Brunak, Tugce Karaderi, Agnete Troen Lundgaard, Joachim Johansen, Ramneek Gupta, Peter Wad Sackett, Joachim Tillner, Thorsten Lehr, Nina Scherer, Christiane Dings, Iryna Sihinevich, Heather Loftus, Louise Cabrelli, Donna McEvoy, Andrea Mari, Roberto Bizzotto, Andrea Tura, Leen 't Hart, Koen Dekkers, Nienke van Leeuwen, Roderick Slieker, Femke Rutters, Joline Beulens, Giel Nijpels, Anitra Koopman, Sabine van Oort, Lenka Groeneveld, Leif Groop, Petra Elders, Ana Viñuela, Anna Ramisch, Emmanouil Dermitzakis, Beate Ehrhardt, Christopher Jennison, Philippe Froguel, Mickaël Canouil, Amélie Boneford, Ian McVittie, Dianne Wake, Francesca Frau, Hans-Henrik Staerfeldt, Kofi Adragni, Melissa Thomas, Han Wu, Imre Pavo, Birgit Steckel-Hamann, Henrik Thomsen, Giuseppe Nicola Giordano, Hugo Fitipaldi, Martin Ridderstråle, Azra Kurbasic, Naeimeh Atabaki Pasdar, Hugo Pomares-Millan, Pascal Mutie, Robert Koivula, Nicky McRobert, Mark McCarthy, Agata Wesolowska-Andersen, Anubha Mahajan, Moustafa Abdalla, Juan Fernandez, Reinhard Holl, Alison Heggie, Harshal Deshmukh, Anita Hennige, Susanna Bianzano, Barbara Thorand, Sapna Sharma, Harald Grallert, Jonathan Adam, Martina Troll, Andreas Fritsche, Anita Hill, Claire Thorne, Michelle Hudson, Teemu Kuulasmaa, Jagadish Vangipurapu, Markku Laakso, Henna Cederberg, Tarja Kokkola, Yunlong Jiao, Stephen Gough, Neil Robertson, Helene Verkindt, Violeta Raverdi, Robert Caiazzo, Francois Pattou, Margaret White, Louise Donnelly, Andrew Brown, Colin Palmer, David Davtian, Adem Dawed, Ian Forgie, Ewan Pearson, Hartmut Ruetten, Petra Musholt, Jimmy Bell, Elizabeth Louise Thomas, Brandon Whitcher, Mark Haid, Claudia Nicolay, Miranda Mourby, Jane Kaye, Nisha Shah, Harriet Teare, Gary Frost, Bernd Jablonka, Mathias Uhlen, Rebeca Eriksen, Josef Vogt, Avirup Dutta, Anna Jonsson, Line Engelbrechtsen, Annemette Forman, Nadja Sondertoft, Nathalie de Preville, Tania Baltauss, Mark Walker, Johann Gassenhuber, Maria Klintenberg, Margit Bergstrom, Jorge Ferrer; Adamski, Jerzy; Franks, Paul W.; Pedersen, Oluf; Segal, Eran
Nature (Lond.), 2020
DOI: 10.1038/s41586-020-2896-2
The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties
De Rosa Matteo; Barbiroli Alberto; Bonì Francesco; Scalone Emanuele; Mattioni Davide; Vanoni Maria A.; Patrone Marco; Bollati Michela; Mastrangelo Eloise; Giorgino Toni; Milani Mario
European biophysics journal, 2020
DOI: 10.1007/s00249-019-01409-9
Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly
Cossu Federica; Sorrentino Luca; Fagnani Elisa; Zaffaroni Mattia; Milani Mario; Giorgino Toni; Mastrangelo Eloise
Journal of chemical information and modeling (Online), 2020
DOI: 10.1021/acs.jcim.0c00518
Different mechanisms of GIP and GLP-1 action explain their different therapeutic efficacy in type 2 diabetes
Grespan, Eleonora ; Giorgino, Toni; Natali, Andrea; Ferrannini, Ele; Mari, Andrea
Metabolism, clinical and experimental (Print), 2020
DOI: 10.1016/j.metabol.2020.154415
Exploring the role of interdisciplinarity in physics: Success, talent and luck
Pluchino Alessandro; Burgio Giulio; Rapisarda Andrea; Biondo Alessio Emanuele; Pulvirenti Alfredo; Ferro Alfredo; Giorgino Toni
