Publications

Peer-reviewed only

Legend: [P] Computational physics; [B] Biostatistics/bioengineering.

2024

• [P] Callea L, Caprai C, Bonati L, Giorgino T, Motta S. Self-Organizing Maps of Unbiased Ligand-Target Binding Pathways and Kinetics. Journal of Chemical Physics 2024. Available from: http://arxiv.org/abs/2409.12603 

• [P] Mirarchi A, Giorgino T, De Fabritiis G. mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics [Internet]. arXiv; 2024 [cited 2024 Sep 23]. Available from: http://arxiv.org/abs/2407.14794 

• [P] Nerín-Fonz F, Caprai C, Morales-Pastor A, Lopez-Balastegui M, Aranda-García D, Giorgino T, et al. AlloViz: A tool for the calculation and visualisation of protein allosteric communication networks. Computational and Structural Biotechnology Journal. 2024 Dec;23:1938–44. 

• [B] Samant R, Giorgino T, Jarochowska E, Vleeschouwer DD. Advantages of DTW windowing function in automated correlation of stratigraphic time series [Internet]. EGU General Assembly 2024; 2024 Mar [cited 2024 Mar 12]. Report No.: EGU24-8374. https://doi.org/10.5194/egusphere-egu24-8374

2023

• [P] Majewski M, Pérez A, Thölke P, Doerr S, Charron NE, Giorgino T, et al. Machine learning coarse-grained potentials of protein thermodynamics. Nat Commun. 2023 Sep 15;14(1):5739. 

• [B] Dawed AY, Mari A, Brown A, McDonald TJ, Li L, Wang S, et al. Pharmacogenomics of GLP-1 receptor agonists: a genome-wide analysis of observational data and large randomised controlled trials. The Lancet Diabetes & Endocrinology. 2023 Jan 1;11(1):33–41. 

• [B] Allesøe RL, Lundgaard AT, Hernández Medina R, Aguayo-Orozco A, Johansen J, Nissen JN, et al. Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models. Nat Biotechnol. 2023 Mar;41(3):399–408. 

2022

• [B] Rasile M, Lauranzano E, Faggiani E, Ravanelli MM, Colombo FS, Mirabella F, et al. Maternal immune activation leads to defective brain–blood vessels and intracerebral hemorrhages in male offspring. The EMBO Journal. 2022 Oct 31;n/a(n/a):e111192. doi:10.15252/embj.2022111192

• [P] Nicoli A, Dunkel A, Giorgino T, de Graaf C, Di Pizio A. Classification Model for the Second Extracellular Loop of Class A GPCRs. J Chem Inf Model [Internet]. 2022 Feb 3 [cited 2022 Feb 4]; doi:10.1021/acs.jcim.1c01056

• [B] Maffioli M, Mora B, Ball S, Iurlo A, Elli EM, Finazzi MC, et al. A Prognostic Model to Predict Survival After 6 Months of Ruxolitinib in Patients with Myelofibrosis. Blood Advances. 2022 Feb 7; doi:10.1182/bloodadvances.2021006889

• [B] Torrens-Fontanals M, Peralta-García A, Talarico C, Guixà-González R, Giorgino T* and Selent J*. SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. Nucleic Acids Research. Breakthrough article. doi:10.1093/nar/gkab977 (* shared corresponding).

• [B] Retelletti Brogi S, Cossarini G, Bachi G, Balestra C, Camatti E, Casotti R, et al. Evidence of Covid-19 lockdown effects on riverine dissolved organic matter dynamics provides a proof-of-concept for needed regulations of anthropogenic emissions. Science of The Total Environment. 2022 Mar 15;152412. doi:10.1016/j.scitotenv.2021.152412

2021

• [P] Bollati M et al. A novel hotspot of gelsolin instability and aggregation propensity triggers a new mechanism of amyloidosis. Computational and Structural Biotechnology Journal. arXiv:2109.07190 doi:10.1016/j.csbj.2021.11.025

• [B] Grespan E, Giorgino T, Natali A, Ferrannini E, Mari A. Different mechanisms of GIP and GLP-1 action explain their different therapeutic efficacy in type 2 diabetes. Metabolism - Clinical and Experimental. Volume 114, January 2021, 154415. doi:10.1016/j.metabol.2020.154415 [Share link (time-limited)]

• [P] Doerr S, Majewsk M, Pérez A, Krämer A, Clementi C, Noe F, et al. TorchMD: A deep learning framework for molecular simulations.  Journal of Chemical Theory and Computation. doi:10.1021/acs.jctc.0c01343; Available from: arXiv:2012.12106 

2020

• [P] 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)

• [B] Bar N, Korem T, Weissbrod O, Zeevi D, Rothschild D, Leviatan S, et al. A reference map of potential determinants for the human serum metabolome. Nature. 2020 Dec;588(7836):135–40. doi:10.1038/s41586-020-2896-2

• [P] Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J.K.S. et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat Methods (2020).  doi:10.1038/s41592-020-0884-y [Preprint] 

• [P] De Rosa M, et al. The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties. European Biophysics Journal (2020) doi:10.1007/s00249-019-01409-9 [arXiv:1911.08194]

2019

• [P] 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

• [B] Maffioli M, Giorgino T, ..., Passamonti F. Second Primary Malignancies In Ruxolitinib-Treated Myelofibrosis: Real-World Evidence From 219 Consecutive Patients. Blood Advances. (2019) 3 (21): 3196-3200. doi:10.1182/bloodadvances.2019000646, OA

• [P] Giorgino T, (2019). Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD. Journal of Open Source Software, 4(41), 1698, doi:10.21105/joss.01698, OA

• [P] De Rosa M, et al. High-resolution crystal structure of gelsolin domain 2 in complex with the physiological calcium ion. Biochemical and Biophysical Research Communications (BBRC). 518 (1) 94-99 doi:10.1016/j.bbrc.2019.08.013 [arXiv:1911.08188]

• [P] Giorgino T, Analysis libraries for molecular trajectories: a cross-language synopsis. Chapter 20 in:  Biomolecular Simulations: Methods and Protocols Edited by M. Bonomi and C. Camilloni (Springer, ISBN 978-1-4939-9608-7). doi:10.1007/978-1-4939-9608-7_20 [Preprint 1,  Preprint 2]

• [P] The PLUMED consortium. A community effort to promote transparency and reproducibility in enhanced molecular simulations. Nature Methods 16, 670 (2019). doi:10.1038/s41592-019-0506-8 [online]

• [P] 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. doi:10.1016/j.bbadis.2019.01.010  [arXiv:1903.07308]

• [P] Pluchino A, Burgio G, Rapisarda A, Biondo AE, Pulvirenti A, Ferro A, Giorgino T (2019) Exploring the role of interdisciplinarity in physics: Success, talent and luck. PLOS ONE 14(6): e0218793. doi:10.1371/journal.pone.0218793, OA

• [B] Mora B, Rumi E, Guglielmelli P, Barraco D, Maffioli M, Rambaldi A, et al. Second primary malignancies in postpolycythemia vera and postessential thrombocythemia myelofibrosis: A study on 2233 patients. Cancer Medicine. 2019. doi:10.1002/cam4.2107

• [B] Wilman HR, Parisinos CA, Atabaki-Pasdar N, Kelly M, Thomas EL, Neubauer S, et al. Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration. Journal of Hepatology. 2019 Volume 71, Issue 3, September 2019,  594-602 . doi:10.1016/j.jhep.2019.05.032

2018

• [P] Giorgino T, How to Differentiate Collective Variables in Free Energy Codes: Computer-Algebra Code Generation and Automatic Differentiation. Computer Physics Communications. doi:10.1016/j.cpc.2018.02.017 [arXiv:1709.06780]

• [B] Mora B*, Giorgino T*, […], Value of cytogenetic abnormalities in post-polycythemia vera and post-essential thrombocythemia myelofibrosis: a study of the MYSEC project. Haematologica, 2018. doi:10.3324/haematol.2017.185751 (* shared first)

• [B] Grespan E, Giorgino T, Arslanian S, Natali A, Ferrannini E, Mari A. Defective Amplifying Pathway of β-cell Secretory Response to Glucose in Type 2 Diabetes: Integrated Modeling of in vitro and in vivo Evidence. Diabetes. Diabetes 2018 Mar; 67(3): 496-506.  doi:10.2337/db17-1039

• [P] Stepniewski TM, Torrens-Fontanals M, Rodríguez-Espigares I, Giorgino T, Primdahl KG, Vik A, et al. Synthesis, molecular modelling studies and biological evaluation of new oxoeoicosanoid receptor 1 agonists. Bioorganic & Medicinal Chemistry. 2018 doi:10.1016/j.bmc.2018.05.036

