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Items: 1 to 50 of 88

1.

Membrane Electroporation and Electropermeabilization: Mechanisms and Models.

Kotnik T, Rems L, Tarek M, Miklavčič D.

Annu Rev Biophys. 2019 May 6;48:63-91. doi: 10.1146/annurev-biophys-052118-115451. Epub 2019 Feb 20.

PMID:
30786231
2.

Sexual and Religious Obsessions in Relation to Suicidal Ideation in Bipolar Disorder.

Abdel Hamid AAL, Nasreldin M, Gohar SM, Saleh AA, Tarek MA.

Suicide Life Threat Behav. 2019 Feb 6. doi: 10.1111/sltb.12540. [Epub ahead of print]

PMID:
30729568
3.

The contribution of lipid peroxidation to membrane permeability in electropermeabilization: A molecular dynamics study.

Rems L, Viano M, Kasimova MA, Miklavčič D, Tarek M.

Bioelectrochemistry. 2019 Feb;125:46-57. doi: 10.1016/j.bioelechem.2018.07.018. Epub 2018 Aug 4.

PMID:
30265863
4.

Computational prediction of vaccine potential epitopes and 3-dimensional structure of XAGE-1b for non-small cell lung cancer immunotherapy.

Tarek MM, Shafei AE, Ali MA, Mansour MM.

Biomed J. 2018 Apr;41(2):118-128. doi: 10.1016/j.bj.2018.04.002. Epub 2018 May 21.

5.

Ant Lion Optimization algorithm for kidney exchanges.

Hamouda E, El-Metwally S, Tarek M.

PLoS One. 2018 May 3;13(5):e0196707. doi: 10.1371/journal.pone.0196707. eCollection 2018.

6.

Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer - insights from molecular dynamics and free-energy calculations.

Bonhenry D, Dehez F, Tarek M.

Phys Chem Chem Phys. 2018 Apr 4;20(14):9101-9107. doi: 10.1039/C8CP00312B.

PMID:
29565093
7.

Studying Kv Channels Function using Computational Methods.

Deyawe A, Kasimova MA, Delemotte L, Loussouarn G, Tarek M.

Methods Mol Biol. 2018;1684:321-341. doi: 10.1007/978-1-4939-7362-0_24.

PMID:
29058202
8.

Atomistic Simulations of Electroporation of Model Cell Membranes.

Tarek M.

Adv Anat Embryol Cell Biol. 2017;227:1-15. doi: 10.1007/978-3-319-56895-9_1. Review.

PMID:
28980037
9.

Role of microRNA-7 and selenoprotein P in hepatocellular carcinoma.

Tarek M, Louka ML, Khairy E, Ali-Labib R, Zakaria Zaky D, Montasser IF.

Tumour Biol. 2017 May;39(5):1010428317698372. doi: 10.1177/1010428317698372.

PMID:
28459371
10.

Epigenetic regulation of immune checkpoints: another target for cancer immunotherapy?

Ali MA, Matboli M, Tarek M, Reda M, Kamal KM, Nouh M, Ashry AM, El-Bab AF, Mesalam HA, Shafei AE, Abdel-Rahman O.

Immunotherapy. 2017 Jan;9(1):99-108. doi: 10.2217/imt-2016-0111. Review.

PMID:
28000527
11.

Properties of lipid electropores II: Comparison of continuum-level modeling of pore conductance to molecular dynamics simulations.

Rems L, Tarek M, Casciola M, Miklavčič D.

Bioelectrochemistry. 2016 Dec;112:112-24. doi: 10.1016/j.bioelechem.2016.03.005. Epub 2016 Apr 6.

PMID:
27091314
12.

A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields.

Casciola M, Tarek M.

Biochim Biophys Acta. 2016 Oct;1858(10):2278-2289. doi: 10.1016/j.bbamem.2016.03.022. Epub 2016 Mar 24.

13.

Properties of lipid electropores I: Molecular dynamics simulations of stabilized pores by constant charge imbalance.

Casciola M, Kasimova MA, Rems L, Zullino S, Apollonio F, Tarek M.

Bioelectrochemistry. 2016 Jun;109:108-16. doi: 10.1016/j.bioelechem.2016.01.006. Epub 2016 Jan 29.

PMID:
26883056
14.

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN.

J Membr Biol. 2015 Aug;248(4):611-40. doi: 10.1007/s00232-015-9802-0. Epub 2015 Jun 11. Review.

15.

PIP₂-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6.

Kasimova MA, Zaydman MA, Cui J, Tarek M.

Sci Rep. 2015 Jan 6;5:7474. doi: 10.1038/srep07474.

16.

Domain-domain interactions determine the gating, permeation, pharmacology, and subunit modulation of the IKs ion channel.

Zaydman MA, Kasimova MA, McFarland K, Beller Z, Hou P, Kinser HE, Liang H, Zhang G, Shi J, Tarek M, Cui J.

Elife. 2014 Dec 23;3:e03606. doi: 10.7554/eLife.03606.

17.

Free-energy landscape of ion-channel voltage-sensor-domain activation.

Delemotte L, Kasimova MA, Klein ML, Tarek M, Carnevale V.

Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):124-9. doi: 10.1073/pnas.1416959112. Epub 2014 Dec 22.

18.

Electroporation threshold of POPC lipid bilayers with incorporated polyoxyethylene glycol (C12E8).

Polak A, Velikonja A, Kramar P, Tarek M, Miklavčič D.

J Phys Chem B. 2015 Jan 8;119(1):192-200. doi: 10.1021/jp509789m. Epub 2014 Dec 26.

PMID:
25495217
19.

Functional interaction between S1 and S4 segments in voltage-gated sodium channels revealed by human channelopathies.

Amarouch MY, Kasimova MA, Tarek M, Abriel H.

Channels (Austin). 2014;8(5):414-20. doi: 10.4161/19336950.2014.958922.

20.

Molecular dynamics simulation of short-wavelength collective dynamics of phospholipid membranes.

Conti Nibali V, D'Angelo G, Tarek M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 May;89(5):050301. Epub 2014 May 12.

PMID:
25353727
21.

Effect of 13q deletion on IL-6 production in patients with multiple myeloma: a hypothesis may hold true.

Neemat K, Rania K, Tarek M, Hamdy AA.

Clin Lab. 2014;60(8):1393-9.

PMID:
25185427
22.

Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study.

Polak A, Tarek M, Tomšič M, Valant J, Ulrih NP, Jamnik A, Kramar P, Miklavčič D.

Langmuir. 2014 Jul 22;30(28):8308-15. doi: 10.1021/la5014208. Epub 2014 Jul 7.

PMID:
25000416
23.

Human retinal transmitochondrial cybrids with J or H mtDNA haplogroups respond differently to ultraviolet radiation: implications for retinal diseases.

Malik D, Hsu T, Falatoonzadeh P, Cáceres-del-Carpio J, Tarek M, Chwa M, Atilano SR, Ramirez C, Nesburn AB, Boyer DS, Kuppermann BD, Jazwinski SM, Miceli MV, Wallace DC, Udar N, Kenney MC.

PLoS One. 2014 Jun 11;9(2):e99003. doi: 10.1371/journal.pone.0099003. eCollection 2014.

24.

Detecting well casing leaks in Bangladesh using a salt spiking method.

Stahl MO, Ong JB, Harvey CF, Johnson CD, Badruzzaman AB, Tarek MH, van Geen A, Anderson JA, Lane JW.

Ground Water. 2014 Sep;52 Suppl 1:195-200. doi: 10.1111/gwat.12200. Epub 2014 Jun 4.

25.

High-yield nontoxic gene transfer through conjugation of the CM₁₈-Tat₁₁ chimeric peptide with nanosecond electric pulses.

Salomone F, Breton M, Leray I, Cardarelli F, Boccardi C, Bonhenry D, Tarek M, Mir LM, Beltram F.

Mol Pharm. 2014 Jul 7;11(7):2466-74. doi: 10.1021/mp500223t. Epub 2014 Jun 4.

PMID:
24865174
26.

Safety profiles of anti-VEGF drugs: bevacizumab, ranibizumab, aflibercept and ziv-aflibercept on human retinal pigment epithelium cells in culture.

Malik D, Tarek M, Caceres del Carpio J, Ramirez C, Boyer D, Kenney MC, Kuppermann BD.

Br J Ophthalmol. 2014 Jun;98 Suppl 1:i11-16. doi: 10.1136/bjophthalmol-2014-305302.

27.

Lipid Peroxidation in Membranes: The Peroxyl Radical Does Not "Float".

Garrec J, Monari A, Assfeld X, Mir LM, Tarek M.

J Phys Chem Lett. 2014 May 15;5(10):1653-8. doi: 10.1021/jz500502q. Epub 2014 Apr 25.

PMID:
26270361
28.

A molecular dynamic study of cholesterol rich lipid membranes: comparison of electroporation protocols.

Casciola M, Bonhenry D, Liberti M, Apollonio F, Tarek M.

Bioelectrochemistry. 2014 Dec;100:11-7. doi: 10.1016/j.bioelechem.2014.03.009. Epub 2014 Mar 28.

PMID:
24731593
29.

On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water.

Conti Nibali V, D'Angelo G, Paciaroni A, Tobias DJ, Tarek M.

J Phys Chem Lett. 2014 Apr 3;5(7):1181-6. doi: 10.1021/jz500023e. Epub 2014 Mar 20.

PMID:
26274468
30.

Inherited mitochondrial DNA variants can affect complement, inflammation and apoptosis pathways: insights into mitochondrial-nuclear interactions.

Kenney MC, Chwa M, Atilano SR, Falatoonzadeh P, Ramirez C, Malik D, Tarek M, Cáceres-del-Carpio J, Nesburn AB, Boyer DS, Kuppermann BD, Vawter M, Jazwinski SM, Miceli M, Wallace DC, Udar N.

Hum Mol Genet. 2014 Jul 1;23(13):3537-51. doi: 10.1093/hmg/ddu065. Epub 2014 Feb 28.

31.

Voltage-gated ion channel modulation by lipids: insights from molecular dynamics simulations.

Kasimova MA, Tarek M, Shaytan AK, Shaitan KV, Delemotte L.

Biochim Biophys Acta. 2014 May;1838(5):1322-31. doi: 10.1016/j.bbamem.2014.01.024. Epub 2014 Feb 8.

32.

Electroporation of archaeal lipid membranes using MD simulations.

Polak A, Tarek M, Tomšič M, Valant J, Ulrih NP, Jamnik A, Kramar P, Miklavčič D.

Bioelectrochemistry. 2014 Dec;100:18-26. doi: 10.1016/j.bioelechem.2013.12.006. Epub 2014 Jan 9.

PMID:
24461702
33.

Prerequisites to proton transport in the bacterial ClC-ec1 Cl-/H+ exchanger.

Tarek M.

Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1668-9. doi: 10.1073/pnas.1323186111. Epub 2014 Jan 23. No abstract available.

34.

Computational tools to investigate genetic cardiac channelopathies.

Abriel H, de Lange E, Kucera JP, Loussouarn G, Tarek M.

Front Physiol. 2013 Dec 26;4:390. doi: 10.3389/fphys.2013.00390. eCollection 2013.

35.

Evaluation of matrix metalloproteinase-2 in lung cancer.

Ali-Labib R, Louka ML, Galal IH, Tarek M.

Proteomics Clin Appl. 2014 Apr;8(3-4):251-7. doi: 10.1002/prca.201300086. Epub 2014 Feb 13.

PMID:
24415566
36.

Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane.

Bonhenry D, Tarek M, Dehez F.

J Chem Theory Comput. 2013 Dec 10;9(12):5675-84. doi: 10.1021/ct400576e. Epub 2013 Nov 23.

PMID:
26592298
37.

Molecular and bioenergetic differences between cells with African versus European inherited mitochondrial DNA haplogroups: implications for population susceptibility to diseases.

Kenney MC, Chwa M, Atilano SR, Falatoonzadeh P, Ramirez C, Malik D, Tarek M, Del Carpio JC, Nesburn AB, Boyer DS, Kuppermann BD, Vawter MP, Jazwinski SM, Miceli MV, Wallace DC, Udar N.

Biochim Biophys Acta. 2014 Feb;1842(2):208-19. doi: 10.1016/j.bbadis.2013.10.016. Epub 2013 Nov 4.

38.

How do functionalized carbon nanotubes land on, bind to and pierce through model and plasma membranes.

Lacerda L, Ali-Boucetta H, Kraszewski S, Tarek M, Prato M, Ramseyer C, Kostarelos K, Bianco A.