PloS one, 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, Henry R.; Parisinos, Constantinos A.; Atabaki-Pasdar, Naeimeh; Kelly, Matt; Thomas, E. Louise; Neubauer, Stefan; Jennison, Christopher; Ehrhardt, Beate; Baum, Patrick; Schoelsch, Corinna; Freijer, Jan; Grempler, Rolf; Graefe-Mody, Ulrike; Hennige, Anita; Dings, Christiane; Lehr, Thorsten; Scherer, Nina; Sihinecich, Iryna; Pattou, Francois; Raverdi, Violeta; Caiazzo, Robert; Torres, Fanelly; Verkindt, Helene; Mari, Andrea; Tura, Andrea; Giorgino, Toni; Bizzotto, Roberto; Froguel, Philippe; Bonneford, Amelie; Canouil, Mickael; Dhennin, Veronique; Brorsson, Caroline; Brunak, Soren; De Masi, Federico; Gudmundsdóttir, Valborg; Pedersen, Helle; Banasik, Karina; Thomas, Cecilia; Sackett, Peter; Staerfeldt, Hans Henrik; Lundgaard, Agnete; Nilsson, Birgitte; Nielsen, Agnes; Mazzoni, Gianluca; Karaderi, Tugce; Rasmussen, Simon; Johansen, Joachim; Allesøe, Rosa; Fritsche, Andreas; Thorand, Barbara; Adamski, Jurek; Grallert, Harald; Haid, Mark; Sharma, Sapna; Troll, Martina; Adam, Jonathan; Ferrer, Jorge; Eriksen, Heather; Frost, Gary; Haussler, Ragna; Hong, Mun gwan; Schwenk, Jochen; Uhlen, Mathias; Nicolay, Claudia; Pavo, Imre; Steckel-Hamann, Birgit; Thomas, Melissa; Adragni, Kofi; Wu, Han; Hart, Leen't; Roderick, Slieker; van Leeuwen, Nienke; Dekkers, Koen; Frau, Francesca; Gassenhuber, Johann; Jablonka, Bernd; Musholt, Petra; Ruetten, Hartmut; Tillner, Joachim; Baltauss, Tania; Bernard Poenaru, Oana; de Preville, Nathalie; Rodriquez, Marianne; Arumugam, Manimozhiyan; Allin, Kristine; Engelbrechtsen, Line; Hansen, Torben; Hansen, Tue; Forman, Annemette; Jonsson, Anna; Pedersen, Oluf; Dutta, Avirup; Vogt, Josef; Vestergaard, Henrik; Laakso, Markku; Kokkola, Tarja; Kuulasmaa, Teemu; Franks, Paul; Giordano, Nick; Pomares-Millan, Hugo
Journal of hepatology (Print), 2019
DOI: 10.1016/j.jhep.2019.05.032
Second primary malignancies in postpolycythemia vera and postessential thrombocythemia myelofibrosis: A study on 2233 patients
Mora Barbara; Rumi Elisa; Guglielmelli Paola; Barraco Daniela; Maffioli Margherita; Rambaldi Alessandro; Caramella Marianna; Komrokji Rami; Gotlib Jason; Kiladjian Jean Jacques; Cervantes Francisco; Devos Timothy; Palandri Francesca; De Stefano Valerio; Ruggeri Marco; Silver Richard T.; Benevolo Giulia; Albano Francesco; Cavalloni Chiara; Pietra Daniela; Barbui Tiziano; Rotunno Giada; Cazzola Mario; Vannucchi Alessandro Maria; Giorgino Toni and Passamonti Francesco
Cancer Medicine, 2019
DOI: 10.1002/cam4.2107
Promoting transparency and reproducibility in enhanced molecular simulations
Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth A. Tribello, Pavel Baná?, Alessandro Barducci, Mattia Bernetti, Peter G. Bolhuis, Sandro Bottaro, Davide Branduardi, Riccardo Capelli, Paolo Carloni, Michele Ceriotti, Andrea Cesari, Haochuan Chen, Wei Chen, Francesco Colizzi, Sandip De, Marco De La Pierre, Davide Donadio, Viktor Drobot, Bernd Ensing, Andrew L. Ferguson, Marta Filizola, James S. Fraser, Haohao Fu, Piero Gasparotto, Francesco Luigi Gervasio, Federico Giberti, Alejandro Gil-Ley, Toni Giorgino, Gabriella T. Heller, Glen M. Hocky, Marcella Iannuzzi, Michele Invernizzi, Kim E. Jelfs, Alexander Jussupow, Evgeny Kirilin, Alessandro Laio, Vittorio Limongelli, Kresten Lindorff-Larsen, Thomas Löhr, Fabrizio Marinelli, Layla Martin-Samos, Matteo Masetti, Ralf Meyer, Angelos Michaelides, Carla Molteni, Tetsuya Morishita, Marco Nava, Cristina Paissoni, Elena Papaleo, Michele Parrinello, Jim Pfaendtner, Pablo Piaggi, GiovanniMaria Piccini, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Davide Provasi, David Quigley, Paolo Raiteri, Stefano Raniolo, Jakub Rydzewski, Matteo Salvalaglio, Gabriele Cesare Sosso, Vojt?ch Spiwok, Ji?í ?poner, David W. H. Swenson, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A. Voth, Andrew White
