Systems Biology

 

F.N. Kalkan*,. M.S. Yildiz*, E. Wood, M.F. Farid, M.K. McCoy, C.C. Zhang, B. Posner, S.S. Chung, E. Toprak, "Synergistic and antagonistic drug-drug interactions are prevalent but not conserved across acute myeloid leukemia cell lines.", Biorxiv, 2024, *Equal Contribution. bioRxiv 2024.02.23.581821;  doi: https://doi.org/10.1101/2024.02.23.581821

 

Kantarcioglu, I.K. Gaszek, T.F. Guclu, M.S. Yildiz, A.R. Atilgan, E. Toprak*, C. Atilgan*, “Elucidating TolC Protein Dynamics: Structural Shifts Facilitate Efflux Mediated β-lactam Resistance.”, Biorxiv, 2024. *Corresponding authors https://www.biorxiv.org/content/10.1101/2024.02.22.581573v1

 

M. Rodrigues, P. Sabaeifard, M.S. Yildiz, L. Coughlin, S. Ahmed, N. Poulides, A.C. Toprak, C. Behrendt, X. Wang, M. Monogue, J. Kim, S. Gan, X. Zhan, L. Filkins, N.S. Williams, L. Hooper, A.Y. Koh*, E. Toprak*, “Susceptible bacteria can survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance.”, Cell Host & Microbe, 2024, *Corresponding authors. https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(24)00016-7

 

E. Cetin, T.F. Guclu, I. Kantarcioglu, I.K. Gaszek, E. Toprak, A.R. Atilgan, B. Dedeoglu, C. Atilgan, “Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR”, Chem. Inf. Model. 2023, 63, 15, 4839–4849 https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c00818

 

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 https://www.frontiersin.org/articles/10.3389/fbioe.2022.884200/full

 

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). https://www.nature.com/articles/s41467-021-23191-z

 

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. https://academic.oup.com/mbe/article/38/10/4493/6310175

 

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. https://www.cell.com/molecular-therapy-family/methods/fulltext/S2329-0501(19)30082-8

 

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. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000291

 

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. https://academic.oup.com/mbe/article/36/7/1533/5458069

 

Y.T. Tamer, E. Toprak, “On the Race to Starvation: How Do Bacteria Survive High Doses of Antibiotics?”, Molecular Cell, 2017 (Preview). https://www.cell.com/molecular-cell/pdf/S1097-2765(17)30932-2.pdf

 

M.F. Cansizoglu, E. Toprak, “Fighting against evolution of antibiotic resistance by utilizing evolvable antimicrobial drugs”, Current Genetics, 2017 (invited review). https://link.springer.com/article/10.1007/s00294-017-0703-x

 

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. https://pubs.rsc.org/en/content/articlelanding/2017/cp/c7cp01458a/unauth

 

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. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002552

 

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. https://www.nature.com/articles/ncomms11641

 

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. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002299

 

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). https://www.nature.com/articles/ncomms8385

 

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. https://academic.oup.com/mbe/article/31/9/2387/2925782

 

B. Okumus, S. Yildiz, E. Toprak, “Fluidic and microfluidic tools for quantitative systems biology”, Current Opinion in Biotechnology, 2014 (invited review).  https://www.sciencedirect.com/science/article/pii/S095816691300640X

 

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). https://www.nature.com/articles/nprot.2013.021

 

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. https://www.nature.com/articles/ng.1034

 

Single Molecule Biophysics

 

E. Toprak, C. Kural, P. R. Selvin, "Super-accuracy and super-resolution getting around the diffraction limit.", Methods in Enzymology, 2010. https://www.sciencedirect.com/science/article/pii/S0076687910750011

 

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

 

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). https://www.pnas.org/doi/full/10.1073/pnas.0900005106

 

E. Toprak, H. Balci, B.H. Blehm, P.R. Selvin, “3D Particle Tracking via Bifocal Imaging”, Nano Letters, 2007. https://pubs.acs.org/doi/full/10.1021/nl0709120

 

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. https://www.annualreviews.org/doi/full/10.1146/annurev.biophys.36.040306.132700

 

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

 

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.

 

J. Enderlein, E. Toprak, P. R. Selvin, “Polarization effect on position accuracy of fluorophore localization”, Optics Express, 2006. https://opg.optica.org/oe/fulltext.cfm?uri=oe-14-18-8111

 

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. https://www.pnas.org/doi/full/10.1073/pnas.0507134103

 

Theoretical Physics

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

 

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

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