Homepage of Michael Y. Tolstorukov

 

 

Center for Biomedical Informatics, Harvard Medical School

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA

e-mail: tolstorukov@gmail.com  -  tel: + 1 ( 617 ) 432 7376

 

 

 

 

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Updated: 03 Nov 2011

Publications

 BOOK CHAPTERS and REVIEWS

Tolstorukov, M.Y., Kharchenko, P.V. & Park, P.J. “Analysis of primary structure of chromatin with next generation sequencing” Epigenomics (2010), 2:187-197. [publisher]

Zhurkin, V.B., Tolstorukov, M.Y., Xu, F., Colasanti, A.V. & Olson, W.K. “Sequence-dependent variability of B-DNA: An update on bending and curvature.” In: T. Ohyama (ed.) DNA Conformation and Transcription. Austin, TX: LANDES Bioscience; 2005. [publisher]

Tolstorukov, M.Y. & Virnik, K.M. “Mathematical model of the nucleic acids conformational transitions with hysteresis over hydration-dehydration cycle.”  In: P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, R.D. Skeel (eds.) Computational Molecular Dynamics: Challenges, Methods, Ideas -- Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, 1997; in Series: Lecture Notes in Computational Science and Engineering, Vol. 4, Berlin, Springer-Verlag, 1998. [publisher]

 

 modENCODE CONSORTIUM PAPERS

1.   The modENCODE Consortium, et al. “Identification of functional elements and regulatory circuits by Drosophila modENCODE” Science (2010), 330:1787-1797.

2.   Kharchenko P.V., et al. “Comprehensive analysis of the chromatin landscape in Drosophila melanogaster” Nature (2011), 471(7339):480-485.

3.   Riddle N.C., et al. “Dynamic patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin” Genome Research (2011), 21:147-163.

 

 RESEARCH PAPERS

1.     Tolstorukov, M.Y., Volfovsky, N., Stephens, R.M. & Park, P.J. “Impact of chromatin structure on sequence variability in the human genome” Nature Structural and Molecular Biology (2011), 18:510-515.

2.     Jagani, Z, Mora-Blanco, E.L., Sansam, C.G., McKenna, E.S., Wilson, B., Chen, D., Klekota, J., Tamayo, P., Nguyen, P.T., Tolstorukov, M., Park, P.J., Cho, Y.J., Hsiao, K., Buonamici, S., Pomeroy, S.L., Mesirov, J.P., Ruffner, H., Bouwmeester, T., Luchansky, S.J., Murtie, J., Kelleher, J.F., Warmuth, M., Sellers, W.R., Roberts, C.W. & Dorsch, M. “Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway” Nature Medicine (2010), 16:1429-1433.

3.      Blackledge, N.P., Zhou, J.C., Tolstorukov, M.Y., Park, P.J. & Klose, R.J. “CpG islands recruit a histone H3 lysine 36 demethylase” Molecular Cell (2010), 38:179-190.

4.      Babbitt, G.A., Tolstorukov, M.Y., Kim, Y. “The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer” Journal of Biomolecular Structure and Dynamics (2010), 27:765-780.

5.     Tolstorukov, M.Y., Kharchenko, P.V., Goldman, J.A., Kingston, R.E. & Park, P.J. “Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes,” Genome Research (2009), 19:967-977, (cover paper).

6.     Kharchenko, P.V., Tolstorukov, M.Y. & Park, P.J. “Design and analysis of ChIP-seq experiments for DNA-binding proteins,” Nature Biotechnology (2008), 26:1351-1359.

7.     Kharchenko, P.V., Woo, C.J., Tolstorukov, M.Y., Kingston, R.E. & Park, P.J. “Nucleosome positioning in human HOX gene clusters,” Genome Research (2008), 18:1554-1561.

8.     Tolstorukov, M.Y., Choudhary, V., Olson, W.K., Zhurkin, V.B. & Park, PJ. “nuScore: a web-interface for nucleosome positioning predictions,” Bioinformatics (2008), 24:1456-1458.

9.     Tolstorukov M.Y., Colasanti, A.V., McCandlish, D., Olson, W.K. & Zhurkin, V.B. “A Novel ‘Roll-and-Slide’ Mechanism of DNA Folding in Chromatin. Implications for Nucleosome Positioning,” Journal of Molecular Biology (2007), 371:725-738.

10.  Tolstorukov, M.Y., Virnik, K.M., Adhya, S. & Zhurkin, V.B. “A-tract clustering may facilitate DNA packaging in bacterial nucleoid,” Nucleic Acids Research (2005), 33:3907–3918.

11.  Semsey, S., Tolstorukov, M.Y., Virnik, K., Zhurkin, V.B. & Adhya, S. “DNA Trajectory in the Gal Repressosome,” Genes & Development (2004), 18:1898-1907.

12.  Liu, M., Tolstorukov, M.Y., Zhurkin, V.B., Adhya, S. & Garges, S. “A new promoter element, UP2, makes the E.coli Plac promoter hyperactive and CRP independent,” Proceedings of the National Academy of Sciences of the USA (2004), 101:6911-6916.

13.  Tolstorukov, M.Y., Jernigan, R.L. & Zhurkin, V.B. “Protein – DNA hydrophobic recognition in the minor groove is facilitated by sugar switching,” Journal of Molecular Biology (2004), 337:65-76.

14.  Virnik, K., Lyubchenko, Y.L., Karymov, M.A., Dahlgren, P., Tolstorukov, M.Y., Semsey, S., Zhurkin, V.B. & Adhya, S. “’Antiparallel’ DNA Loop in Gal Repressosome Visualized by Atomic Force Microscopy,” Journal of Molecular Biology (2003), 334:53-63.

