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|
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Haldane, A., Manhart, M. and Morozov, A.V. (2014) |
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Biophysical fitness landscapes for transcription factor binding sites Software |
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PLoS Comp. Biol., in press
|
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Tsitron, J., Kreller, C.R., Sekhar, P.K., Mukundan, R., Garzon, F.H.,
Brosha, E.L. and Morozov, A.V. (2014) |
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Bayesian decoding of the ammonia response of a zirconia-based mixed-potential sensor in the presence of hydrocarbon interference |
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Sensors and Actuators B: Chemical 192, 283-293
|
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Manhart, M. and Morozov, A.V. (2013) |
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Path-based approach to random walks on networks characterizes how proteins evolve new functions |
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Phys. Rev. Lett. 111, 088102
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Drsata, T., Perez, A., Orozco, M., Morozov, A.V., Sponer J. and Lankas, F. (2013) |
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Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer |
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J. Chem. Theory Comput. 9, 707-721
|
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Locke, G., Haberman, D., Johnson, S.M. and Morozov, A.V. (2013) |
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Global remodeling of nucleosome positions in C. elegans |
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BMC Genomics 14, 284
|
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Petrenko, N., Chereji, R.V., McClean, M.N., Morozov, A.V. and Broach, J.R. (2013) |
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Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses |
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Mol. Biol. Cell 24, 2045-2057
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Morozov, A.V. (2013) |
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Thermodynamic models of nucleosome positioning: comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by Pasquale De Santis and Anita Scipioni |
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Phys. Life Rev. 10, 75-77; discussion 82-84
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Haq, O., Andrec, M., Morozov, A.V. and Levy, M.R. (2012) |
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Correlated electrostatic mutations provide a reservoir of stability in HIV protease |
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PLoS Comp. Biol. 8, e1002675
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Tolkunov, D. and Morozov, A.V. (2012) |
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Single temperature for Monte Carlo optimization on complex landscapes |
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Phys. Rev. Lett. 108, 250602
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Manhart, M., Haldane, A. and Morozov, A.V. (2012) |
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A universal scaling law determines time reversibility and steady state of substitutions under selection |
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Theor. Popul. Biol. 82, 66-76
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Tsitron, J., Ault, A.D., Broach, J.R. and Morozov, A.V. (2011) |
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Decoding complex chemical mixtures with a physical model of a sensor array |
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PLoS Comp. Biol. 7, e1002224
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Tolkunov, D., Zawadzki, K.A., Singer, C., Elfving, N., Morozov, A.V. and Broach, J.R. (2011) |
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Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters |
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Mol. Biol. Cell 22, 2106-2118
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Chereji, R.V. and Morozov, A.V. (2011) |
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Statistical mechanics of nucleosomes constrained by higher-order chromatin structure |
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J. Stat. Phys. 144, 379-404
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Chereji, R.V., Tolkunov, D., Locke, G. and Morozov, A.V. (2011) |
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Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions |
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Phys. Rev. E Rapid Comm. 83, 050903
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Morozov, A.V. (2011) |
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Sequence determinants of histone-DNA binding preferences: comment on "Cracking the chromatin code: precise rule of nucleosome positioning" by Edward N. Trifonov |
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Phys Life Rev. 8, 62-63; discussion 69-72
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Locke, G., Tolkunov, D., Moqtaderi, Z., Struhl, K. and Morozov, A.V. (2010) |
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High-throughput sequencing reveals a simple model of nucleosome energetics |
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Proc. Nat. Acad. Sci. USA 107, 20998-21003
