Publications

  1. M.F. Cansizoglu, Y.T. Tamer, M. Farid, A.Y. Koh, E. Toprak ,“Rapid-Ultra-Sensitive-Detection (RUSD) platform for antimicrobial sensitivity testing”, 2019, , (under revision).

  2. Y.T. Tamer, I.K. Gaszek, H. Abdizadeh, T. Batur, K. Reynolds,  A.R. Atilgan, C. Atilgan,  E. Toprak, “High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection”, Biorxiv, 2019, https://doi.org/10.1101/398065, (under revision).

  3. Y.T. Tamer, E. Toprak, “On the Race to Starvation: How Do Bacteria Survive High Doses of Antibiotics?”, Molecular Cell, 2017 Dec 21;68(6):1019-1021. doi: 10.1016/j.molcel.2017.12.004.

  4. M.F. Cansizoglu, E. Toprak, “Fighting against evolution of antibiotic resistance by utilizing evolvable antimicrobial drugs”, Current Genetics, 2017 (invited review).

  5. H. Abdizadeh, Y.T. Tamer, O. Acar, E. Toprak, A.R. Atilgan, C. Atilgan, “Increased Substrate Affinity in the Escherichia Coli L28R Dihydrofolate Reductase Mutant Causes Trimethoprim Resistance”, Physical Chemistry Chemical Physics, 2017.

  6. D.H. Ayhan, Y.T. Tamer, M. Akbar, S.M. Bailey, M. Wong, S.M. Daly, D.E. Greenberg, E. Toprak, “Sequence-Specific Targeting of Bacterial Resistance Genes Increases Antibiotic Efficacy”, PLOS Biology, September 15, 2016.

  7. Okumus B, Landgraf D, Lai GC, Bakhsi S, Arias-Castro JC, Yildiz S, Huh D, Fernandez-Lopez R, Peterson CN, Toprak E, El Karoui M, Paulsson J. Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells. Nature communications. 2016.

  8. G. Chevereau, M. Dravecka, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, and T. Bollenbach, “Quantifying the determinants of evolutionary dynamics leading to drug resistance”, PLOS Biology, 2015.

  9. A.C. Palmer*, E. Toprak*, M. Baym, S. Kim, A. Veres, S. Bershtein, & R. Kishony. “Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes”, Nature communications, 6, 2015.  doi:10.1038/ncomms8385  

  10. Oz, T., Guvenek, A., Yildiz, S., Karaboga, E., Tamer, Y.T., Mumcuyan, N., Ozan, V.B., Senturk, G.H., Cokol, M., Yeh, P., Toprak, E.*, “Selection strength contributes to the complexity of antibiotic resistance evolution”, Molecular Biology and Evolution, (Published online: June 24, 2014, * corresponding author). doi:10.1093/molbev/msu191

  11. B. Okumus, S. Yildiz, E. Toprak*, “Fluidic and microfluidic tools for quantitative systems biology”, Current Opinion in Biotechnology, 2014, * corresponding author. doi:10.1016/j.copbio.2013.08.016

  12. E. Toprak*, A. Veres, S. Yildiz, J.M. Pedraza, R. Chait, J. Paulsson, R. Kishony*, “Building a Morbidostat: An automated high-throughput fluidic system for studying bacterial drug resistance in dynamically sustained drug environments”, Nature Protocols, 2013; E.T. and R.K. are corresponding authors). doi:10.1038/nprot.2013.021

  13. E. Toprak, A. Veres, J.B. Michel, R. Chait, D.L. Hartl, R. Kishony, “Evolutionary paths to strong antibiotic resistance under dynamically sustained drug stress”, Nature Genetics, 2012. doi:10.1038/ng.1034

  14. E. Toprak, C. Kural, P. R. Selvin, "Super-accuracy and super-resolution getting around the diffraction limit.", Methods in Enzymology, 2010.doi: 10.1016/S0076-6879(10)75001-1

  15. E. Toprak, A. Yildiz, M.T. Hoffman, S.S. Rosenfeld, P.R. Selvin, “Why kinesin is so processive”, PNAS, 2009doi: 10.1073/pnas.0808396106

  16. J. G. Reifenberger, E. Toprak, H. Kim, D. Safer, H.L. Sweeney, P.R. Selvin, “Myosin VI undergoes a 180° Power stroke implying an uncoupling of the front lever arm”, PNAS, 2009, (J.G.R. and E.T. contributed equally).doi: 10.1073/pnas.0900005106

  17. E. Toprak, H. Balci, B.H. Blehm, P.R. Selvin, “3D Particle Tracking via Bifocal Imaging”, Nano Letters, 2007.PMID: 17583964

  18. E. Toprak and P.R. Selvin, “New Fluorescent Tools for Watching Nanometer-Scale Conformational Changes of Single Molecules”, Annual Review of Biophysics and Biomolecular Structure, 2007.PMID: 17298239

  19. H. Park, E. Toprak, P. R. Selvin, “Single-molecule fluorescence to study molecular motors”, Quarterly Reviews of Biophysics, 2007.PMID: 17666122

  20. P.R. Selvin, T. Lougheed, M.T. Hoffman, H. Park, H. Balci, B.H. Blehm, E. Toprak, “In vitro & in vivo FIONA and other acronyms for watching molecular motors walk”, Single Molecules: A Laboratory Manual. Cold Spring Harbor Press. Edited by Selvin, P.R., Taekjip Ha, Univ. of Illinois, 2007.doi: 10.1101/pdb.top27

  21. J. Enderlein, E. Toprak, P. R. Selvin, “Polarization effect on position accuracy of fluorophore localization”, Optics Express, 2006.PMID: 19529183

  22. E. Toprak, J. Enderlein, S. Syed, S.A. McKinney, R.G. Petschek, T. Ha, Y.E. Goldman, P.R. Selvin, “Defocused Orientation and Position Imaging of Myosin V”, PNAS, 2006.PMID: 16614073

  23. E. Toprak and O.T. Turgut, “Large N limit of SO(N) Scalar Gauge Theory”, Journal of Mathematical Physics, 2002.

  24. E. Toprak and O.T. Turgut, “Large N limit of SO(N) Gauge Theory of Fermions and Bosons”, Journal of Mathematical Physics, 2002.

 © 2019 by Ahmet Toprak. 

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