Nature methods (Online), 2019
DOI: 10.1038/s41592-019-0506-8
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, 2019
DOI: 10.1016/j.bbadis.2019.01.010
Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD
Toni Giorgino
Journal of open source software On line, 2019
DOI: 10.21105/joss.01698
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 (Print), 2019
DOI: 10.1016/j.bbrc.2019.08.013
PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python
Toni Giorgino
Journal of open source software On line, 2019
DOI: 10.21105/joss.01773
Second primary malignancies in ruxolitinib-treated myelofibrosis: real-world evidence from 219 consecutive patients
Margherita Maffioli; Toni Giorgino; Barbara Mora; Alessandra Iurlo; Elena Elli; Maria Chiara Finazzi; Marianna Caramella; Elisa Rumi; Maria Cristina Carraro; Nicola Polverelli; Mariella D'Adda; Simona Malato; Marianna Rossi; Alfredo Molteni; Alessandro Vismara; Cinzia Sissa; Francesco Spina; Michela Anghilieri; Daniele Cattaneo; Rossella Renso; Marta Bellini; Maria Luisa Pioltelli; Chiara Cavalloni; Daniela Barraco; Raffaella Accetta; Lorenza Bert`u; Matteo Giovanni Della Porta and Francesco Passamonti
Blood advances, 2019
DOI: 10.1182/bloodadvances.2019000646
Synthesis, molecular modelling studies and biological evaluation of new oxoeoicosanoid receptor 1 agonists
Tomasz Maciej Stepniewski and Mariona Torrens-Fontanals and Ismael Rodriguez-Espigares and Toni Giorgino and Karoline G. Primdahl and Anders Vik and Yngve Stenstrom and Jana Selent and Trond Vidar Hansen
Bioorganic & medicinal chemistry (Print), 2018
DOI: 10.1016/j.bmc.2018.05.036
How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation
Giorgino T
Computer physics communications, 2018
DOI: 10.1016/j.cpc.2018.02.017
Defective amplifying pathway of ?-cell secretory response to glucose in type 2 diabetes: Integrated modeling of in vitro and in vivo evidence
Grespan, Eleonora; Giorgino, Toni; Arslanian, Silva; Arslanian, Silva; Natali, Andrea; Ferrannini, Ele; Mari, Andrea
Diabetes (N.Y.N.Y.), 2018
DOI: 10.2337/db17-1039
High-throughput automated preparation and simulation of membrane proteins with HTMD
Doerr, S.; Giorgino, T.; Martinez-Rosell, G.; Damas, JM.; De Fabritiis, G.
Journal of chemical theory and computation, 2017
DOI: 10.1021/acs.jctc.7b00480
Driver mutations' effect in secondary myelofibrosis: An international multicenter study based on 781 patients
Passamonti, F. and Mora, B. and Giorgino, T. and Guglielmelli, P. and Cazzola, M. and Maffioli, M. and Rambaldi, A. and Caramella, M. and Komrokji, R. and Gotlib, J. and Kiladjian, J. J. and Cervantes, F. and Devos, T. and Palandri, F. and De Stefano, V. and Ruggeri, M. and Silver, R. and Benevolo, G. and Albano, F. and Caramazza, D. and Rumi, E. and Merli, M. and Pietra, D. and Casalone, R. and Barbui, T. and Pieri, L. and Vannucchi, A. M.