• [B] Barraco D, Mora B, Guglielmelli P, Rumi E, Maffioli M, Rambaldi A, et al. Gender effect on phenotype and genotype in patients with post-polycythemia vera and post-essential thrombocythemia myelofibrosis: results from the MYSEC project. Blood Cancer Journal. 2018 Sep 21;8(10):89. doi:10.1038/s41408-018-0128-x

• [B] Mora B, Giorgino T, Guglielmelli P, Rumi E, Maffioli M, Rambaldi A, et al. 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. Leukemia Research. 2018 doi:10.1016/j.leukres.2018.04.012

2017

• [P] Stefan Doerr*, Toni Giorgino*, Gerard Martinez-Rosell, João M. Damas, and Gianni De Fabritiis, High-throughput automated preparation and simulation of membrane proteins with HTMD, J. Chem. Theory Comput. 2017, doi:10.1021/acs.jctc.7b00480 (* shared first)

• [P] Gerard Martinez-Rosell, Toni Giorgino*, and Gianni De Fabritiis*, PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations Journal of Chemical Information and Modeling 2017 doi:10.1021/acs.jcim.7b00190 (* shared corresponding)

• [B] Passamonti F*, Giorgino T*, […] A clinical-molecular prognostic model to predict survival in patients with post polycythemia vera and post essential thrombocythemia myelofibrosis. Leukemia, 2017. (* shared first) doi:10.1038/leu.2017.169

• [P] Martínez-Rosell G, Giorgino T, Harvey MJ, de Fabritiis G. Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale. Current Topics in Medicinal Chemistry. (2017) 23;17:1–1. doi:10.2174/1568026617666170414142549

• [P] Giorgino T, Laio A, Rodriguez A. METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations. Computer Physics Communications 217 (2017). doi:10.1016/j.cpc.2017.04.009

2016 and before

• [B] Passamonti F, Mora B*, Giorgino T*, Guglielmelli P, Cazzola M, Maffioli M, et al. Driver mutations’ effect in secondary myelofibrosis: An international multicenter study based on 781 patients. Leukemia [Internet]. 2016 Nov 25 doi:10.1038/leu.2016.351 * equal contribution

• [P] Mazzitelli, S. et al. Amyloid-β 1–24 C-terminal truncated fragment promotes amyloid-β 1–42 aggregate formation in the healthy brain. Acta Neuropathologica Communications 4, 110 (2016). doi:10.1186/s40478-016-0381-9

• [B] Swat, M., […] (2015), Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. CPT: Pharmacometrics & Systems Pharmacology. doi: 10.1002/psp4.57

• [B] Kröger N, Giorgino T, Scott BL, Ditschkowski M, Alchalby H, Cervantes F, et al. Impact of allogeneic stem cell transplantation on survival of patients less than 65 years with primary myelofibrosis. Blood May 2015, 125 (21) 3347-3350;doi:10.1182/blood-2014-10-608315

• [P] Ramon Guixa-Gonzalez; Ismael Rodriguez-Espigares; Juan Manuel Ramirez-Anguita; Pau Carrio-Gaspar; Hector Martinez-Seara; Toni Giorgino*; Jana Selent*. MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics (2014) 30 (10): 1478-1480; doi:10.1093/bioinformatics/btu037 * shared senior

• [B] Maffioli, M., A. Genoni, D. Caramazza, B. Mora, A. Bussini, M. Merli, T. Giorgino, R. Casalone, F. Passamonti. Looking for CALR mutations in familial myeloproliferative neoplasms. Leukemia. 2014 Jan 20; doi:10.1038/leu.2014.33

• [P] Toni Giorgino, Plumed-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts (2014) Computer Physics Communications,Volume 185, Issue 3, March 2014, Pages 1109–1114 doi:10.1016/j.cpc.2013.11.019  [arxiv:1312.3190].

• [P] Enrico Dainese, Gianni De Fabritiis, Annalaura Sabatucci, Sergio Oddi, Clotilde Beatrice Angelucci, Chiara Di Pancrazio, Toni Giorgino, Nathaniel Stanley, Michele Del Carlo, Benjamin Cravatt and Mauro Maccarrone Membrane lipids are key-modulators of the endocannabinoid-hydrolase FAAH Biochem. J. (2014) 457 (463–472) doi:10.1042/BJ20130960

• [P] Giorgino, T. Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD. Computer Physics Communications. Volume 185, Issue 1, January 2014, Pages 317–322doi:10.1016/j.cpc.2013.08.022 or arXiv:1308.5873

• [P] Guillermo Perez-Hernandez, Fabian Paul, Toni Giorgino, Gianni de Fabritiis, Frank Noé, Identification of slow molecular order parameters for Markov model construction, The Journal of Chemical Physics, 139, 015102 (2013) doi:10.1063/1.4811489, arxiv:1302.6614

• [P] Giorgino, T., I. Buch, e G. De Fabritiis. Visualizing the Induced Binding of SH2-Phosphopeptide. J. Chem. Theory Comput., 2012, 8 (4), pp 1171–1175. doi:10.1021/ct300003f.

• [P] Buch, I., Giorgino, T., & De Fabritiis, G. (2011). Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proceedings of the National Academy of Sciences, 108(25), 10184-10189. doi:10.1073/pnas.1103547108

• [P] T. Giorgino and G. De Fabritiis, An high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A, Journal of Chemical Theory and Computation, 2011, 7 (6), pp 1943–1950, doi:10.1021/ct100707s

• [P] Cooper J, Cervenansky F, De Fabritiis G, Fenner J, Friboulet D, Giorgino T, et al. The Virtual Physiological Human ToolKit. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2010;368(1925):3925-3936. doi:10.1098/rsta.2010.0144

• [P] Giorgino T., Harvey M.J. and De Fabritiis G., Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations, Computer Physics Communications, Volume 181, Issue 8, August 2010, Pages 1402-1409. Preprint @ U Berkeley; doi:10.1016/j.cpc.2010.04.007

• [P] Buch I, Harvey MJ, Giorgino T, Anderson DP, De Fabritiis G. High-throughput all-atom molecular dynamics simulations using distributed computing. J Chem Inf Model. 2010 Mar 22;50(3):397-403. doi:10.1021/ci900455r.

• [B] Giorgino T, Tormene P, Maggioni G, Pistarini C, Quaglini S. Wireless Support to Post-Stroke Rehabilitation: MyHeart’s Neurological Rehabilitation Concept. IEEE Transactions on Information Technology in Biomedicine. 2009 Nov;13(6):1012-1018. doi:10.1109/TITB.2009.2028020. 

• [B] Giorgino T. Computing and Visualizing Dynamic Time Warping Alignments in R: the dtw Package. Journal of Statistical Software. 2009 August;31(7). www.jstatsoft.org/v31/i07

• [B] Tormene P, Giorgino T, Quaglini S, Stefanelli M. Matching incomplete time series with dynamic time warping: an algorithm and an application to post-stroke rehabilitation. Artificial Intelligence in Medicine. 2009 Jan;45(1):11–34. (* shared first) doi:10.1016/j.artmed.2008.11.007. [Preprint]

• [B] Giorgino T, Tormene P, Maggioni G, Capozzi D, Quaglini S, Pistarini C. Assessment of sensorized garments as a flexible support to self-administered post-stroke physical rehabilitation. Eur J Phys Rehabil Med. 2009 Mar;45(1):75–84. PMID: 19293756

• [B] Rojas-Barahona LM, Giorgino T. Adaptable dialog architecture and runtime engine (AdaRTE): a framework for rapid prototyping of health dialog systems. International Journal of Medical Informatics. 2009 Apr;78 Suppl 1:S56–S68. doi:10.1016/j.ijmedinf.2008.07.017.

• [B] Giorgino T, Tormene P, Lorussi F, Rossi DD, Quaglini S. Sensor evaluation for wearable strain gauges in neurological rehabilitation. IEEE Trans Neural Syst Rehabil Eng. 2009 Aug;17(4):409–415. doi:10.1109/TNSRE.2009.2019584.

• [B] Quaglini S, Giorgino T, Rojas-Barahona LM, Caffi E, De Vito M, Persico A, et al. An automated voice response system for anticoagulant therapy management. Stud Health Technol Inform. (MEDINFO) 2009;150:453-457. doi:10.3233/978-1-60750-044-5-453

• [B] Giorgino T, Tormene P, Cattani B, Pistarini C, Quaglini S. Remote Support for Stroke Rehabilitation: MyHeart’s Neurological Rehabilitation Concept. In: MEDINFO 2007 - Proceedings of the 12th World Congress on Health (Medical) Informatics. pp. 1063-1067. Brisbane (Australia). ISBN 978-1-58603-774-1. PMID: 17911685

• [B] Rojas-Barahona LM, Giorgino T. AdaRTE: adaptable dialogue architecture and runtime engine. A new architecture for health-care dialogue systems. Stud Health Technol Inform. 2007;129(Pt 2):1063-7. (Medinfo 2007) Brisbane (Australia). ISBN 978-1-58603-774-1. PMID: 17911878.

