M. Mellul, S. Lahav, M. Imashimizu, Y. Tokunaga, D. B. Lukatsky, and O. Ram, Repetitive DNA Symmetry Elements Negatively Regulate Gene Expression in Embryonic Stem Cells, Biophys. J. 121(16), 3126-3135 (2022).
S . Lacham-Hartman, Y. Shmidov, E. S. Radisky, R. Bitton, D. B. Lukatsky, and N. Papo, Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site, PLoS One 16(11), e0249616 (2021).
M. Imashimizu, Yuji Tokunaga, A. Afek, Hiroki Takahashi, Nobuo Shimamoto, and D. B. Lukatsky, Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences, Biomolecules, 10(9), 1299 (2020).
D. B. Lukatsky, Understanding the Robustness of Protein Diffusion on DNA and Microtubules, Biophys. J. 118(12), 2870-2871 (2020).
M. Godstein, M. Mellul, G. Deutch, M. Imashimizu, K. Takeuchi, E. Meshorer, O. Ram, and D. B. Lukatsky, Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry, Biophys. J. 118(8), 2015-2026 (2020).
S. Ilic, S. Cohen, A. Afek, R. Gordan, D. B. Lukatsky, and B. Akabayov, DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling. J. Vis. Exp. Oct 8, (152) (2019).
A. Afek, S. Ilic, J. Horton, D. B. Lukatsky, R. Gordan, and B. Akabayov, DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase. iScience 2, 141-147 (2018).
A. Afek, L. Tagliafierro, O. C. Glenn, D. B. Lukatsky, R. Gordan, and O. Chiba-Falek, Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene. Neorogenetics 19(3) 135-144 (2018).
M. Imashimizu, and D. B. Lukatsky, Transcription pausing: biological significance of thermal fluctuations biased by repetitive genomic sequences. Transcription. 9(3) 196-203 (2018).
M. Godstein and D. B. Lukatsky, Specificity-determining DNA triplet code for positioning of human pre-initiation complex, Biophys. J. 112(14) 2047-2050 (2017).
M. Imashimizu, A. Afek, H. Takahashi, L. Lubkowska, and D. B. Lukatsky, Control of Transcriptional Pausing by Biased Thermal Fluctuations on Repetitive Genomic Sequences, Proc. Natl. Acad. Sci. USA (PNAS Plus) 113(47) E7409–E7417 (2016).
A. Afek, H. Cohen, R. Gordan, and D. B. Lukatsky, Nonconsensus protein binding to repetitive DNA sequence elements significantly affects eukaryotic genomes, PLoS computational biology 11(8) e1004429 (2015).
A. Afek, J. L. Schipper, J. Horton, R. Gordan, and D. B. Lukatsky, Protein-DNA binding in the absence of specific base-pair recognition, Proc. Natl. Acad. Sci. USA 111(48) 17140-17145 (2014).
A. Afek and D. B. Lukatsky, Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites, Biophys. J. 105 1653-1660 (2013).
A. Afek and D. B. Lukatsky, Genome-wide organization of eukaryotic pre-initiation complex is influenced by nonconsensus protein-DNA binding, Biophys. J. 104 1107-1115 (2013). Reviewed in New and Notable section of the journal issue.
A. Afek and D. B. Lukatsky, Nonspecific Protein-DNA Binding is Widespread in the Yeast Genome, Biophys. J. 102, 1881-1888 (2012).
M. Elkin, I. Andre, and D. B. Lukatsky, Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions, J. Stat. Phys. 146, 870-877 (2012).
A. Afek, I. Sela, N. Musa-Lempel, and D. B. Lukatsky, Nonspecific Transcription Factor-DNA Binding Influences Nucleosome Occupancy in Yeast, Biophys. J. 101, 2465-2475 (2011).
D. B. Lukatsky A. Afek, and E. I. Shakhnovich, Sequence Correlations Shape Protein Promiscuity, J. Chem. Phys. 135, 065104 (2011).
I. Sela and D. B. Lukatsky, DNA Sequence Correlations Shape Nonspecific Transcription Factor-DNA Binding Affinity,Biophys. J. 101, 160-166 (2011).
A. Afek, E. I. Shakhnovich, and D. B. Lukatsky, Multi-Scale Sequence Correlations Increase Proteome Structural Disorder and Promiscuity, J. Mol. Biol. 409, 439-449 (2011).
D. B. Lukatsky and E. I. Shakhnovich, Statistically Enhanced Promiscuity of Structurally Correlated Patterns, Phys. Rev. E 77, 020901(R) (2008).
D. B. Lukatsky, B. E. Shakhnovich, J. Mintseris, and E. I. Shakhnovich, Structural Similarity Enhances Interaction Propensity of Proteins, J. Mol. Biol. 365, 1596 (2007).
D. B. Lukatsky, K. B. Zeldovich, and E. I. Shakhnovich, Statistically Enhanced Self-Attraction of Random Patterns, Phys. Rev. Lett. 97, 178101 (2006).
D. B. Lukatsky, B. Mulder, and D. Frenkel, Designing Ordered DNA-linked Nanoparticle Assemblies, J. Phys. Cond. Mat. 18, S567 (2006).
D. B. Lukatsky and D. Frenkel, Surface and Bulk Dissolution Properties and Selectivity of DNA-linked Nanoparticle Assemblies, J. Chem. Phys. 122, 214904 (2005).
D. B. Lukatsky and D. Frenkel, Phase Behavior and Selectivity of DNA-Linked Nanoparticle Assemblies, Phys. Rev. Lett. 92, 068302 (2004). Reviewed in Nature Materials Nanozone, The Physics of DNA detection, Feb. 19, (2004).
D. B. Lukatsky and D. Frenkel, Multiple Stalk Formation as a Pathway of Defect-Induced Membrane Fusion, Eur. Phys. J. E 14, 3 (2004).
D. B. Lukatsky, G. Haran, and S. A. Safran, Slow Fluctuations in Enhanced Raman Scattering and Surface Roughness Relaxation, Phys. Rev E 67, 062402 (2003).
D. B. Lukatsky and S. A. Safran, Universal Reduction of Pressure Between Charged Surfaces by Long-Wavelength Surface Charge Modulation, Europhys. Lett. 60, 629 (2002).
D. B. Lukatsky, S. A. Safran, A.W.C. Lau, and P. Pincus, Enhanced Counterion Localization Induced by Surface Charge Modulation, Europhys. Lett. 58, 785 (2002).
A.W.C. Lau, D. B. Lukatsky, P. Pincus, and S. A. Safran, Charge Fluctuations and Counterion Condensation, Phys. Rev. E 65, 051502 (2002).
D. B. Lukatsky and S. A. Safran, Fluctuations and Ordering in Macroion Suspensions, Phys. Rev. E 63, 011405 (2001).
D. B. Lukatsky and S. A. Safran, Pressure of Correlated Layer-Charge and Counterion Fluctuations in Charged Thin Films, Phys. Rev. E 60, 5848 (1999).
D. B. Lukatsky and V. N. Bondarev, Model for the Order-Disorder Transition in Charged Colloidal Suspension, Physica A 249, 369 (1998).