PAOLO TIERI                                                                   home

Main publications

1.    Palumbo MC, Morettini M, Tieri P, Diele F, Sacchetti M, Castiglione F (2018) Personalizing physical exercise in a computational model of fuel homeostasis, PLoS Computational Biology, accepted for publication

2.    Tieri P, Farina L, Petti M, Astolfi L, Paci P, Castiglione F (2018) Network inference and reconstruction in Bioinformatics, in Encyclopedia of Bioinformatics and Computational Biology, 1st Ed., Editors-in-Chiefs: Ranganathan S, Nakai K, Schonbach C, in press

3.    Zanin M, Chorbev I, Stres B, Stalidzans E, Vera J, Tieri P, Castiglione F, Groen D, Zheng H, Baumbach J, Schmid JA, Basilio J, Klimek P, Debeljak N, Rozman D, Schmidt HHW (2017) Community effort endorsing multiscale modeling, multiscale data science and multiscale computing for systems medicine, Briefing in Bioinformatics, accepted for publication

4.    Ribeiro H, Maioli TU, de Freitas LM, Tieri P, Castiglione F. (2017) Modeling immune response to leishmania species indicates adenosine as an important inhibitor of Th-Cell activation. Frontiers in Cell and Infect Microbiol, doi:10.3389/fcimb.2017.00309 here

5.    Moreau JF, Pradeu T, Grignolio A, Nardini C, Castiglione F, Tieri P, Capri M, Salvioli S, Taupin JL, Garagnani P, Franceschi C. (2016) The emerging role of ECM crosslinking in T cell mobility as a hallmark of immunosenescence in humans. Ageing Research Reviews, 35:322-335, doi:10.1016/j.arr.2016.11.005 here

6.    Mendez T, Castiglione F, Tieri P, Felicori L. Systems and Synthetic Biology applied to Health (2016), Curr Dev Biotech Bioeng, Elsevier, doi:10.1016/B978-0-444-63660-7.00009-7 here

7.    Castiglione F, Tieri P, Palma A, Jarrah AS (2016) Statistical ensemble of gene regulatory networks of macrophage differentiation. BMC Bioinformatics, 17:506, doi:10.1186/s12859-016-1363-4 here

8.    Bartoletti-Stella A, Chiaro G, Calandra-Buonaura G, Contin M, Scaglione C, Barletta G, Cecere A, Garagnani P, Tieri P, Ferrarini A, Piras S, Franceschi C, Delledonne M, Cortelli P, Capellari S. (2015) A patient with PMP22-related hereditary neuropathy and DBH-gene-related dysautonomia. J Neurol. PMID: 26410747, here

9.    Tieri P, Nardini C, Dent JE, editors (2015) Multi-omic Data Integration, Publisher: Frontiers Media SA, ISBN: 978-2-88919-648-7 here

10. Nardini C, Dent J, Tieri P (2015). Editorial: Multi-omic Data Integration. Front. Cell Dev. Biol. 3:46. doi: 10.3389/fcell.2015.00046 here

11. Cappuccio A, Tieri P, Castiglione F (2015) Multiscale modelling in immunology: a review. Briefings in Bioinformatics, doi: 10.1093/bib/bbv012 here

12. Tieri P, Prana V, Colombo T, Santoni D, Castiglione F. (2014) Multi-scale Simulation of T Helper Lymphocyte Differentiation. In: Campos S, editor. Advances in Bioinformatics and Computational Biology. Lecture Notes in Computer Science. 8826: Springer International Publishing; 2014. p. 123-34 DOI: 10.1007/978-3-319-12418-6_16 here

13. Tieri P, Zhou XY, Zhu L, Nardini C. (2014) Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects. Front. Cell Dev. Biol., 2:59. doi: 10.3389/fcell.2014.00059 here

14. Grignolio A, Mishto M, Faria AMC, Garagnani P, Franceschi C, Tieri P. (2014) Towards a liquid self: how time, geography, and life experiences reshape the biological identity. Front. Immunol, 5:153. doi: 10.3389/fimmu.2014.00153 here

15. Castiglione F, Tieri P, De Graaf A, Franceschi C, Liò P, Van Ommen B, Mazzà C, Tuchel A, Bernaschi M, Samson C, Colombo T, Castellani GC, Capri M, Garagnani P, Salvioli S, Nguyen VA, Bobeldijk-Pastorova I, Krishnan S, Cappozzo A, Sacchetti M, Morettini M, Ernst M. (2013) The onset of type 2 diabetes: proposal for a multi-scale model. JMIR Res Protoc. Oct 31;2(2):e44. doi: 10.2196/resprot.2854. PubMed PMID: 24176906 here

16. Tieri P, Nardini C. (2013) Signalling Pathway Databases Usability: Lessons Learned. Mol BioSyst, 2013 Oct;9(10):2401-7. doi: 10.1039/c3mb70242a. PubMed PMID: 23942525 here

17. Garagnani P, Giuliani C, Pirazzini C, Olivieri F, Bacalini MG, Ostan R, Mari D, Passarino G, Monti D, Bonfigli AR, Boemi M, Ceriello A, Genovese S, Sevini FLuiselli D, Tieri P, Capri M, Salvioli S, Vijg J, Suh Y, Delledonne M, Testa R, Franceschi C. (2013) Centenarians as super-controls to assess the biological relevance of genetic risk factors for common age-related diseases: A proof of principle on  type 2 diabetes. Aging; 5(5): 373-85 PMID: 23804578 here

