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Items: 1 to 50 of 57

1.

Insights into the mechanisms of K+ permeation in K+-channels from computer simulations.

Oakes V, Furini S, Domene C.

J Chem Theory Comput. 2019 Dec 6. doi: 10.1021/acs.jctc.9b00971. [Epub ahead of print]

PMID:
31809048
2.

New frontiers to cure Alport syndrome: COL4A3 and COL4A5 gene editing in podocyte-lineage cells.

Daga S, Donati F, Capitani K, Croci S, Tita R, Giliberti A, Valentino F, Benetti E, Fallerini C, Niccheri F, Baldassarri M, Mencarelli MA, Frullanti E, Furini S, Conticello SG, Renieri A, Pinto AM.

Eur J Hum Genet. 2019 Nov 21. doi: 10.1038/s41431-019-0537-8. [Epub ahead of print]

PMID:
31754267
3.

Modulation of the potassium channel KcsA by anionic phospholipids: Role of arginines at the non-annular lipid binding sites.

Poveda JA, Giudici AM, Renart ML, Millet O, Morales A, González-Ros JM, Oakes V, Furini S, Domene C.

Biochim Biophys Acta Biomembr. 2019 Oct 1;1861(10):183029. doi: 10.1016/j.bbamem.2019.183029. Epub 2019 Jul 24.

PMID:
31351058
4.

Identification via Numerical Computation of Transcriptional Determinants of a Cell Phenotype Decision Making.

Cortesi M, Pasini A, Furini S, Giordano E.

Front Genet. 2019 Jun 21;10:575. doi: 10.3389/fgene.2019.00575. eCollection 2019.

5.

Non-collagen genes role in digenic Alport syndrome.

Daga S, Fallerini C, Furini S, Pecoraro C, Scolari F, Ariani F, Bruttini M, Mencarelli MA, Mari F, Renieri A, Pinto AM.

BMC Nephrol. 2019 Feb 26;20(1):70. doi: 10.1186/s12882-019-1258-5.

6.

Ion-triggered selectivity in bacterial sodium channels.

Furini S, Domene C.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):5450-5455. doi: 10.1073/pnas.1722516115. Epub 2018 May 7.

7.

iPSC-derived neurons profiling reveals GABAergic circuit disruption and acetylated α-tubulin defect which improves after iHDAC6 treatment in Rett syndrome.

Landucci E, Brindisi M, Bianciardi L, Catania LM, Daga S, Croci S, Frullanti E, Fallerini C, Butini S, Brogi S, Furini S, Melani R, Molinaro A, Lorenzetti FC, Imperatore V, Amabile S, Mariani J, Mari F, Ariani F, Pizzorusso T, Pinto AM, Vaccarino FM, Renieri A, Campiani G, Meloni I.

Exp Cell Res. 2018 Jul 15;368(2):225-235. doi: 10.1016/j.yexcr.2018.05.001. Epub 2018 May 4.

PMID:
29730163
8.

Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca2+ Selectivity in Calcium Release-Activated Calcium Channels.

Alavizargar A, Berti C, Ejtehadi MR, Furini S.

J Phys Chem B. 2018 Apr 26;122(16):4407-4417. doi: 10.1021/acs.jpcb.7b12453. Epub 2018 Apr 11.

PMID:
29600712
9.

Burden-driven feedback control of gene expression.

Ceroni F, Boo A, Furini S, Gorochowski TE, Borkowski O, Ladak YN, Awan AR, Gilbert C, Stan GB, Ellis T.

Nat Methods. 2018 May;15(5):387-393. doi: 10.1038/nmeth.4635. Epub 2018 Mar 26.

10.

Omic Approach in Non-smoker Female with Lung Squamous Cell Carcinoma Pinpoints to Germline Susceptibility and Personalized Medicine.

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.

Cancer Res Treat. 2018 Apr;50(2):356-365. doi: 10.4143/crt.2017.125. Epub 2017 May 26.

11.

A structural bioinformatics investigation on protein-DNA complexes delineates their modes of interaction.

Gardini S, Furini S, Santucci A, Niccolai N.

Mol Biosyst. 2017 May 2;13(5):1010-1017. doi: 10.1039/c7mb00071e.

PMID:
28418051
12.

Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up.

Cortesi M, Bandiera L, Pasini A, Bevilacqua A, Gherardi A, Furini S, Giordano E.

J Biol Eng. 2017 Feb 20;11:8. doi: 10.1186/s13036-017-0050-y. eCollection 2017.

13.

Exome sequencing coupled with mRNA analysis identifies NDUFAF6 as a Leigh gene.

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.

Mol Genet Metab. 2016 Nov;119(3):214-222. doi: 10.1016/j.ymgme.2016.09.001. Epub 2016 Sep 3.

PMID:
27623250
14.

Combined ultrasound and exome sequencing approach recognizes Opitz G/BBB syndrome in two malformed fetuses.

Pinto AM, Imperatore V, Bianciardi L, Baldassarri M, Galluzzi P, Furini S, Centini G, Renieri A, Mari F.