Nanoscale. 2013 Nov 7;5(21):10242-50. doi: 10.1039/c3nr03184e. Epub 2013 Sep 5.

PMID:
24056765
39.

On the electroporation thresholds of lipid bilayers: molecular dynamics simulation investigations.

Polak A, Bonhenry D, Dehez F, Kramar P, Miklavčič D, Tarek M.

J Membr Biol. 2013 Nov;246(11):843-50. doi: 10.1007/s00232-013-9570-7. Epub 2013 Jun 19.

PMID:
23780415
40.

Omega currents in voltage-gated ion channels: what can we learn from uncovering the voltage-sensing mechanism using MD simulations?

Tarek M, Delemotte L.

Acc Chem Res. 2013 Dec 17;46(12):2755-62. doi: 10.1021/ar300290u. Epub 2013 May 22. Review.

PMID:
23697886
41.

An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations.

Vargas E, Yarov-Yarovoy V, Khalili-Araghi F, Catterall WA, Klein ML, Tarek M, Lindahl E, Schulten K, Perozo E, Bezanilla F, Roux B.

J Gen Physiol. 2012 Dec;140(6):587-94. doi: 10.1085/jgp.201210873.

42.

Mechanisms of Ion Channels Voltage-Dependency: All about Molecular Sensors, Gates, Levers, Locks, and Grease.

Loussouarn G, Tarek M.

Front Pharmacol. 2012 Sep 27;3:174. doi: 10.3389/fphar.2012.00174. eCollection 2012. No abstract available.

43.

Dual effect of phosphatidylinositol (4,5)-bisphosphate PIP(2) on Shaker K(+) [corrected] channels.

Abderemane-Ali F, Es-Salah-Lamoureux Z, Delemotte L, Kasimova MA, Labro AJ, Snyders DJ, Fedida D, Tarek M, Baró I, Loussouarn G.

J Biol Chem. 2012 Oct 19;287(43):36158-67. doi: 10.1074/jbc.M112.382085. Epub 2012 Aug 29. Erratum in: J Biol Chem. 2013 Apr 12;288(15):10951.

44.

Molecular-level characterization of lipid membrane electroporation using linearly rising current.

Kramar P, Delemotte L, Maček Lebar A, Kotulska M, Tarek M, Miklavčič D.

J Membr Biol. 2012 Oct;245(10):651-9. doi: 10.1007/s00232-012-9487-6. Epub 2012 Aug 11.

PMID:
22886207
45.

Transport of siRNA through lipid membranes driven by nanosecond electric pulses: an experimental and computational study.

Breton M, Delemotte L, Silve A, Mir LM, Tarek M.

J Am Chem Soc. 2012 Aug 29;134(34):13938-41. doi: 10.1021/ja3052365. Epub 2012 Aug 16.

PMID:
22880891
46.

Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion.

Kraszewski S, Bianco A, Tarek M, Ramseyer C.

PLoS One. 2012;7(7):e40703. doi: 10.1371/journal.pone.0040703. Epub 2012 Jul 16.

47.

Molecular dynamics simulations of voltage-gated cation channels: insights on voltage-sensor domain function and modulation.

Delemotte L, Klein ML, Tarek M.

Front Pharmacol. 2012 May 25;3:97. doi: 10.3389/fphar.2012.00097. eCollection 2012.

48.

Molecular dynamics simulations of lipid membrane electroporation.

Delemotte L, Tarek M.

J Membr Biol. 2012 Sep;245(9):531-43. doi: 10.1007/s00232-012-9434-6. Epub 2012 May 30.

PMID:
22644388
49.

Uptake and translocation mechanisms of cationic amino derivatives functionalized on pristine C60 by lipid membranes: a molecular dynamics simulation study.

Kraszewski S, Tarek M, Ramseyer C.

ACS Nano. 2011 Nov 22;5(11):8571-8. doi: 10.1021/nn201952c. Epub 2011 Oct 13.

PMID:
21981729
50.

Ethanol enhances collective dynamics of lipid membranes.

Kaye MD, Schmalzl K, Nibali VC, Tarek M, Rheinstädter MC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 May;83(5 Pt 1):050907. Epub 2011 May 25.

PMID:
21728483

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