18. Tieri P, Bellavista E, Termanini A, Salvioli S, Capri M, Franceschi C (2012) Charting the NF-kB interactome map. PLoS ONE, 7(3): e32678. doi:10.1371/journal.pone.0032678. here

19. Tieri P, de la Fuente A, Termanini A, Franceschi C (2011) Integrating omics data for signaling pathways, interactome reconstruction, and functional analysis. Methods Mol. Biol. 719, 415-33 rated “must read” by   FACULTYof1000 here, here and here

20. Tieri P, Grignolio A, Zaikin A, Mishto M, Remondini D, Castellani GC, Franceschi C (2010) Network, degeneracy and bow tie: integrating paradigms and architectures to grasp the complexity of the immune system. Theoretical Biology and Medical Modelling, 7, 32 here

21. Termanini A, Tieri P, Franceschi C (2010) Encoding the states of interacting proteins to facilitate biological pathways reconstruction. Biology Direct, 5, 52  here

22. Grignolio A, Tieri P, Castellani GC (2010) Networks, Degeneracy and Bow ties: A Unifying Perspective of Immunological Paradigms and Architectures, in: Immunology Today - Three Historical Perspectives under Three Theoretical Horizons, Grignolio A Ed., Bononia University Press, Quaderni del CIG series, 2, 53-68.

23. Cevenini E, Bellavista E, Tieri P, Castellani G, Lescai F, Francesconi M, Mishto M, Santoro A, Valensin S, Salvioli S, Capri M, Zaikin A, Monti D, de Magalhães JP, Franceschi C (2010) Systems Biology and Longevity: an emerging approach to identify innovative anti-aging targets and strategies, Curr. Pharm. Des.,16, 802-813. here and here

24. Tieri P, Grignolio A, (2009) Paradigms and architectures in the immune system: from degeneracy to bow ties, in: ACUME2 Living Texts conference series proceedings, PNW Polish Scientific Publishers, 57-70.

25. Capri M, Salvioli S, Cevenini E, Celani L, Sevini F, Bellavista E, Lanzarini C, Lukas S, Lescai F, Tieri P, Monti D, Franceschi C (2009) Aging and Longevity in Animal Models and Humans, in: Life-Span Extension, Aging Medicine, Sell C et al. eds., Springer/Humana Press, DOI: 10.1007/978-1-60327-507-1_11, 175-191 here and here

26. Tieri P (2008) The immune system: look who's talking, in: Biocomplexity at the cutting edge of Physics, Systems Biology and Humanities, Bononia University Press, Quaderni del CIG series, 1, 145-154 here

27. Cevenini E, Invidia L, Lescai F, Salvioli S, Tieri P, Castellani GC, Franceschi C (2008) Human models of aging and longevity. Expert Opin. Biol. Ther. 8 (9), 1393-1405 here

28. Salvioli S, Capri M, Tieri P, Loroni J, Barbi C, Invidia L, Altilia S, Santoro A, Pirazzini C, Pierini MBellavista E, Alberghina L, Franceschi C (2008) Different types of cell death in organismal aging and longevity: state of the art and possible systems biology approach, Curr. Pharm. Des., 14, 226-236 here and here

29. Salvioli S, Tieri P, Castellani GC, Capri M, Barbi C, Santoro A, Altilia S, Invidia L, Pierini M, Bellavista E, Monti D, Franceschi C (2007) Longevity genes across species: conservation versus evolvability, Inv. Surviv. J., 4, 112-118 here

30. Remondini D, Neretti N, Sedivy JM, Franceschi C, Milanesi L, Tieri P, Castellani GC (2007) Networks from gene expression time series: characterization of correlation patterns, Int. J. Bifurcat. Chaos, 17 (7), 2477-2483 here

31. Tieri P, Castellani GC, Remondini D, Valensin S, Loroni J, Salvioli S, Franceschi C (2007) Capturing Degeneracy in the Immune System, in: In silico Immunology, D. Flower and J. Timmis Eds., Springer Verlag, New York, ISBN 9780387392387, pp 109-118 here

32. Remondini D, Tieri P, Valensin S, Verondini E, Franceschi C, Bersani F, Castellani GC (2006) A general learning rule for network modeling of neuroimmune interactome, in: Neural Nets, WIRN/NAIS 2005 Proceedings, Lecture Notes in Computer Science, Springer Verlag, 3931, pp 286-292 here

33. Salvioli S, Capri M, Valensin S, Tieri P, Monti D, Ottaviani E, Franceschi C (2006) Inflamm-aging, Cytokines and Aging: state of the art, new hypotheses on the role of mitochondria and new perspectives from systems biology, Curr. Pharm. Des., 12, 3161-71 here and here

34. Tieri P, Valensin S, Latora V, Castellani GC, Marchiori M, Remondini D, Franceschi C (2005) Quantifying the relevance of different mediators in the human immune cell network, Bioinformatics, 21, 1639-1643 here

35. Tieri P, Valensin S, Franceschi C, Morandi C, Castellani GC (2003) Memory and selectivity in evolving scale-free immune networks, in Artificial Immune Systems, ICARIS 2003 Proceedings, Lecture Notes in Computer Science, Springer-Verlag, 2787, pp.93-101 here


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