• [B] Giorgino T, Tormene P, Quaglini S. A Multivariate Time-Warping Based Classifier for Gesture Recognition with Wearable Strain Sensors. In: Proc. 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBS 2007. p. 4903–4906. Los Alamitos, CA, USA. doi:10.1109/IEMBS.2007.4353439.

• [B] Giorgino T, Quaglini S, Lorussi F, De Rossi D. Experiments in the Detection of Upper Limb Posture through Kinestetic Strain Sensor. In: Wearable and Implantable Body Sensor Networks, International Workshop on. Boston, MA (USA): IEEE Computer Society; 2006. p. 9-12. doi:10.1109/BSN.2006.25.

• [B] Lorussi F, Tognetti A, Giorgino T, Quaglini S. Wearable system for post stroke rehabilitation of the upper-limb. Biomedicine & Pharmacotherapy. Volume 60, Issue 8, September 2006, Pages 473-474, doi:10.1016/j.biopha.2006.07.030.

• [B] Giorgino T, Lorussi F, De Rossi D, Quaglini S. Posture Classification via Wearable Strain Sensors for Neurological Rehabilitation. In: Engineering in Medicine and Biology Society, 2006. EMBS ’06. 28th Annual International Conference of the IEEE. p. 6273–6276. Los Alamitos, CA, USA doi:10.1109/IEMBS.2006.260620.

• [B] Bickmore T, Giorgino T. Health dialog systems for patients and consumers. Journal of Biomedical Informatics. 2006;39(5):556–571 (Methodological review). doi:10.1016/j.jbi.2005.12.004.

• [B] Giorgino T, Azzini I, Rognoni C, Quaglini S, Stefanelli M, Gretter R, et al. Automated spoken dialogue system for hypertensive patient home management. International Journal of Medical Informatics. 2005 Mar; 74(2-4):159–167. doi:10.1016/j.ijmedinf.2004.04.026.

• [B] Bellazzi R, Giorgino T, Azzini I, Larizza C, Quaglini S, Hernando E. New frontiers of telemedicine systems for chronic patients monitoring: Adaptive systems and multi-access services. Measurement + Control. 2004 Giu; 37(5) pp. 146-150. The institute of measurement and control, London, UK. doi: 10.1177/002029400403700502

Special issues

• Bickmore T, Giorgino T, Green N, Picard R. Special issue on dialog systems for health communication (guest editorial). Journal of Biomedical Informatics. 2006;39(5):465–467. doi:10.1016/j.jbi.2006.02.002.

Book chapters

• Giorgino T, Analysis libraries for molecular trajectories: a cross-language synopsis. Chapter 20 in:  Biomolecular Simulations: Methods and Protocols Edited by M. Bonomi and C. Camilloni (Springer, ISBN 978-1-4939-9608-7). doi:10.1007/978-1-4939-9608-7_20 [Code and preprint on GitHub]

• Giorgino T, Tormene P, Quaglini S. Indumenti sensorizzati per la neuroriabilitazione motoria: analisi del movimento con feedback in tempo reale. In: Bonfiglio A, Cerutti S, De Rossi D, Magenes G, editors. Sistemi indossabili per la salute e la protezione dell’uomo; Patron, Bologna, Settembre 2008. ISBN 978-88-555-2994-5.

• Azzini I, Giorgino T, Falavigna D, Gretter R. Application of Spoken Dialogue Technology in a Medical Domain. In: Text, Speech and Dialogue. Lecture Notes in Computer Science 2448/2002 p. 177-196. Springer Berlin / Heidelberg. ISBN 978-3-540-44129-8. doi:10.1007/3-540-46154-X.