Leukemia, 2017
DOI: 10.1038/leu.2016.351
Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale.
Martinez-Rosell, Gerard; Giorgino, Toni; Harvey, Matt J; de Fabritiis, Gianni
Current topics in medicinal chemistry (Print), 2017
DOI: 10.2174/1568026617666170414142549
METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations
Giorgino, T.; Laio, A.; Rodriguez, A.
Computer physics communications, 2017
DOI: 10.1016/j.cpc.2017.04.009
A clinical-molecular prognostic model to predict survival in patients with post polycythemia vera and post essential thrombocythemia myelofibrosis
Passamonti, F; Giorgino, T; Mora, B; Guglielmelli, P; Rumi, E; Maffioli, M; Rambaldi, A; Caramella, M; Komrokji, R; Gotlib, J; Kiladjian, J J; Cervantes, F; Devos, T; Palandri, F; De Stefano, V; Ruggeri, M; Silver, R T; Benevolo, G; Albano, F; Caramazza, D; Merli, M; Pietra, D; Casalone, R; Rotunno, G; Barbui, T; Cazzola, M; Vannucchi, A M
Leukemia (Basingstoke, Online), 2017
DOI: 10.1038/leu.2017.169
PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations
Gerard Martinez-Rosell, Toni Giorgino, and Gianni De Fabritiis
Journal of chemical information and modeling, 2017
DOI: 10.1021/acs.jcim.7b00190
Amyloid-beta 1-24 C-terminal truncated fragment promotes amyloid-beta 1-42 aggregate formation in the healthy brain
Mazzitelli S.; Filipello F.; Rasile M.; Lauranzano E.; Starvaggi-Cucuzza C.; Tamborini M.; Pozzi D.; Barajon I.; Giorgino T.; Natalello A.; Matteoli M.
Acta Neuropathologica Communications, 2016
DOI: 10.1186/s40478-016-0381-9
Pharmacometrics Markup Language (PharmML): Opening new perspectives for model exchange in drug development
Swat M.J.; Moodie S.; Wimalaratne S.M.; Kristensen N.R.; Lavielle M.; Mari A.; Magni P.; Smith M.K.; Bizzotto R.; Pasotti L.; Mezzalana E.; Comets E.; Sarr C.; Terranova N.; Blaudez E.; Chan P.; Chard J.; Chatel K.; Chenel M.; Edwards D.; Franklin C.; Giorgino T.; Glont M.; Girard P.; Grenon P.; Harling K.; Hooker A.C.; Kaye R.; Keizer R.; Kloft C.; Kok J.N.; Kokash N.; Laibe C.; Laveille C.; Lestini G.; Mentre F.; Munafo A.; Nordgren R.; Nyberg H.B.; Parra-Guillen Z.P.; Plan E.; Ribba B.; Smith G.; Troconiz I.F.; Yvon F.; Milligan P.A.; Harnisch L.; Karlsson M.; Hermjakob H.; Le Novere N.
CPT: Pharmacometrics & Systems Pharmacology, 2015
DOI: 10.1002/psp4.57
Impact of allogeneic stem cell transplantation on survival of patients less than 65 years of age with primary myelofibrosis
Kroger, N.; Giorgino, T.; Scott, B.L.; Ditschkowski, M.; Alchalby, H.; Cervantes, F.; Vannucchi, A.; Cazzola, M.; Morra, E.; Zabelina, T.; Maffioli, M.; Pereira, A.; Beelen, D.; Deeg, H.J.; Passamonti, F.
Blood, 2015
DOI: 10.1182/blood-2014-10-608315
PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts
Giorgino, T.
Computer physics communications, 2014
DOI: 10.1016/j.cpc.2013.11.019
MEMBPLUGIN: studying membrane complexity in VMD
Guixà-González, R.;Rodriguez-Espigares, I.;Ramírez-Anguita, J.M.;Carrió-Gaspar, P.;Martinez-Seara, H.;Giorgino, T.;Selent, J.
Bioinformatics (Oxf., Print), 2014
DOI: 10.1093/bioinformatics/btu037
Looking for CALR mutations in familial myeloproliferative neoplasms
Maffioli, M.;Genoni, A.;Caramazza, D.;Mora, B.;Bussini, A.;Merli, M.;Giorgino, T.;Casalone, R.;Passamonti, F.,
Leukemia, 2014
DOI: 10.1038/leu.2014.33
Computing 1-D atomic densities in macromolecular simulations: the Density Profile tool for VMD
Giorgino, T.
Computer physics communications, 2014
DOI: 10.1016/j.cpc.2013.08.022
Membrane lipids are key-modulators of the endocannabinoid-hydrolase FAAH
Dainese, E.;De Fabritiis, G.;Sabatucci, A.;Oddi, S.;Angelucci, C.A.;Di Pancrazio, C.;Giorgino, T.;Stanley, N.;Del Carlo, M.;Cravatt, B.;Maccarrone, M.
Biochemical journal (Online), 2013
DOI: 10.1042/BJ20130960
Identification of slow molecular order parameters for Markov model construction
Pérez-Hernández, G.; Paul, F.; Giorgino, T.; De Fabritiis, G.; Noe, F.
The Journal of chemical physics, 2013
DOI: 10.1063/1.4811489
Visualizing the Induced Binding of SH2-Phosphopeptide
Giorgino, T.;Buch, I.;de Fabritiis, G.
Journal of chemical theory and computation, 2012
DOI: 10.1021/ct300003f
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Buch, I.; Giorgino, T.; De Fabritiis, G.
Proceedings of the National Academy of Sciences of the United States of America, 2011
DOI: 10.1073/pnas.1103547108
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
Giorgino, T,: De Fabritiis, G.
Journal of chemical theory and computation, 2011
DOI: 10.1021/ct100707s
The Virtual Physiological Human TOOLKIT
Cooper, J.; Cervenansky, F.; De Fabritiis, G.; Fenner, J.; Friboulet, D.; Giorgino, T.; Manos, S.; Martelli, Y.; Villà-Freixa, J.; Zasada, S.; Lloyd, S.; McCormack, K.; Coveney, P. V.
Philosophical transactions - Royal Society. Mathematical, Physical and engineering sciences (Print), 2010
DOI: 10.1098/rsta.2010.0144
Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations
Giorgino, T.; Harvey, M.J.; De Fabritiis, G.
Computer physics communications, 2010
DOI: 10.1016/j.cpc.2010.04.007
High-throughput all-atom molecular dynamics simulations using distributed computing
Buch, I.; Harvey, MJ.; Giorgino, T.; Anderson, DP.; De Fabritiis, G.
Journal of chemical information and modeling, 2010
DOI: 10.1021/ci900455r
Wireless Support to Post-Stroke Rehabilitation: MyHeart's Neurological Rehabilitation Concept
Giorgino, T.; Tormene, P.; Maggioni, G.; Pistarini, C.; Quaglini, S.
IEEE transactions on information technology in biomedicine, 2009
DOI: 10.1109/TITB.2009.2028020
Computing and Visualizing Dynamic Time Warping Alignments in R: the dtw Package
Giorgino, T.
Journal of statistical software, 2009
Matching incomplete time series with dynamic time warping: an algorithm and an application to post-stroke rehabilitation
Tormene, P.; Giorgino, T.; Quaglini, S.; Stefanelli, M.
Artificial intelligence in medicine (Print), 2009
DOI: 10.1016/j.artmed.2008.11.007
Assessment of sensorized garments as a flexible support to self-administered post-stroke physical rehabilitation
Giorgino, T.; Tormene, P.; Maggioni, G.; Capozzi, D.; Quaglini, S.; Pistarini, C.
European Journal of Physical and Rehabilitation Medicine (Testo stamp.), 2009
Adaptable dialog architecture and runtime engine (AdaRTE): a framework for rapid prototyping of health dialog systems.
Rojas-Barahona, LM.; Giorgino, T.
International journal of medical informatics, 2009
DOI: 10.1016/j.ijmedinf.2008.07.017
Sensor evaluation for wearable strain gauges in neurological rehabilitation
Giorgino, T.; Tormene, P.; Lorussi, F.; Rossi, DD.; Quaglini, S.