Clin Dysmorphol. 2017 Jan;26(1):18-25.

PMID:
27749392
15.

Energetics of Ion Permeation in an Open-Activated TRPV1 Channel.

Jorgensen C, Furini S, Domene C.

Biophys J. 2016 Sep 20;111(6):1214-1222. doi: 10.1016/j.bpj.2016.08.009.

16.

Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations.

Oakes V, Furini S, Domene C.

Curr Top Membr. 2016;78:183-214. doi: 10.1016/bs.ctm.2015.12.002. Epub 2016 Mar 14. Review.

PMID:
27586285
17.

Exploring the Dynamics of the TWIK-1 Channel.

Oakes V, Furini S, Pryde D, Domene C.

Biophys J. 2016 Aug 23;111(4):775-784. doi: 10.1016/j.bpj.2016.07.009.

18.

Phenotypic Variability in Synthetic Biology Applications: Dealing with Noise in Microbial Gene Expression.

Bandiera L, Furini S, Giordano E.

Front Microbiol. 2016 Apr 8;7:479. doi: 10.3389/fmicb.2016.00479. eCollection 2016. Review.

19.

Potentially Treatable Disorder Diagnosed Post Mortem by Exome Analysis in a Boy with Respiratory Distress.

Imperatore V, Mencarelli MA, Fallerini C, Bianciardi L, Ariani F, Furini S, Renieri A, Mari F, Frullanti E.

Int J Mol Sci. 2016 Feb 27;17(3):306. doi: 10.3390/ijms17030306.

20.

PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations.

Berti C, Furini S, Gillespie D.

J Chem Theory Comput. 2016 Mar 8;12(3):925-9. doi: 10.1021/acs.jctc.5b01044. Epub 2016 Feb 19.

PMID:
26891893
21.

Computational studies of transport in ion channels using metadynamics.

Furini S, Domene C.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1733-40. doi: 10.1016/j.bbamem.2016.02.015. Epub 2016 Feb 15. Review.

22.

Experimental measurements and mathematical modeling of biological noise arising from transcriptional and translational regulation of basic synthetic gene circuits.

Bandiera L, Pasini A, Pasotti L, Zucca S, Mazzini G, Magni P, Giordano E, Furini S.

J Theor Biol. 2016 Apr 21;395:153-160. doi: 10.1016/j.jtbi.2016.02.004. Epub 2016 Feb 10.

PMID:
26874228
23.

Exome sequencing analysis in a pair of monozygotic twins re-evaluates the genetics behind their intellectual disability and reveals a CHD2 mutation.

Pinto AM, Bianciardi L, Mencarelli MA, Imperatore V, Di Marco C, Furini S, Suppiej A, Salviati L, Tenconi R, Ariani F, Mari F, Renieri A.

Brain Dev. 2016 Jun;38(6):590-6. doi: 10.1016/j.braindev.2015.12.006. Epub 2016 Jan 2.

PMID:
26754451
24.

Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels.

Domene C, Barbini P, Furini S.

J Chem Theory Comput. 2015 Apr 14;11(4):1896-906. doi: 10.1021/ct501053x.

PMID:
26574394
25.

Blocking the passage: C60 geometrically clogs K(+) channels.

Calvaresi M, Furini S, Domene C, Bottoni A, Zerbetto F.

ACS Nano. 2015 May 26;9(5):4827-34. doi: 10.1021/nn506164s. Epub 2015 Apr 20.

26.

Permeation and dynamics of an open-activated TRPV1 channel.

Darré L, Furini S, Domene C.

J Mol Biol. 2015 Jan 30;427(2):537-49. doi: 10.1016/j.jmb.2014.11.016. Epub 2014 Dec 3.

PMID:
25479373
27.

Combined action potential- and dynamic-clamp for accurate computational modelling of the cardiac IKr current.

Bartolucci C, Altomare C, Bennati M, Furini S, Zaza A, Severi S.

J Mol Cell Cardiol. 2015 Feb;79:187-94. doi: 10.1016/j.yjmcc.2014.11.011. Epub 2014 Nov 18.

PMID:
25446181
28.

DNA recognition process of the lactose repressor protein studied via metadynamics and umbrella sampling simulations.

Furini S, Domene C.

J Phys Chem B. 2014 Nov 20;118(46):13059-65. doi: 10.1021/jp505885j. Epub 2014 Nov 6.

PMID:
25341013
29.

A straightforward approach to designing a scoring system for predicting length-of-stay of cardiac surgery patients.

Barbini P, Barbini E, Furini S, Cevenini G.

BMC Med Inform Decis Mak. 2014 Oct 13;14:89. doi: 10.1186/1472-6947-14-89.

30.

Three-Dimensional Brownian Dynamics Simulator for the Study of Ion Permeation through Membrane Pores.

Berti C, Furini S, Gillespie D, Boda D, Eisenberg RS, Sangiorgi E, Fiegna C.

J Chem Theory Comput. 2014 Aug 12;10(8):2911-26. doi: 10.1021/ct4011008.

PMID:
26588267
31.

Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel.

