Furini Simone

1. Alavizargar, A., Berti, C., Ejtehadi, M. R. & Furini, S. Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca 2+ Selectivity in CRAC Channels. J. Phys. Chem. B acs.jpcb.7b12453 (2018). doi:10.1021/acs.jpcb.7b12453
2. Ceroni, F. et al. Burden-driven feedback control of gene expression. Nat. Methods (2018).
3. Baldassarri, M. et al. Omic Approach in Non-smoker Female with Lung Squamous Cell Carcinoma Pinpoints to Germline Susceptibility and Personalized Medicine. J Korean Cancer Assoc 0, 0 (2017).
4. Gardini, S., Furini, S., Santucci, A. & Niccolai, N. A structural bioinformatics investigation on protein–DNA complexes delineates their modes of interaction. Mol. BioSyst. 13, 1010–1017 (2017).
5. Cortesi, M. et al. Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up. J. Biol. Eng. 11, 8 (2017).
6. Pinto, A. M. et al. Combined ultrasound and exome sequencing approach recognizes Opitz G/BBB syndrome in two malformed fetuses. Clin. Dysmorphol. 26, 18–25 (2017).
7. Bianciardi, L. et al. Exome sequencing coupled with mRNA analysis identifies NDUFAF6 as a Leigh gene. Mol. Genet. Metab. 119, 214–222 (2016).
8. Jorgensen, C., Furini, S. & Domene, C. Energetics of Ion Permeation in an Open-Activated TRPV1 Channel. Biophys. J. 111, 1214–1222 (2016).
9. Oakes, V., Furini, S., Pryde, D. & Domene, C. Exploring the Dynamics of the TWIK-1 Channel. Biophys. J. 111, 775–784 (2016).
10. Berti, C., Furini, S. & Gillespie, D. PACO: PArticle COunting Method to Enforce Concentrations in Dynamic Simulations. J. Chem. Theory Comput. 12, 925–929 (2016).
11. Bandiera, L., Furini, S. & Giordano, E. Phenotypic variability in synthetic biology applications: Dealing with noise in microbial gene expression. Front. Microbiol. 7, 1–7 (2016).
12. Imperatore, V. et al. Potentially treatable disorder diagnosed post Mortem by exome analysis in a boy with respiratory distress. Int. J. Mol. Sci. 17, (2016).
13. Oakes, V., Furini, S. & Domene, C. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations. Curr. Top. Membr. 78, 183–214 (2016).
14. Furini, S. & Domene, C. Computational studies of transport in ion channels using metadynamics. Biochim. Biophys. Acta - Biomembr. 1858, 1733–1740 (2016).
15. Bandiera, L. et al. Experimental measurements and mathematical modeling of biological noise arising from transcriptional and translational regulation of basic synthetic gene circuits. J. Theor. Biol. 395, 153–160 (2016).
16. Pinto, A. M. et al. Exome sequencing analysis in a pair of monozygotic twins re-evaluates the genetics behind their intellectual disability and reveals a CHD2 mutation. Brain Dev. 38, 590–596 (2016).
17. Calvaresi, M., Furini, S., Domene, C., Bottoni, A. & Zerbetto, F. Blocking the Passage: C 60 Geometrically Clogs K + Channels. ACS Nano 9, 4827–4834 (2015).
18. Domene, C., Barbini, P. & Furini, S. Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels. J. Chem. Theory Comput. 11, 1896–1906 (2015).
19. Darré, L., Furini, S. & Domene, C. Permeation and dynamics of an open-activated TRPV1 channel. J. Mol. Biol. 427, 537–549 (2015).
20. Furini, S. & Domene, C. DNA recognition process of the lactose repressor protein studied via metadynamics and umbrella sampling simulations. J. Phys. Chem. B 118, 13059–13065 (2014).
21. Berti, C. et al. Three-dimensional Brownian dynamics simulator for the study of ion permeation through membrane pores. J. Chem. Theory Comput. 10, 2911–2926 (2014).
22. Barbini, P., Barbini, E., Furini, S. & Cevenini, G. A straightforward approach to designing a scoring system for predicting length-of-stay of cardiac surgery patients. BMC Med. Inform. Decis. Mak. 14, 89 (2014).
23. Pessoa, J., Fonseca, F., Furini, S. & Morais-Cabral, J. H. Determinants of ligand selectivity in a cyclic nucleotide–regulated potassium channel. J. Gen. Physiol. 144, 41–54 (2014).
24. Renieri, A. et al. Oligogenic germline mutations identified in early non-smokers lung adenocarcinoma patients. Lung Cancer 85, 168–174 (2014).
25. Furini, S., Barbini, P. & Domene, C. Effects of the protonation state of the EEEE motif of a bacterial Na +-channel on conduction and pore structure. Biophys. J. 106, 2175–2183 (2014).
26. Bartolucci, C. et al. Combined action potential- and dynamic-clamp for accurate computational modelling of the cardiac IKr current. J. Mol. Cell. Cardiol. 79, 835–838 (2015).
27. Furini, S. & Domene, C. K+ and Na+ Conduction in Selective and Nonselective Ion Channels Via Molecular Dynamics Simulations. Biophys. J. 105, 1737–1745 (2013).
28. Furini, S., Barbini, P. & Domene, C. DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence. Nucleic Acids Res. 41, 3963–3972 (2013).
29. Grillo, E. et al. Revealing the Complexity of a Monogenic Disease: Rett Syndrome Exome Sequencing. PLoS One 8, e56599 (2013).
30. Barbini, P., Cevenini, G., Furini, S. & Barbini, E. A naive approach for deriving scoring systems to support clinical decision making. J. Eval. Clin. Pract. 20, 1–6 (2014).
31. Furini, S. & Domene, C. Nonselective Conduction in a Mutated NaK Channel with Three Cation-Binding Sites. Biophys. J. 103, 2106–2114 (2012).
32. Ceroni, F., Furini, S., Stefan, A., Hochkoeppler, A. & Giordano, E. A synthetic Post-transcriptional controller to explore the modular design of gene circuits. ACS Synth. Biol. 1, 163–171 (2012).
33. Furini, S. & Domene, C. On conduction in a bacterial sodium channel. PLoS Comput. Biol. 8, e1002476 (2012).
34. Domene, C. & Furini, S. Molecular Dynamics Simulations of the TrkH Membrane Protein. Biochemistry 51, 1559–1565 (2012).
35. Furini, S. & Domene, C. Gating at the selectivity filter of ion channels that conduct Na \n + and K \n + ions. Biophys. J. 101, 1623–1631 (2011).
36. Furini, S. & Domene, C. Selectivity and Permeation of Alkali Metal Ions in K+-channels. J. Mol. Biol. 409, 867–878 (2011).
37. Illingworth, C. J. R., Furini, S. & Domene, C. Computational Studies on Polarization Effects and Selectivity in K + Channels. J. Chem. Theory Comput. 6, 3780–3792 (2010).
38. Ceroni, F., Furini, S., Giordano, E. & Cavalcanti, S. Rational design of modular circuits for gene transcription: A test of the bottom-up approach. J. Biol. Eng. 4, 14 (2010).
39. Domene, C. & Furini, S. On ionic conduction in potassium channels. Proc. Natl. Acad. Sci. 107, E128–E128 (2010).
40. Furini, S., Domen, C. & Cavalcanti, S. Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. J. Phys. Chem. B 114, 2238–2245 (2010).
41. Ceroni, F., Furini, S. & Cavalcanti, S. A computational model of gene expression in an inducible synthetic circuit. Pacific Symp. Biocomput. 2010, PSB 2010 409–420 (2010).
42. Furini, S. & Domene, C. Atypical mechanism of conduction in potassium channels. Proc. Natl. Acad. Sci. 16074–16077 (2009).
43. Domene, C. & Furini, S. Dynamics, Energetics, and Selectivity of the Low-K+ KcsA Channel Structure. J. Mol. Biol. 389, 637–645 (2009).
44. Furini, S., Beckstein, O. & Domene, C. Permeation of water through the KcsA K + channel. Proteins Struct. Funct. Bioinforma. 74, 437–448 (2009).
45. Furini, S., Domene, C., Rossi, M., Tartagni, M. & Cavalcanti, S. Model-Based Prediction of the α-Hemolysin Structure in the Hexameric State. Biophys. J. 95, 2265–2274 (2008).
46. Grandi, E. et al. Induction of NO synthase 2 in ventricular cardiomyocytes incubated with a conventional bicarbonate dialysis bath. Nephrol. Dial. Transplant. 23, 2192–2197 (2008).
47. Domene, C., Vemparala, S., Furini, S., Sharp, K. & Klein, M. L. The Role of Conformation in Ion Permeation in a K + Channel. J. Am. Chem. Soc. 130, 3389–3398 (2008).
48. Furini, S., Zerbetto, F. & Cavalcanti, S. Role of the Intracellular Cavity in Potassium Channel Conductivity. J. Phys. Chem. B 111, 13993–14000 (2007).
49. Furini, S., Zerbetto, F. & Cavalcanti, S. Application of the Poisson-Nernst-Planck Theory with Space-Dependent Diffusion Coefficients to KcsA. Biophys. J. 91, 3162–3169 (2006).
50. Gómez-Varela, D. et al. Different relevance of inactivation and F468 residue in the mechanisms of hEag1 channel blockage by astemizole, imipramine and dofetilide. FEBS Lett. 580, 5059–5066 (2006).

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