Congresses, workshops and symposia (peer-reviewed)

• Giorgino T. How to differentiate collective variables in free energy codes. Open source software for enhanced-sampling simulations; 2019 Jul 22; CECAM-Lugano, Lugano, Switzerland. [Code and slides]

• Giorgino T, Session 3: Protein preparation, protonation and building; and Bonus Session: Using PLUMED2 Metrics, at the 3rd Workshop on High Throughput Molecular Dynamics (2016)

• Kröger N, Giorgino T, Scott BL, Ditschkowski M, Alchalby H, Cervantes F, et al. Decision-finding for allogeneic stem cell Transplantation in PMF according to DIPSS. Bone Marrow Transplant. 2015 Mar;50:S71–S71.

• Mora B, Guglielmelli P, Cazzola M, Maffioli M, Rambaldi A, Caramella M, et al. An International Multicenter Project on Secondary Myelofibrosis. Clinical Lymphoma Myeloma and Leukemia. 2016 Sep 1;16:S91.

• Maffioli M, Cervantes F, Cazzola M, Vannucchi AM, Morra E, Caramazza D, et al. Low Risk IPSS/DIPSS Primary Myelofibrosis: Identification of Patients with Higher Risk of Progression. Blood. 2014 Dec 6;124(21):3187–3187. Available from: http://www.bloodjournal.org/content/124/21/3187

• Kröger N, Giorgino T, Scott BL, Ditschkowski M, Alchalby H, Cervantes F, et al. Survival of Allogeneic Stem Cell Transplantation Vs Conventional Therapies per DIPSS Stratification in Patients with Primary Myelofibrosis Younger Than 65 Years: A Retrospective Analysis on 673 Patients. Blood. 2014 Dec 6;124(21):633–633. Available from: http://www.bloodjournal.org/content/124/21/633

• T. Giorgino.PLUMED-GUI 2.0: a GUI for the Rapid Prototyping of PLUMED Analysis and Biasing Script.Enhancing molecular simulations with PLUMED (May 28-June 2, 2014). Belfast, United Kingdom

• Enrico Dainese, Gianni De Fabritiis, Annalaura Sabatucci, Sergio Oddi, Clotilde Beatrice Angelucci, Chiara Di Pancrazio, Toni Giorgino, Nathaniel Stanley, Michele Del Carlo, Benjamin Cravatt, Mauro Maccarrone, Key role for membrane lipids in orchestrating the endocannabinoid hydrolase (FAAH) function and subcellular localization, SW02.S7–73, FEBS Journal 280 (Suppl. 1) 135 (FEBS congress 2013)

• T. Giorgino, I. Buch, G. De Fabritiis, Molecular recognition of SH2-phosphopeptide by molecular dynamics, XI Jornadas de Bioinformática, Barcelona, Spain, 23-25 Jan (2012).

• Giorgino T, D’Abramo M, Gervasio FL, De Fabritiis G. Exploring the Kinetics of Drug Binding to the hERG Channel through Large-Scale Simulations. In: First Virtual Physiological Human conference, VPH2010. Bruxelles, Belgium, 2010.

• I. Buch, T. Giorgino, G. De Fabritiis, High-throughput all-atom molecular dynamics simulations using distributed computing, 24th Molecular Modeling Workshop, Erlangen (Germany), 15-16th March 2010.

• I. Buch, T. Giorgino, G. De Fabritiis, Reliable and accurate prediction of ligand binding by high-throughput molecular dynamics simulations, 1st Prize-awarded presentation XVIII Jornades de Biologia Molecular, Barcelona (Spain), 29-30th June 2010.

• I. Buch, T. Giorgino, G. De Fabritiis, Energetics, kinetics and binding pathway reconstruction for enzyme-inhibitor complex from high-throughput molecular dynamics simulations IV Meeting on High Performance Computing in Molecular Simulations, Madrid (Spain), 30th September-1st October 2010.

• T. Giorgino, G. De Fabritiis, Submitting and managing distributed computations: the researcher’s interface to a BOINC project 5th BOINC Workshop, Barcelona (Spain), 22-23th October 2009.

• Silvana Quaglini, Toni Giorgino, Paolo Tormene, Giorgio Maggioni, Caterina Pistarini, Barbara Cattani, Maria Cristina Mazzoleni, Telemedicine Systems for Delivering Patient-specific Motor and Cognitive Rehabilitation, Travel Health Informatics and Telehealth Selected Papers from EFMI Special Topic Conference Antalya, Turkey, November 12 – 15, 2009, European Notes in Medical Informatics ENMI Vol V No 1, p. 48, ISSN 1861-3179.

