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Alexandre V. Morozov, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
protein structure prediction
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Ballal A, Laurendon C, Salmon M, Vardakou M, Cheema J, Defernez M, O'Maille PE, Morozov AV. Sparse epistatic patterns in the evolution of terpene synthases. Molecular Biology and Evolution. PMID 32119077 DOI: 10.1093/Molbev/Msaa052  0.318
2017 Chereji RV, Bharatula V, Elfving N, Blomberg J, Larsson M, Morozov AV, Broach JR, Björklund S. Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly. Nucleic Acids Research. PMID 28575439 DOI: 10.1093/Nar/Gkx491  0.341
2016 Manhart M, Morozov AV. Erratum: Scaling properties of evolutionary paths in a biophysical model of protein adaptation (2015Phys. Biol.12045001) Physical Biology. 13: 019601. DOI: 10.1088/1478-3975/13/1/019601  0.343
2015 Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM. Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. Nucleic Acids Research. PMID 26429969 DOI: 10.1093/Nar/Gkv978  0.354
2015 Locke G, Morozov AV. A Biophysical Approach to Predicting Protein-DNA Binding Energetics. Genetics. 200: 1349-61. PMID 26081193 DOI: 10.1534/Genetics.115.178384  0.441
2015 Manhart M, Morozov AV. Scaling properties of evolutionary paths in a biophysical model of protein adaptation. Physical Biology. 12: 045001. PMID 26020812 DOI: 10.1088/1478-3975/12/4/045001  0.377
2015 Manhart M, Morozov AV. Protein folding and binding can emerge as evolutionary spandrels through structural coupling. Proceedings of the National Academy of Sciences of the United States of America. 112: 1797-802. PMID 25624494 DOI: 10.1073/Pnas.1415895112  0.422
2015 Chereji RV, Morozov AV. Functional roles of nucleosome stability and dynamics. Briefings in Functional Genomics. 14: 50-60. PMID 25275099 DOI: 10.1093/Bfgp/Elu038  0.332
2014 Haldane A, Manhart M, Morozov AV. Biophysical fitness landscapes for transcription factor binding sites. Plos Computational Biology. 10: e1003683. PMID 25010228 DOI: 10.1371/Journal.Pcbi.1003683  0.379
2014 Chereji RV, Morozov AV. Ubiquitous nucleosome crowding in the yeast genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 5236-41. PMID 24706846 DOI: 10.1073/Pnas.1321001111  0.365
2013 Manhart M, Morozov AV. Path-based approach to random walks on networks characterizes how proteins evolve new functions. Physical Review Letters. 111: 088102. PMID 24010480 DOI: 10.1103/Physrevlett.111.088102  0.353
2013 Dršata T, Pérez A, Orozco M, Morozov AV, Sponer J, Lankaš F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of Chemical Theory and Computation. 9: 707-721. PMID 23976886 DOI: 10.1021/Ct300671Y  0.388
2013 Locke G, Haberman D, Johnson SM, Morozov AV. Global remodeling of nucleosome positions in C. elegans. Bmc Genomics. 14: 284. PMID 23622142 DOI: 10.1186/1471-2164-14-284  0.309
2013 Morozov AV. 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. Physics of Life Reviews. 10: 75-7; discussion 82-. PMID 23403270 DOI: 10.1016/J.Plrev.2013.01.014  0.324
2013 Chereji RV, Morozov AV. New Insights into Nucleosome Unwrapping Biophysical Journal. 104: 579a-580a. DOI: 10.1016/J.Bpj.2012.11.3218  0.352
2012 Manhart M, Haldane A, Morozov AV. A universal scaling law determines time reversibility and steady state of substitutions under selection. Theoretical Population Biology. 82: 66-76. PMID 22838027 DOI: 10.1016/J.Tpb.2012.03.007  0.309
2011 Chereji RV, Morozov AV. Statistical Mechanics of Nucleosomes Constrained by Higher-Order Chromatin Structure. Journal of Statistical Physics. 144: 379-404. PMID 21857746 DOI: 10.1007/S10955-011-0214-Y  0.387
2011 Chereji RV, Tolkunov D, Locke G, Morozov AV. Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 83: 050903. PMID 21728479 DOI: 10.1103/Physreve.83.050903  0.375
2011 Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR. Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters. Molecular Biology of the Cell. 22: 2106-18. PMID 21508315 DOI: 10.1091/Mbc.E10-10-0826  0.311
2011 Morozov AV. Sequence determinants of histone-DNA binding preferences: comment on "Cracking the chromatin code: precise rule of nucleosome positioning" by Edward N. Trifonov. Physics of Life Reviews. 8: 62-3; discussion 69-. PMID 21296039 DOI: 10.1016/J.Plrev.2011.01.013  0.385
2010 Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV. High-throughput sequencing reveals a simple model of nucleosome energetics. Proceedings of the National Academy of Sciences of the United States of America. 107: 20998-1003. PMID 21084631 DOI: 10.1073/Pnas.1003838107  0.388
2010 Bai L, Morozov AV. Gene regulation by nucleosome positioning. Trends in Genetics : Tig. 26: 476-83. PMID 20832136 DOI: 10.1016/J.Tig.2010.08.003  0.305
2010 Tolkunov D, Morozov AV. Genomic studies and computational predictions of nucleosome positions and formation energies. Advances in Protein Chemistry and Structural Biology. 79: 1-57. PMID 20621280 DOI: 10.1016/S1876-1623(10)79001-5  0.39
2009 Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED. Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Research. 37: 4707-22. PMID 19509309 DOI: 10.1093/Nar/Gkp475  0.609
2007 Morozov AV, Siggia ED. Connecting protein structure with predictions of regulatory sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 7068-73. PMID 17438293 DOI: 10.1073/Pnas.0701356104  0.618
2006 Foat BC, Morozov AV, Bussemaker HJ. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics (Oxford, England). 22: e141-9. PMID 16873464 DOI: 10.1093/Bioinformatics/Btl223  0.613
2006 Morozov AV, Tsemekhman K, Baker D. Electron density redistribution accounts for half the cooperativity of alpha helix formation. The Journal of Physical Chemistry. B. 110: 4503-5. PMID 16526672 DOI: 10.1021/Jp057161F  0.449
2005 Morozov AV, Kortemme T. Potential functions for hydrogen bonds in protein structure prediction and design. Advances in Protein Chemistry. 72: 1-38. PMID 16581371 DOI: 10.1016/S0065-3233(05)72001-5  0.622
2005 Morozov AV, Havranek JJ, Baker D, Siggia ED. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research. 33: 5781-98. PMID 16246914 DOI: 10.1093/Nar/Gki875  0.742
2004 Misura KM, Morozov AV, Baker D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of Molecular Biology. 342: 651-64. PMID 15327962 DOI: 10.1016/J.Jmb.2004.07.038  0.748
2004 Morozov AV, Kortemme T, Tsemekhman K, Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proceedings of the National Academy of Sciences of the United States of America. 101: 6946-51. PMID 15118103 DOI: 10.1073/Pnas.0307578101  0.657
2003 Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53: 76-87. PMID 12945051 DOI: 10.1002/Prot.10454  0.731
2003 Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins. 52: 118-22. PMID 12784377 DOI: 10.1002/Prot.10384  0.702
2003 Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Journal of Molecular Biology. 326: 1239-59. PMID 12589766 DOI: 10.1016/S0022-2836(03)00021-4  0.682
2003 Morozov AV, Kortemme T, Baker D. Evaluation of models of electrostatic interactions in proteins Journal of Physical Chemistry B. 107: 2075-2090. DOI: 10.1021/Jp0267555  0.66
2002 Alm E, Morozov AV, Kortemme T, Baker D. Simple physical models connect theory and experiment in protein folding kinetics. Journal of Molecular Biology. 322: 463-76. PMID 12217703 DOI: 10.1016/S0022-2836(02)00706-4  0.728
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