15.  Tolstorukov, M.Y., Ivanov, V.I., Malenkov, G.G., Jernigan, R.L. & Zhurkin, V.B. “Sequence-dependent B«A transition in DNA evaluated with dimeric and trimeric scales,” Biophysical Journal (2001), 81:3409-3421.

16.  Tolstorukov, M.Y. & Maleev, V.Y. “Conformational transitions of DNA induced by changing water content of the sample: A theoretical study,” Journal of Biomolecular Structure and Dynamics (2000), 17:913-920.

17.  Tolstorukov, M.Y. & Gatash, S.V. “Self-organization and nonlinear dynamics of nucleic acid-water system,” Special Issue of International Journal on Bifurcation and Chaos (1999), 9:371-381.

18.  Virnik, K.M. & Tolstorukov, M.Y. “Binding energy differentiation of water molecules in DNA hydration shell,” Digest of Kharkov State University, Biophysical Bulletin (1998), 422:35-38.

19.  Virnik, K.M. Tolstorukov, M.Y. & Maleev, V.Y. “Surface diffusion of bound water in hydrate surroundings of DNA,“ Digest of Kharkov State University, Biophysical Bulletin (1998), 422:23-28.

20.  Tolstorukov, M.Y. & Virnik, K.M. “Experimental study of hysteresis phenomenon in the process of hydration-dehydration of NaDNA,” Biopolymers and Cell (1998), 14:524-528 (in Russian).

21.  Tolstorukov, M.Y., Gatash, S.V. & Maleev, V.Y. “Parameter distributed model of the conformational transitions induced with change of relative humidity in the nucleic acid samples,” Digest of Kharkov State University, Biophysical Bulletin (1998), 410:33-40 (in Russian).

22.  Tolstorukov, M.Y., Gatash, S.V. & Maleev, V.Y. “Mathematical model of nucleic acids' conformational dynamics in wetted samples,” Vestnik Problem Biologii i Mediciny (1998), 16:6-12 (in Russian).

23.  Virnik, K.M. & Tolstorukov, M.Y. “Calculation of fractal dimensions of DNA in various conformations,” Vestnik Problem Biologii i Mediciny (1998), 2:5-15, (in Russian).

24.  Tolstorukov, M.Y., Gasan, A.I., Gatash, S.V., & Maleev, V.Y. “The molecular mechanism of the sorption hysteresis in the DNA - water system,” Biophysics (1997), 42:847-857.

 

 

 MANUSCRIPTS IN PREPARATION

1.     Sansam, C.G., Tolstorukov, M.Y., Helming, K., Koellhoffer, E.C., Evans, J.A., Wilson, B.G., Park, P.J. & Roberts, CWM. “Swi/Snf sculpts the chromatin landscape at promoters” – research paper

 

 CONFERENCE PAPERS

Tolstorukov, M.Y., Kharchenko, P.V., Goldman, J.A., Kingston, R.E., Park, P.J. “Comparative analysis of nucleosome sequence organization in human and yeast genomes” Journal of Biomolecular Structure and Dynamics (2009), 26:917.

Tolstorukov, M.Y., Zhurkin, V.B., Olson, W.K. “Structural properties of GC-rich sequences may hinder nucleosome positioning in CpG islands” Journal of Biomolecular Structure and Dynamics (2007), 24:624-625.

Shashel, Y.V., Anishkin, A.G., Tolstorukov, M.Y. “Cross-correlations of base-pair and dimer step parameters of DNA” Journal of Biomolecular Structure and Dynamics (2007), 24:739-740.

Tolstorukov, M.Y., Colasanti, A.V., McCandlish, D., Olson, W.K. & Zhurkin, V.B. “Superhelical path of nucleosomal DNA is controlled by base-pair slide,” Journal of Biomolecular Structure and Dynamics (2005), 22:854-855.

Virnik, K., Tolstorukov, M., Zhurkin, V. & Adhya, S. “Structural organization of bacterial nucleoid,” Journal of Biomolecular Structure and Dynamics (2005), 22:848.

Tolstorukov, M., Virnik, K., Adhya, S. & Zhurkin, V. “Genome-wide A-tract distribution and DNA packaging in pro- and eukaryotes,” Journal of Biomolecular Structure and Dynamics (2003), 20: 869-870.

Tolstorukov, M.Y., Jernigan, R.L. & Zhurkin, V.B. “Effect of sugar puckering on protein-DNA interactions in DNA minor groove,” Biophysical Journal (2002), 82: 2265.

Tolstorukov, M.Y., Jernigan, R.L., & Zhurkin, V.B. “Non-random distribution of A-tracts in pro- and eukaryotic genomes,”  In: Chakravarti, A., Eisen, M., and Zhang, M., (Eds.):  Proceedings of the 2001 Meeting on Integrating Genome Sequence, Sequence Variation and Gene Expression.  Cold Spring Harbor, NY (2001), p. 67.

 

12th Conversation in Stereodynamics, Albany, NY, June 2001

 

Tolstorukov, M.Y., Jernigan, R.L. & Zhurkin, V.B. “Protein-DNA minor groove recognition,” Journal of Biomolecular Structure and Dynamics (2001), 18: 944-945.

Tolstorukov, M.Y., Jernigan, R.L. & Zhurkin, V.B. “Minor groove interaction profiles of protein/DNA complexes,” Biophysical Journal (2001), 80: 568a.

Tolstorukov, M.Y., Ivanov, V.I., Minchenkova, L.E., Krylov, D.Y., Jernigan, R.L. & Zhurkin, V.B. “Trimeric model for the B-A transition in DNA,” Biophysical Journal (2001), 80: 484a.

Tolstorukov, M.Y., