• Alavizargar, A.,, Berti, C.,, Ejtehadi, M. R., Furini, S. (2018). Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca2+ Selectivity in CRAC Channels. Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.7b12453.
  • Ceroni, F., Boo, A., Furini, S., Gorochowski, T.E., Borkowski O., Ladak Y.N., Awan, A.R., Gilbert, C., Stan. G.B., Ellis, T. (2018). Burden-driven feedback control of gene expression. Nat Methods. 2018 Mar 26. doi: 10.1038/nmeth.4635


  • Gardini, S., Furini, S., Santucci, A. & Niccolai, N. (2017). A structural bioinformatics investigation on protein–DNA complexes delineates their modes of interaction. Molecular BioSystems. 13, 1010–1017.
  • Baldassarri, M., Fallerini, C., Cetta, F., Ghisalberti, M., Bellan, C., Furini, S., Spiga, O., Crispino, S., Gotti, G., Ariani, F., Paladini, P., Renieri, A., Frullanti, E. (2017). "Omic" Approach in Non-Smoker Female with Lung Squamous Cell Carcinoma Pinpoints to Germline Susceptibility and Personalized Medicine. Cancer Res Treat. May 26. doi: 10.4143/crt.2017.125.
  • Cortesi, M., Bandiera, L., Pasini, A., Bevilacqua, A., Gherardi, A., Furini, S., Giordano, E. (2017). Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up. Journal of Biological Engineering. 11, 8.
  • Pinto, Anna Maria; Imperatore, Valentina; Bianciardi, Laura; Baldassarri, Margherita; Galluzzi, Paolo; Furini, Simone; Centini, Giovanni; Renieri, Alessandra; Mari, Francesca. (2017). Combined ultrasound and exome sequencing approach recognizes Opitz G/BBB syndrome in two malformed fetuses. Clinical Dysmorphology 26, 18-25.


  • Bianciardi, L., Imperatore, V., Fernandez-Vizarra, E., Lopomo, A., Falabella, M., Furini, S., Galluzzi, P., Grosso, S., Zeviani, M., Renieri, A., Mari, F. & Frullanti, E. (2016). Exome sequencing coupled with mRNA analysis identifies NDUFAF6 as a Leigh gene. Molecular Genetics and Metabolism 119, 214-222.
  • Jorgensen, C., Furini, S. & Domene, C. (2016). Energetics of Ion Permeation in an Open-Activated TRPV1 Channel. Biophysical Journal 111, 1214-1222.
  • Oakes, V., Furini, S., Pryde, D. & Domene, C. (2016). Exploring the Dynamics of the TWIK-1 Channel. Biophysical Journal 111, 775-784.
  • 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.
  • 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.
  • 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.
  • Oakes, V., Furini, S. & Domene, C. (2016). Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations. Current Topics in Membranes. 78, 183–214 .
  • Furini, S. & Domene, C. (2016). Computational studies of transport in ion channels using metadynamics. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 1733-1740.
  • 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.
  • 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.


  • Calvaresi, M., Furini, S., Domene, C., Bottoni, A. & Zerbetto, F. (2015). Blocking the Passage: C60 Geometrically Clogs K+ Channels. ACS Nano 9, 4827-4834.
  • 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.
  • 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.
  • Darre, L., Furini, S. & Domene, C. (2015). Permeation and dynamics of an open-activated TRPV1 channel. Journal of Molecular Biology 427, 537-49.


  • Furini, S. & Domene, C. (2014). DNA Recognition Process of the Lactose Repressor Protein Studied via Metadynamics and Umbrella Sampling Simulations. The Journal of Physical Chemistry B 118, 13059-13065.
  • 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.
  • Barbini, P., Barbini, E., Furini, S. & Cevenini, G. (2014). A straightforward approach to designing a scoring system for predicting length-of-stay of cardiac surgery patients. BMC Medical Informatics and Decision Making 14, 89.
  • Pessoa, J., Fonseca, F., Furini, S. & Morais-Cabral, J. H. (2014). Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel. The Journal of General Physiology 144, 41-54.
  • Renieri, A., Mencarelli, M. A., Cetta, F., Baldassarri, M., Mari, F., Furini, S., Piu, P., Ariani, F., Dragani, T. A. & Frullanti, E. (2014). Oligogenic germline mutations identified in early non-smokers lung adenocarcinoma patients. Lung Cancer 85, 168-74.
  • 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. Biophysical Journal 106, 2175-83.
  • Barbini, P., Cevenini, G., Furini, S. & Barbini, E. (2014). A naive approach for deriving scoring systems to support clinical decision making. Journal of evaluation in clinical practice 20, 1-6.


