ISI pubblications

My account on ResearchGate
  1. Berti, C., Furini, S. & Gillespie, D. (2016). PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations. Journal of Chemical Theory and Computation 12, 925-929.
  2. Bandiera, L., Furini, S. & Giordano, E. (2016). Phenotypic Variability in Synthetic Biology Applications: Dealing with Noise in Microbial Gene Expression. Frontiers in Microbiology 7, 479.
  3. Imperatore, V., Mencarelli, M. A., Fallerini, C., Bianciardi, L., Ariani, F., Furini, S., Renieri, A., Mari, F. & Frullanti, E. (2016). Potentially Treatable Disorder Diagnosed Post Mortem by Exome Analysis in a Boy with Respiratory Distress. International Journal of Molecular Sciences 17, 306.
  4. Furini, S. & Domene, C. (2016). Computational studies of transport in ion channels using metadynamics. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 1733-1740.
  5. Bandiera, L., Pasini, A., Pasotti, L., Zucca, S., Mazzini, G., Magni, P., Giordano, E. & Furini, S. (2016). Experimental measurements and mathematical modeling of biological noise arising from transcriptional and translational regulation of basic synthetic gene circuits. Journal of Theoretical Biology 395, 153-160.
  6. Pinto, A. M., Bianciardi, L., Mencarelli, M. A., Imperatore, V., Di Marco, C., Furini, S., Suppiej, A., Salviati, L., Tenconi, R., Ariani, F., Mari, F. & Renieri, A. (2016). Exome sequencing analysis in a pair of monozygotic twins re-evaluates the genetics behind their intellectual disability and reveals a CHD2 mutation. Brain and Development 38, 590-596.
  7. Calvaresi, M., Furini, S., Domene, C., Bottoni, A. & Zerbetto, F. (2015). Blocking the Passage: C Geometrically Clogs K Channels. ACS Nano 9(5),4827-34
  8. Domene, C., Barbini, P. & Furini, S. (2015). Bias-exchange metadynamics simulations: An efficient strategy for the analysis of conduction and selectivity in ion channels. Journal of Chemical Theory and Computation 11, 1896-1906. 
  9. Bartolucci, C., Altomare, C., Bennati, M., Furini, S., Zaza, A. & Severi, S. (2015). Combined action potential- and dynamic-clamp for accurate computational modelling of the cardiac IKr current. Journal of Molecular and Cellular Cardiology 79, 187-194.
  10. Darre, L., Furini, S. & Domene, C. (2015). Permeation and dynamics of an open-activated TRPV1 channel. J Mol Biol 427, 537-49.
  11. Furini, S., Domene, C. (2014). DNA recognition process of the lactose repressor protein studied via metadynamics and umbrella sampling simulations. J Phys Chem B 118(46):13059-65          
  12. Berti, C., Furini, S., Gillespie, D., Boda, D., Eisenberg, R. S., Sangiorgi, E. & Fiegna, C. (2014). Three-Dimensional Brownian Dynamics Simulator for the Study of Ion Permeation through Membrane Pores. Journal of Chemical Theory and Computation 10, 2911-2926.
  13. Pessoa J, Fonseca F, Furini S, Morais-Cabral JH. (2014). Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel. J Gen Physiol. 144:41-54.
  14. Renieri A, Mencarelli MA, Cetta F, Baldassarri M, Mari F, Furini S, Piu P, Ariani F, Dragani TA, Frullanti E. (2014). Oligogenic germline mutations identified in early non-smokers lung adenocarcinoma patients. Lung Cancer.
  15. Furini S, Barbini P, Domene C. (2014). Effects of the protonation state of the EEEE motif of a bacterial Na(+)-channel on conduction and pore structure. Biophys J 106, 2175-83.
  16. Barbini, P., Cevenini, G., Furini, S. & Barbini, E. (2014). A naive approach for deriving scoring systems to support clinical decision making. J Eval Clin Pract 20, 1-6.
  17. Furini, S. & Domene, C. (2013). K+ and Na+ conduction in selective and nonselective ion channels via Molecular Dynamics simulations. Biophys J 105, 1737-1745.
  18. Grillo, E., Lo Rizzo, C., Bianciardi, L., Bizzarri, V., Baldassarri, M., Spiga, O., Furini, S., De Felice, C., Signorini, C., Leoncini, S., Pecorelli, A., Ciccoli, L., Mencarelli, M. A., Hayek, J., Meloni, I., Ariani, F., Mari, F. & Renieri, A. (2013). Revealing the complexity of a monogenic disease: rett syndrome exome sequencing. PLoS One 8, e56599
  19. Furini, S., Barbini, P. & Domene, C. (2013). DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence. Nucl Acids Res 41, 3963-3972
  20. Furini, S. & Domene, C. (2012). Nonselective conduction in a mutated NaK channel with three cation-binding sites. Biophys J 103, 2106-14.
  21. Ceroni, F., Furini, S., Stefan, A., Hochkoeppler, A. & Giordano, E. (2012). A Synthetic Post-transcriptional Controller To Explore the Modular Design of Gene Circuits. ACS Synth. Biol. 1, 163-171.
  22. Furini, S. & Domene, C. (2012). On conduction in a bacterial sodium channel. PLoS Comput Biol 8, e1002476.
  23. Domene, C. & Furini, S. (2012). Molecular dynamics simulations of the TrkH membrane protein. Biochemistry 51, 1559-65.
  24. Furini, S. & Domene, C. (2011). Gating at the selectivity filter of ion channels that conduct Na+ and K+ ions. Biophys J 101, 1623-31.
  25. Furini, S. & Domene, C. (2011). Selectivity and permeation of alkali metal ions in K+-channels. J Mol Biol 409, 867-78.
  26. Illingworth, C. J. R., Furini, S. & Domene, C. (2010). Computational Studies on Polarization Effects and Selectivity in K+ Channels. J. Chem. Theory Comput. 6, 3780–3792.
  27. Ceroni, F., Furini, S., Giordano, E. & Cavalcanti, S. (2010). Rational design of modular circuits for gene transcription: A test of the bottom-up approach. J Biol Eng 4, 14.
  28. Domene, C. & Furini, S. (2010). On ionic conduction in potassium channels. Proc Natl Acad Sci U S A 107, E128; author reply E129.
  29. Furini, S., Domene, C. & Cavalcanti, S. (2010). Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. J Phys Chem B 114, 2238-45.
  30. Furini, S. & Domene, C. (2009). Atypical mechanism of conduction in potassium channels. Proc Natl Acad Sci U S A 106, 16074-7.
  31. Domene, C. & Furini, S. (2009). Dynamics, Energetics, and Selectivity of the Low-K+ KcsA Channel Structure. Journal of Molecular Biology 389, 637-645.
  32. Furini, S., Beckstein, O. & Domene, C. (2009). Permeation of water through the KcsA K+ channel. Proteins 74, 437-48.
  33. Domene, C., Furini, S., Michael, L. J., Gary, K. A. & Jo, M. H. (2009). Examining Ion Channel Properties Using Free-Energy Methods. In Methods in Enzymology, Vol. Volume 466, pp. 155-177. Academic Press.
  34. Furini, S., Domene, C., Rossi, M., Tartagni, M. & Cavalcanti, S. (2008). Model-based prediction of the alpha-hemolysin structure in the hexameric state. Biophys J 95, 2265-74.
  35. Grandi, E., Govoni, M., Furini, S., Severi, S., Giordano, E., Santoro, A. & Cavalcanti, S. (2008). Induction of NO synthase 2 in ventricular cardiomyocytes incubated with a conventional bicarbonate dialysis bath. Nephrol Dial Transplant 23, 2192-7.
  36. Domene, C., Vemparala, S., Furini, S., Sharp, K. & Klein, M. L. (2008). The role of conformation in ion permeation in a K+ channel. J Am Chem Soc 130, 3389-98.
  37. Furini, S., Zerbetto, F. & Cavalcanti, S. (2007). Role of the intracellular cavity in potassium channel conductivity. Journal of Physical Chemistry B 111, 13993-14000.
  38. Furini, S., Zerbetto, F. & Cavalcanti, S. (2006). Application of the Poisson-Nernst-Planck theory with space-dependent diffusion coefficients to KcsA. Biophys J 91, 3162-9.
  39. Gómez-Varela, D., Contreras-Jurado, C., Furini, S., García-Ferreiro, R., Stühmer, R. & Pardo, L., A. (2006). Different relevance of inactivation and F468 residue in the mechanisms of hEag1 channel blockage by astemizole, imipramine and dofetilide. FEBS Letters 580, 5059-5066.