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Tolkunov, D. and Morozov, A.V. (2010) |
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Genomic studies and computational predictions of nucleosome positions and formation energies |
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Adv. Prot. Chem. Struc. Biol. 79, 1-57
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Bai, L. and Morozov, A.V. (2010) |
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Gene regulation by nucleosome positioning |
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Trends Genet. 26, 476-483
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Haq, O., Levy, R.M., Morozov, A.V. and Andrec, M. (2009) |
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Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease |
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BMC Bioinformatics 10 (Suppl. 8), S10
|
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Morozov, A.V., Fortney, K., Gaykalova, D.A., Studitsky, V.M., Widom, J. and Siggia, E.D. (2009) |
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Using DNA mechanics to predict in vitro nucleosome positions and formation energies |
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Nucl. Acids Res. 37, 4707-4722
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Zawadzki, K.A., Morozov, A.V. and Broach, J.R. (2009) |
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Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae
|
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InCytes from MBC
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Mol. Biol. Cell 20, 3503-3513
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Morozov, A.V., Fortney, K., Gaykalova, D.A., Studitsky, V.M., Widom, J. and Siggia, E.D. (2008) |
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Extrinsic and intrinsic nucleosome positioning signals |
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arXiv:0805.4017
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Morozov, A.V. and Siggia, E.D. (2007) |
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Connecting protein structure with predictions of regulatory sites |
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Proc. Nat. Acad. Sci. USA 104, 7068-7073
|
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Foat, B.C., Morozov, A.V. and Bussemaker, H.J. (2006) |
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Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE |
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Bioinformatics 22, e141-e149
|
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Morozov, A.V., Tsemekhman, K. and Baker, D. (2006) |
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Electron density redistribution accounts for half the cooperativity of alpha helix formation |
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J. Phys. Chem. B Lett. 110, 4503-4505
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Morozov, A.V., Havranek, J.J., Baker, D. and Siggia, E.D. (2005) |
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Protein-DNA binding specificity predictions with structural models |
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Nucl. Acids Res. 33, 5781-5798
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Morozov, A.V. and Kortemme, T. (2005) |
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Potential functions for hydrogen bonds in protein structure prediction and design |
| |
Adv. Prot. Chem. 72, 1-38
|
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Misura, K., Morozov, A.V. and Baker, D. (2004) |
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Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction |
| |
J. Mol. Biol. 342, 651-664
|
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Morozov, A.V., Kortemme, T., Tsemekhman, K. and Baker, D. (2004) |
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Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations |
| |
Proc. Nat. Acad. Sci. 101, 6946-6951
|
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Morozov, A.V., Misura, K., Tsemekhman, K. and Baker, D. (2004) |
| |
Comparison of quantum mechanics and molecular mechanics dimerization energy landscapes
for pairs of ring-containing amino acids in proteins |
| |
J. Phys. Chem. B 108, 8489-8496
|
| |
Tsai, J., Bonneau, R., Morozov, A.V., Kuhlman, B., Rohl, C.A. and Baker, D. (2003) |
| |
An improved protein decoy set for testing energy functions for protein structure prediction |
| |
Proteins: Str., Func., Gen. 53, 76-87
|
| |
Gray, J.J., Moughon, S., Kortemme, T., Schueler-Furman, O., Misura, K., Morozov, A.V. and Baker, D. (2003) |
| |
Protein-protein docking predictions for the CAPRI experiment |
| |
Proteins: Str., Func., Gen. 52, 118-122
|
| |
Morozov, A.V., Kortemme, T. and Baker, D. (2003) |
| |
Evaluation of models of electrostatic interactions in proteins |
| |
J. Phys. Chem. B 107, 2075-2090
|
| |
Kortemme, T., Morozov, A.V. and Baker, D. (2003) |
| |
An orientation-dependent hydrogen bonding potential improves prediction of specificity and
structure for proteins and protein-protein complexes |
| |
J. Mol. Biol. 326, 1239-1259
|
| |
Alm, E., Morozov, A.V., Kortemme, T. and Baker, D. (2002) |
| |
Simple physical models connect theory and experiment in protein folding kinetics |
| |
J. Mol. Biol. 322, 463-476
|
| |
Morozov, A.V. (2002) |
| |
Two-frequency mutual coherence function of electromagnetic waves in random media: a path-integral variational solution |
| |
J. Opt. Soc. Am. A 19, 2074-2084
|