Publication List (2002+, reverse chronological order)

  Haldane, A., Manhart, M. and Morozov, A.V. (2014)
  Biophysical fitness landscapes for transcription factor binding sites    Software
  PLoS Comp. Biol., in press

  Tsitron, J., Kreller, C.R., Sekhar, P.K., Mukundan, R., Garzon, F.H., Brosha, E.L. and Morozov, A.V. (2014)
  Bayesian decoding of the ammonia response of a zirconia-based mixed-potential sensor in the presence of hydrocarbon interference
  Sensors and Actuators B: Chemical 192, 283-293

  Manhart, M. and Morozov, A.V. (2013)
  Path-based approach to random walks on networks characterizes how proteins evolve new functions
  Phys. Rev. Lett. 111, 088102

  Drsata, T., Perez, A., Orozco, M., Morozov, A.V., Sponer J. and Lankas, F. (2013)
  Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
  J. Chem. Theory Comput. 9, 707-721

  Locke, G., Haberman, D., Johnson, S.M. and Morozov, A.V. (2013)
  Global remodeling of nucleosome positions in C. elegans
  BMC Genomics 14, 284

  Petrenko, N., Chereji, R.V., McClean, M.N., Morozov, A.V. and Broach, J.R. (2013)
  Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses
  Mol. Biol. Cell 24, 2045-2057

  Morozov, A.V. (2013)
  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
  Phys. Life Rev. 10, 75-77; discussion 82-84

  Haq, O., Andrec, M., Morozov, A.V. and Levy, M.R. (2012)
  Correlated electrostatic mutations provide a reservoir of stability in HIV protease
  PLoS Comp. Biol. 8, e1002675

  Tolkunov, D. and Morozov, A.V. (2012)
  Single temperature for Monte Carlo optimization on complex landscapes
  Phys. Rev. Lett. 108, 250602

  Manhart, M., Haldane, A. and Morozov, A.V. (2012)
  A universal scaling law determines time reversibility and steady state of substitutions under selection
  Theor. Popul. Biol. 82, 66-76

  Tsitron, J., Ault, A.D., Broach, J.R. and Morozov, A.V. (2011)
  Decoding complex chemical mixtures with a physical model of a sensor array
  PLoS Comp. Biol. 7, e1002224

  Tolkunov, D., Zawadzki, K.A., Singer, C., Elfving, N., Morozov, A.V. and Broach, J.R. (2011)
  Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters
  Mol. Biol. Cell 22, 2106-2118

  Chereji, R.V. and Morozov, A.V. (2011)
  Statistical mechanics of nucleosomes constrained by higher-order chromatin structure
  J. Stat. Phys. 144, 379-404

  Chereji, R.V., Tolkunov, D., Locke, G. and Morozov, A.V. (2011)
  Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions
  Phys. Rev. E Rapid Comm. 83, 050903

  Morozov, A.V. (2011)
  Sequence determinants of histone-DNA binding preferences: comment on "Cracking the chromatin code: precise rule of nucleosome positioning" by Edward N. Trifonov
  Phys Life Rev. 8, 62-63; discussion 69-72

  Locke, G., Tolkunov, D., Moqtaderi, Z., Struhl, K. and Morozov, A.V. (2010)
  High-throughput sequencing reveals a simple model of nucleosome energetics
  Proc. Nat. Acad. Sci. USA 107, 20998-21003

  Tolkunov, D. and Morozov, A.V. (2010)
  Genomic studies and computational predictions of nucleosome positions and formation energies
  Adv. Prot. Chem. Struc. Biol. 79, 1-57

  Bai, L. and Morozov, A.V. (2010)
  Gene regulation by nucleosome positioning
  Trends Genet. 26, 476-483

  Haq, O., Levy, R.M., Morozov, A.V. and Andrec, M. (2009)
  Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease
  BMC Bioinformatics 10 (Suppl. 8), S10

  Morozov, A.V., Fortney, K., Gaykalova, D.A., Studitsky, V.M., Widom, J. and Siggia, E.D. (2009)
  Using DNA mechanics to predict in vitro nucleosome positions and formation energies
  Nucl. Acids Res. 37, 4707-4722

  Zawadzki, K.A., Morozov, A.V. and Broach, J.R. (2009)
  Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae
  InCytes from MBC
  Mol. Biol. Cell 20, 3503-3513

  Morozov, A.V., Fortney, K., Gaykalova, D.A., Studitsky, V.M., Widom, J. and Siggia, E.D. (2008)
  Extrinsic and intrinsic nucleosome positioning signals

  Morozov, A.V. and Siggia, E.D. (2007)
  Connecting protein structure with predictions of regulatory sites
  Proc. Nat. Acad. Sci. USA 104, 7068-7073

  Foat, B.C., Morozov, A.V. and Bussemaker, H.J. (2006)
  Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
  Bioinformatics 22, e141-e149

  Morozov, A.V., Tsemekhman, K. and Baker, D. (2006)
  Electron density redistribution accounts for half the cooperativity of alpha helix formation
  J. Phys. Chem. B Lett. 110, 4503-4505

  Morozov, A.V., Havranek, J.J., Baker, D. and Siggia, E.D. (2005)
  Protein-DNA binding specificity predictions with structural models
  Nucl. Acids Res. 33, 5781-5798

  Morozov, A.V. and Kortemme, T. (2005)
  Potential functions for hydrogen bonds in protein structure prediction and design
  Adv. Prot. Chem. 72, 1-38

  Misura, K., Morozov, A.V. and Baker, D. (2004)
  Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction
  J. Mol. Biol. 342, 651-664

  Morozov, A.V., Kortemme, T., Tsemekhman, K. and Baker, D. (2004)
  Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
  Proc. Nat. Acad. Sci. 101, 6946-6951

  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

Alexandre V. Morozov
Last modified: Sun Sep 16 16:39:09 EDT 2012