IEEE transactions on neural systems and rehabilitation engineering, 2009
DOI: 10.1109/TNSRE.2009.2019584
An automated voice response system for anticoagulant therapy management
Quaglini, S.; Giorgino, T.; Rojas-Barahona, L.M.; Caff, E.; Vito, M.D.E.;Persico, A.;Cavallini, A.
Studies in health technology and informatics (Print), 2009
DOI: 10.3233/978-1-60750-044-5-453
Health dialog systems for patients and consumers
Bickmore, T.; Giorgino, T.
Journal of biomedical informatics, 2006
DOI: 10.1016/j.jbi.2005.12.004
Special issue on dialog systems for health communication (guest editorial).
Bickmore, T.; Giorgino, T.; Green, N.; Picard, R.
Journal of biomedical informatics, 2006
DOI: 10.1016/j.jbi.2006.02.002
Automated spoken dialogue system for hypertensive patient home management
Giorgino, T.; Azzini, I.; Rognoni, C.; Quaglini, S.; Stefanelli, M.; Gretter, R.; Falavigna, D.
International journal of medical informatics, 2005
DOI: 10.1016/j.ijmedinf.2004.04.026
New frontiers of telemedicine systems for chronic patients monitoring: Adaptive systems and multi-access service
Bellazzi, R.; Giorgino, T.; Azzini, I.; Larizza, C.; Quaglini, S.; Hernando, E.
Measurement and control (Lond., 1968), 2004
DOI: 10.1177/002029400403700502
APE computers--past, present and future
Bodin, F.; Boucaud, Ph.; Cabibbo, N. Cascino, G.; Calvayrac, F.; Della Morte, M.; Del Re, A.; De Pietri, R.; Deriso, P.; Di Carlo, F.; Di Renzo, F.; Errico, W.; Frezzotti, R.; Gensch, U.; Giorgino, T.; Guagnelli, M.; Hervé, N.; Jansen, K.; Kaldass, H.; Lonardo, A.; Lukyanov, M.; Magazzú, G.; Micheli, J.; Morénas, V.; Mori, L.; Palombi, F.; Paschedag, N.; Pech, J.; Péne, O.; Petronzio, R.; Pleiter, D.; Rapuano, F.; Rossetti, D.; Roiesnel, C.; Sartori, L.; Simma, H.; Schifano, F.; Tripiccione, R.; Vicini, P.; Wegner, W.
Computer physics communications, 2002
DOI: 10.1016/S0010-4655(02)00314-4
Status of APEmille
Bartoloni, A.; Boucaud, P.; Cabibbo, N.; Calvayrac, C.; Della Morte, A.; Del Pietri, R.; De Riso, P.; Di Carlo, F.; Di Renzo, F.; Errico, W.; Frezzotti, R.; Giorgino, T.; Heitger, J.; Lonardo, A.; Loukianov, M.; Magazzú, G.; Micheli, J.; Morenas, V.; Paschedag, N.; Péne, O.; Petronzio, R.; Pleiter, D.; Rapuano, F.; Rolf, J.; Rossetti, D.; Sartori, L.; Simma, H.; Schifano, F.; Torelli, M.; Tripiccione, R.; Vicini, P.; Wegner, P.
Nuclear physics. B, Proceedings supplement (Print), 2002
DOI: 10.1016/S0920-5632(01)01922-3
The apeNEXT project
Bodin, F.; Boucaud, P.; Cabibbo, N.; Calvayrac, F.; Della Morte, M.;De Pietri, R.; De Riso, P.; Di Carlo, F.; Di Renzo, F.; Errico, W.; Frezzotti, R.; Gensch, U.; Giorgino, T.; Guagnelli, M.; Hervé, N.; Kaldass, H.; Lonardo, A.; Lukyanov, M.; Magazzú, G.; Micheli, J.; Morénas, V.; Mori, L.; Palombi, F.; Paschedag, N.; Péne, O.; Petronzio, R.; Pleiter, D.; Rapuano, F.; Rossetti, D.; Sartori, L.; Simma, H.; Schifano, F.; Tripiccione, R.; Vicini, P.
Nuclear physics. B, Proceedings supplement (Print), 2002
DOI: 10.1016/S0920-5632(01)01656-5