Pessoa J, Fonseca F, Furini S, Morais-Cabral JH.

J Gen Physiol. 2014 Jul;144(1):41-54. doi: 10.1085/jgp.201311145.

32.

Oligogenic germline mutations identified in early non-smokers lung adenocarcinoma patients.

Renieri A, Mencarelli MA, Cetta F, Baldassarri M, Mari F, Furini S, Piu P, Ariani F, Dragani TA, Frullanti E.

Lung Cancer. 2014 Aug;85(2):168-74. doi: 10.1016/j.lungcan.2014.05.020. Epub 2014 Jun 4.

PMID:
24954872
33.

Effects of the protonation state of the EEEE motif of a bacterial Na(+)-channel on conduction and pore structure.

Furini S, Barbini P, Domene C.

Biophys J. 2014 May 20;106(10):2175-83. doi: 10.1016/j.bpj.2014.04.005.

34.

K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations.

Furini S, Domene C.

Biophys J. 2013 Oct 15;105(8):1737-45. doi: 10.1016/j.bpj.2013.08.049. Review.

35.

A synthetic post-transcriptional controller to explore the modular design of gene circuits.

Ceroni F, Furini S, Stefan A, Hochkoeppler A, Giordano E.

ACS Synth Biol. 2012 May 18;1(5):163-71. doi: 10.1021/sb200021s. Epub 2012 May 10.

36.

A naïve approach for deriving scoring systems to support clinical decision making.

Barbini P, Cevenini G, Furini S, Barbini E.

J Eval Clin Pract. 2014 Feb;20(1):1-6. doi: 10.1111/jep.12064. Epub 2013 May 7.

PMID:
23648123
37.

Revealing the complexity of a monogenic disease: rett syndrome exome sequencing.

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 MA, Hayek J, Meloni I, Ariani F, Mari F, Renieri A.

PLoS One. 2013;8(2):e56599. doi: 10.1371/journal.pone.0056599. Epub 2013 Feb 28.

38.

DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence.

Furini S, Barbini P, Domene C.

Nucleic Acids Res. 2013 Apr;41(7):3963-72. doi: 10.1093/nar/gkt099. Epub 2013 Feb 20.

39.

Nonselective conduction in a mutated NaK channel with three cation-binding sites.

Furini S, Domene C.

Biophys J. 2012 Nov 21;103(10):2106-14. doi: 10.1016/j.bpj.2012.10.004. Epub 2012 Nov 20.

40.

On conduction in a bacterial sodium channel.

Furini S, Domene C.

PLoS Comput Biol. 2012;8(4):e1002476. doi: 10.1371/journal.pcbi.1002476. Epub 2012 Apr 5.

41.

Molecular dynamics simulations of the TrkH membrane protein.

Domene C, Furini S.

Biochemistry. 2012 Feb 28;51(8):1559-65. doi: 10.1021/bi201586n. Epub 2012 Feb 14.

PMID:
22316140
42.

Gating at the selectivity filter of ion channels that conduct Na+ and K+ ions.

Furini S, Domene C.

Biophys J. 2011 Oct 5;101(7):1623-31. doi: 10.1016/j.bpj.2011.08.035.

43.

Selectivity and permeation of alkali metal ions in K+-channels.

Furini S, Domene C.

J Mol Biol. 2011 Jun 24;409(5):867-78. doi: 10.1016/j.jmb.2011.04.043. Epub 2011 Apr 22.

PMID:
21540036
44.

Rational design of modular circuits for gene transcription: A test of the bottom-up approach.

Ceroni F, Furini S, Giordano E, Cavalcanti S.

J Biol Eng. 2010 Nov 11;4:14. doi: 10.1186/1754-1611-4-14.

45.

On ionic conduction in potassium channels.

Domene C, Furini S.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):E128; author reply E129. doi: 10.1073/pnas.1007693107. Epub 2010 Aug 2. No abstract available.

46.

Insights into the sliding movement of the lac repressor nonspecifically bound to DNA.

Furini S, Domene C, Cavalcanti S.

J Phys Chem B. 2010 Feb 18;114(6):2238-45. doi: 10.1021/jp906504m.

PMID:
20095570
47.

A computational model of gene expression in an inducible synthetic circuit.

Ceroni F, Furini S, Cavalcanti S.

Pac Symp Biocomput. 2010:409-20.

48.

Atypical mechanism of conduction in potassium channels.

Furini S, Domene C.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16074-7. doi: 10.1073/pnas.0903226106. Epub 2009 Sep 4.

49.

Dynamics, energetics, and selectivity of the low-K+ KcsA channel structure.

Domene C, Furini S.

J Mol Biol. 2009 Jun 12;389(3):637-45. doi: 10.1016/j.jmb.2009.04.038. Epub 2009 Apr 23.

PMID:
19393663
50.

Examining ion channel properties using free-energy methods.

Domene C, Furini S.

Methods Enzymol. 2009;466:155-77. doi: 10.1016/S0076-6879(09)66007-9. Epub 2009 Nov 13. Review.

PMID:
21609861

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