• Pasotti L, Giorgino T, Magni P. Movement detection from a wearable system: a deconvolution-based approach. In: Burattini R, Contro R, Dario P, Landini L, editor(s). Primo Congresso Nazionale di Bioingegneria – GNB 2008. Pisa (Italy) 2008. p. 607-608.

• Giorgino T, Maggioni G, Tormene P, Capozzi D, Quaglini S, Pistarini C. Sensorised garments for post-stroke physical rehabilitation. In: International Focus on Stroke. Milan (Italy): 2007.

• Rojas-Barahona LM, Giorgino T. AdaRTE: An Extensible and Adaptable Architecture for Dialog Systems. In: Bridging the Gap: Academic and Industrial Research in Dialog Technologies Workshop Proceedings, NAACL-HLT, pp. 64-67. Rochester, USA. 2007. Association for Computational Linguistics, Morristown, NJ, USA. www.aclweb.org/anthology/W/W07/W07-0309.pdf

• Pistarini C, Maggioni G, Giorgino T, Quaglini S. Instrumental Kinesiology Approach in Neurorehabilitation Follow-up. In: Virtual Rehabilitation, 2007, p. 79-79. IEEE Computer Society, Los Alamitos, CA, USA. doi:10.1109/ICVR.2007.4362135.

• Giorgino T, Quaglini S, Lorussi F. Conductive Elastomer Sensors in Neurological Rehabilitation. In: Proceedings of ISEK. Turin (Italy). 2006.

• Giorgino T, Quaglini S, Lorussi F, Tognetti A. Experiments in the Detection of Upper Limb Posture through Kinestetic Strain Sensors. In: Proceedings of ISEK. Turin (Italy). 2006.

• Quaglini S, Giorgino T, Pistarini C, Maggioni G, Lorussi F. Un sistema basato su indumenti sensorizzati per la rilevazione del movimento nella riabilitazione post ictus. In: XXXIV Congresso Nazionale S.I.M.F.E.R. Firenze (Italy) 2006.

• Tormene P, Viaro F, Giorgino T. Classification of Time Series Acquired by Wearable Sensors for Recognizing Motor Rehabilitation Exercises. Technical Report, 2006.

• Rognoni C, Giorgino T, Quaglini S, Stefanelli M, Marchesi E, Baccheschi J. Adapting an Hypertension Home-Monitoring System to the Patient’s Cardiovascular Risk. In: Druzdzel MJ, Leong T, editor(s). AAAI Press. 2005 Spring Symposium Series. ISBN 978-1-57735-228-0.

• Giorgino T, Quaglini S, Rognoni C, Baccheschi J. The HOMEY project: a telemedicine service for hypertensive patients. In: UM 2005 workshop on Personalisation for e-Health, 29 July 2005, Edinburgh, UK.

• Falavigna D, Giorgino T, Gretter R. A Frame Based Spoken Dialog System for Home Care. In: Interspeech’2005 - Eurospeech, 9th European Conference on Speech Communication and Technology, Lisbon, Portugal, September 4-8, 2005 ISCA Archive, http://www.isca-speech.org/archive/interspeech_2005. p. 201-204.

• Bickmore T, Giorgino T. Some Novel Aspects of Health Communication. In: American Association for Artificial Intelligence, AAAI Fall Symposium 04, Washington DC, USA, 2004. AAAI Press. ISBN 978-1-57735-215-0.

• Giorgino T, Quaglini S, Stefanelli M. Evaluation and Usage Patterns in the Homey Hypertension Management Dialogue System. In: American Association for Artificial Intelligence, AAAI Fall Symposium 04, Washington DC, USA, 2004. AAAI Press. ISBN 978-1-57735-215-0.

• Giorgino T, Spadini E. Machine Learning Techniques for the Evaluation of a Chronic Disease-Management Dialog System. In: Intelligent Data Mining in Medicine IDAMAP 2004, San Francisco, CA, USA.

• Rognoni C, Giorgino T, Quaglini S, Stefanelli M, Marchesi E, Baccheschi J. An hypertension home-monitoring system adapted for cardiovascular risk management. In: 1st EMMIT Euro-Mediterranean Medical Informatics and Telemedicine. Genova, 2004.

• Azzini I, Giorgino T, Nardelli L, Orlandi M, Rognoni C. An architecture for a multi-modal Web Browser. In: IDS 2002. Multi-Modal Dialogue in Mobile Environments, ISCA Tutorial and Research Workshop (ITRW). Kloster Irsee, Germany, June 17-19, 2002: 2002. p. 9. Available from: www.isca-speech.org/archive_open/ids_02/ids2_021.html .

• Azzini I, Giorgino T, Falavigna D, Gretter R. Application of the ITC-irst spoken dialog system in a medical domain. In: TSD 2002: Fifth International Conference on Text, Speech and Dialogue. Brno, Czech Rep., September 9-12, 2002. p. 449.

• Armaroli C, Azzini I, Ferrario L, Giorgino T, Nardelli L, Orlandi M, et al. An architecture for a multi-modal Web Browser. In: 7th International Conference on Spoken Language Processing (ICSLP2002 - INTERSPEECH 2002), Denver, Colorado, USA, September 16-20, 2002, ed. by John H. L. Hansen and Bryan Pellom, ISCA Archive, p. 2553-2556. Available from: www.isca-speech.org/archive/icslp_2002/i02_2553.html.

• Piazza M, Giorgino T, Azzini I, Stefanelli M, Luo R. Cognitive human factors for telemedicine systems. Stud Health Technol Inform. 2004;107(Pt 2):974-8. (Medinfo 2004) PMID: 15360958.

• Azzini I, Falavigna D, Giorgino T, Gretter R, Quaglini S, Rognoni C, et al. Automated Spoken Dialog System for Home Care and Data Acquisition from Chronic Patients. In: Medical Informatics Europe MIE 2003. St. Malo, France. p. 146-151. PMID: 14663978.

• Azzini I, Giorgino T, Quaglini S, Rognoni C, Stefanelli M. Home Monitoring of Hypertensive Patients through Intelligent Dialog System. In: Kohane IS, editor(s). American Medical Informatics Association, AMIA 2002, San Antonio, TX, USA. 2002. PMCID: PMC2244273.

• Bodin, F.; Boucaud, P.; Cabibbo, N.; et al. APE computers - Past, present and future. Computer Physics Communications, 2002, 147, 402-409. doi:10.1016/S0010-4655(02)00314-400314-4).

• Bartoloni A, Boucaud P, Cabibbo N, Calvayrac C, Della Morte A, Del Pietri R, et al. Status of APEmille. Nuclear Physics B - Proceedings Supplements. 2002; 106-1071043-1045. doi:10.1016/S0920-5632(01)01922-301922-3).

• Bodin F, Boucaud P, Cabibbo N, Calvayrac F, Della Morte M, De Pietri R, et al. The apeNEXT project. Nuclear Physics B - Proceedings Supplements. 2002; 106-107173-176. doi:10.1016/S0920-5632(01)01656-501656-5).

Dissemination

• Interview in Proteins are complex molecules essential to life, 2010 (institutional video).

• Giorgino T. Quan les persones col.laboren amb la ciència [When public collaborates with science]. Imima’t - divulguem la ciència. June 2009 (catalan); article also available in Spanish.

• Giorgino T. Technical focus on GPUGRID. Article in the Virtual Physiologial Human Network of Excellence – Newsletter n. 2. June 2009. 

• Giorgino T. Wiki science featured in EMBO reports. Article in the Virtual Physiologial Human Network of Excellence – Newsletter n. 2. June 2009.

• Giorgino T. Wearable sensors for neurological rehabilitation. Presentation video for the MyHeart project, 2008. Available from: www.labmedinfo.org/projects/myheart (Online)

Academic theses

• Giorgino T, Advances in Voice Recognition for Home Care: Technology and Architecture. Tesi di Dottorato discussa presso l’Università degli Studi di Pavia il 10 marzo 2005. Bibl. Nazionale Centrale Firenze TDR 2005 6713

• Giorgino T. ApeNEXT: architettura ed algoritmi di LGT. Tesi di Laurea discussa presso l’Università degli Studi di Pisa il 4 giugno 2001.

Old essays

• Calcolo del coefficiente di diffusione di un sistema di Lennard-Jones (Italian, 1998). An essay submitted for a course in molecular dynamics taken at the Scuola Normale Superiore.

• Giorgino T. An Introduction to Text Classification. Final thesis for the Scuola Avanzata di Formazione Integrata, Istituto Universitario di Studi Superiori di Pavia. December 2004.

• Giorgino T. Language trees, zipping and error estimation. Final thesis for the first year of the Scuola Avanzata di Formazione Integrata, Istituto Universitario di Studi Superiori di Pavia. November 2002.