  • Bartolucci, C., Altomare, C., Bennati, M., Furini, S., Zaza, A. & Severi, S. (2013). Computing in Cardiology, Zaragoza, SPAIN.
  • Furini, S. & Domene, C. (2013). K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations. Biophysical journal 105, 1737-45.
  • 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. Nucleic acids research 41, 3963-72.
  • 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.


  • Furini, S. & Domene, C. (2012). Nonselective conduction in a mutated NaK channel with three cation-binding sites. Biophysical Journal 103, 2106-14.
  • 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 Synthetic Biology 1, 163-171.
  • Furini, S. & Domene, C. (2012). On conduction in a bacterial sodium channel. PLOS Computational Biology 8, e1002476.
  • Domene, C. & Furini, S. (2012). Molecular dynamics simulations of the TrkH membrane protein. Biochemistry 51, 1559-65.


  • Furini, S. & Domene, C. (2011). Gating at the selectivity filter of ion channels that conduct Na+ and K+ ions. Biophysical Journal 101, 1623-31.
  • Furini, S. & Domene, C. (2011). Selectivity and permeation of alkali metal ions in K+-channels. Journal of Molecular Biology 409, 867-78.


  • Illingworth, C. J. R., Furini, S. & Domene, C. (2010). Computational Studies on Polarization Effects and Selectivity in K+ Channels. Journal of Chemical Theory and Computation 6, 3780–3792.
  • Ceroni, F., Furini, S., Giordano, E. & Cavalcanti, S. (2010). Rational design of modular circuits for gene transcription: A test of the bottom-up approach. Journal of Biological Engineering 4, 14.
  • Domene, C. & Furini, S. (2010). On ionic conduction in potassium channels. Proceedings of the National Academy of Sciences of the United States of America 107, E128; author reply E129.
  • Furini, S., Domene, C. & Cavalcanti, S. (2010). Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. The Journal of Physical Chemistry B 114, 2238-45.
  • Ceroni, F., Furini, S. & Cavalcanti, S. (2010). A computational model of gene expression in an inducible synthetic circuit. Pacific Symposium on Biocomputing, 409-20.


  • Furini, S. & Domene, C. (2009). Atypical mechanism of conduction in potassium channels. Proceedings of the National Academy of Sciences of the United States of America 106, 16074-7.
  • Domene, C. & Furini, S. (2009). Dynamics, Energetics, and Selectivity of the Low-K+ KcsA Channel Structure. Journal of Molecular Biology 389, 637-645.
  • Furini, S., Beckstein, O. & Domene, C. (2009). Permeation of water through the KcsA K+ channel. Proteins: Structure, Function, and Bioinformatics 74, 437-48.
  • 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.


  • Furini, S., Domene, C., Rossi, M., Tartagni, M. & Cavalcanti, S. (2008). Model-based prediction of the alpha-hemolysin structure in the hexameric state. Biophysical Journal 95, 2265-74.
  • 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. Nephrology Dialysis Transplantation 23, 2192-7.
  • Domene, C., Vemparala, S., Furini, S., Sharp, K. & Klein, M. L. (2008). The role of conformation in ion permeation in a K+ channel. Journal of the American Chemical Society 130, 3389-98.


  • Furini, S., Zerbetto, F. & Cavalcanti, S. (2007). Role of the intracellular cavity in potassium channel conductivity. The Journal of Physical Chemistry B 111, 13993-14000.


  • Furini, S., Zerbetto, F. & Cavalcanti, S. (2006). Application of the Poisson-Nernst-Planck theory with space-dependent diffusion coefficients to KcsA. Biophysical Journal 91, 3162-9.
  • 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.