Toprak Lab
Publications
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M Farid, M Rodrigues, R England, E Toprak, “Label-Free Optical Detection of Pathogenic Bacteria and Fungi at Extremely Low Cell Densities for Rapid Antibiotic Susceptibility Testing”, Frontiers in Bioengineering and Biotechnology, 2022
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M.S. Manna, Y.T. Tamer, I.K. Gaszek, N. Poulides, A. Ahmed, X. Wang, F.C. Toprak, A.Y. Koh, N.S. Williams, D. Borek, A.R. Atilgan, J.D. Hulleman, C. Atilgan, U. Tambar, E. Toprak, “A trimethoprim derivative impedes antibiotic resistance evolution”. Nature Communications, 12, 2949 (2021).
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Y.T.Tamer, I.K. Gaszek, M. Rodrigues, F.S. Coskun, M. Farid, A.Y. Koh, W. Russ, E. Toprak, “The antibiotic efflux protein TolC is a highly evolvable target under colicin E1 and TLS phage selection”, Molecular Biology and Evolution, msab190, 2021.
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H. Peng, V.Q. Chau, W. Phetsang, R.M. Sebastian, M.R.L. Stone, S. Datta, M. Renwick, Y.T. Tamer, E. Toprak, A.Y. Koh, M.A.T. Blaskovich, J.D. Hulleman, "Non-antibiotic small molecule regulation of dhfr-based destabilizing domains in vivo", Molecular Therapy - Methods & Clinical Development, 2019.
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M.F. Cansizoglu, Y.T. Tamer, M. Farid, A.Y. Koh, E. Toprak ,“Rapid-Ultra-Sensitive-Detection (RUSD) platform for antimicrobial sensitivity testing”, PLOS Biology, 2019.
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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”, Molecular Biology and Evolution, 2019.
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Y.T. Tamer, E. Toprak, “On the Race to Starvation: How Do Bacteria Survive High Doses of Antibiotics?”, Molecular Cell, 2017 (Preview).
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M.F. Cansizoglu, E. Toprak, “Fighting against evolution of antibiotic resistance by utilizing evolvable antimicrobial drugs”, Current Genetics, 2017 (invited review).
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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.
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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, 2016.
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B. Okumus, D. Landgraf, G.C. Lai, S. Bakhsi, J.C. Arias-Castro, S. Yildiz, D. Huh, R. Fernandez-Lopez, C.N. Peterson, E. Toprak, M. El Karoui, J. Paulsson., “Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells”. Nature communications, 2016.
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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.
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A.C. Palmer*, E. Toprak*, M. Baym, S. Kim, A. Veres, S. Bershtein, and R. Kishony, “Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes”, Nature communications, 2015 (* contributed equally).
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T. Oz, A. Guvenek, S. Yildiz, E. Karaboga, Y.T. Tamer, N. Mumcuyan, V.B. Ozan, G.H. Senturk, M. Cokol, P. Yeh, E. Toprak, “Selection strength contributes to the complexity of antibiotic resistance evolution”, Molecular Biology and Evolution, 2014.
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B. Okumus, S. Yildiz, E. Toprak, “Fluidic and microfluidic tools for quantitative systems biology”, Current Opinion in Biotechnology, 2014 (invited review).
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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; (¶ corresponding authors).
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E. Toprak, A. Veres, J.B. Michel, R. Chait, D.L. Hartl, R. Kishony, “Evolutionary paths to strong antibiotic resistance under dynamically sustained drug selection”, Nature Genetics, 2012.
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E. Toprak, C. Kural, P. R. Selvin, "Super-accuracy and super-resolution getting around the diffraction limit.", Methods in Enzymology, 2010.
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E. Toprak, A. Yildiz, M.T. Hoffman, S.S. Rosenfeld, P.R. Selvin, “Why kinesin is so processive”, PNAS, 2009.
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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, (* equal contribution).
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E. Toprak, H. Balci, B.H. Blehm, P.R. Selvin, “3D Particle Tracking via Bifocal Imaging”, Nano Letters, 2007.
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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.
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H. Park, E. Toprak, P. R. Selvin, “Single-molecule fluorescence to study molecular motors”, Quarterly Reviews of Biophysics, 2007.
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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.
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J. Enderlein, E. Toprak, P. R. Selvin, “Polarization effect on position accuracy of fluorophore localization”, Optics Express, 2006.
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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.
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E. Toprak and O.T. Turgut, “Large N limit of SO(N) Scalar Gauge Theory”, Journal of Mathematical Physics, 2002.
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E. Toprak and O.T. Turgut, “Large N limit of SO(N) Gauge Theory of Fermions and Bosons”, Journal of Mathematical Physics, 2002.