Systems Biology

1. Higher-order epistasis drives evolutionary unpredictability toward novel antibiotic resistance
   Ilona K Gaszek, Muhammed Sadık Yıldız, Zhaoxu Meng, Jose Alberto de la Paz, Sophia Maria Alvarez, Faruck Morcos, Milo M Lin, Erdal Toprak
   Biorxiv, 2025.

2. Context-dependent evolutionary dynamics toward bacterial survival during sequential antibiotic treatment
   Adam Lyon, Muhammed Sadık Yıldız, Erdal Toprak
   Biorxiv, 2025.

3. A Simple, Low-Cost, and Efficient Protocol for Rapid Isolation of Pathogenic Bacteria from Human Blood
   FS Coskun, J Quick, E Toprak
   Biorxiv, 2025.

4. Synergistic and antagonistic drug-drug interactions are prevalent but not conserved across acute myeloid leukemia cell lines
   F.N. Kalkan*, M.S. Yıldız*, E. Wood, M.F. Farid, M.K. McCoy, C.C. Zhang, B. Posner, S.S. Chung, E. Toprak
   Scientific Reports, 2025.

5. Elucidating TolC Protein Dynamics: Structural Shifts Facilitate Efflux Mediated β-lactam Resistance
   Kantarcioglu, I.K. Gaszek, T.F. Guclu, M.S. Yıldız, A.R. Atilgan, E. Toprak*, C. Atilgan*
   Communications Biology, 2024.

6. Susceptible bacteria can survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance
   M. Rodrigues, P. Sabaeifard, M.S. Yıldız, 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*
   Cell Host & Microbe, 2024.

7. Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR
   E. Cetin, T.F. Guclu, I. Kantarcioglu, I.K. Gaszek, E. Toprak, A.R. Atilgan, B. Dedeoglu, C. Atilgan
   J. Chem. Inf. Model., 2023.

8. Label-Free Optical Detection of Pathogenic Bacteria and Fungi at Extremely Low Cell Densities for Rapid Antibiotic Susceptibility Testing
   M. Farid, M. Rodrigues, R. England, E. Toprak
   Frontiers in Bioengineering and Biotechnology, 2022.

9. A trimethoprim derivative impedes antibiotic resistance evolution
   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
   Nature Communications, 2021.

10. The antibiotic efflux protein TolC is a highly evolvable target under colicin E1 and TLS phage selection
    Y.T. Tamer, I.K. Gaszek, M. Rodrigues, F.S. Coskun, M. Farid, A.Y. Koh, W. Russ, E. Toprak
    Molecular Biology and Evolution, 2021.

11. Non-antibiotic small molecule regulation of dhfr-based destabilizing domains in vivo
    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
    Molecular Therapy - Methods & Clinical Development, 2019.

12. Rapid-Ultra-Sensitive-Detection (RUSD) platform for antimicrobial sensitivity testing
    M.F. Cansizoglu, Y.T. Tamer, M. Farid, A.Y. Koh, E. Toprak
    PLOS Biology, 2019.

13. High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection
    Y.T. Tamer, I.K. Gaszek, H. Abdizadeh, T. Batur, K. Reynolds, A.R. Atilgan, C. Atilgan, E. Toprak
    Molecular Biology and Evolution, 2019.

14. On the Race to Starvation: How Do Bacteria Survive High Doses of Antibiotics?
    Y.T. Tamer, E. Toprak
    Molecular Cell (Preview), 2017.

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

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

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

18. Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells
    B. Okumus, D. Landgraf, G.C. Lai, S. Bakhsi, J.C. Arias-Castro, S. Yıldız, D. Huh, R. Fernandez-Lopez, C.N. Peterson, E. Toprak, M. El Karoui, J. Paulsson
    Nature Communications, 2016.

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

20. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes
    A.C. Palmer*, E. Toprak*, M. Baym, S. Kim, A. Veres, S. Bershtein, R. Kishony
    Nature Communications, 2015.

21. Selection strength contributes to the complexity of antibiotic resistance evolution
    T. Oz, A. Guvenek, S. Yıldız, E. Karaboga, Y.T. Tamer, N. Mumcuyan, V.B. Ozan, G.H. Senturk, M. Cokol, P. Yeh, E. Toprak
    Molecular Biology and Evolution, 2014.

22. Fluidic and microfluidic tools for quantitative systems biology
    B. Okumus, S. Yıldız, E. Toprak
    Current Opinion in Biotechnology (invited review), 2014.

23. Building a Morbidostat: An automated high-throughput fluidic system for studying bacterial drug resistance in dynamically sustained drug environments
    E. Toprak*, A. Veres, S. Yıldız, J.M. Pedraza, R. Chait, J. Paulsson, R. Kishony*
    Nature Protocols, 2013.

24. Evolutionary paths to strong antibiotic resistance under dynamically sustained drug selection
    E. Toprak, A. Veres, J.B. Michel, R. Chait, D.L. Hartl, R. Kishony
    Nature Genetics, 2012.

Single Molecule Biophysics

1. Super-accuracy and super-resolution getting around the diffraction limit
   E. Toprak, C. Kural, P.R. Selvin
   Methods in Enzymology, 2010.

2. Why kinesin is so processive
   E. Toprak, A. Yildiz, M.T. Hoffman, S.S. Rosenfeld, P.R. Selvin
   PNAS, 2009.

3. Myosin VI undergoes a 180° Power stroke implying an uncoupling of the front lever arm
   J.G. Reifenberger*, E. Toprak*, H. Kim, D. Safer, H.L. Sweeney, P.R. Selvin
   PNAS, 2009.

4. 3D Particle Tracking via Bifocal Imaging
   E. Toprak, H. Balci, B.H. Blehm, P.R. Selvin
   Nano Letters, 2007.

5. New Fluorescent Tools for Watching Nanometer-Scale Conformational Changes of Single Molecules
   E. Toprak, P.R. Selvin
   Annual Review of Biophysics and Biomolecular Structure, 2007.

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

7. In vitro & in vivo FIONA and other acronyms for watching molecular motors walk
   P.R. Selvin, T. Lougheed, M.T. Hoffman, H. Park, H. Balci, B.H. Blehm, E. Toprak
   Single Molecules: A Laboratory Manual, Cold Spring Harbor Press, 2007.

8. Polarization effect on position accuracy of fluorophore localization
   J. Enderlein, E. Toprak, P.R. Selvin
   Optics Express, 2006.

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

Theoretical Physics

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

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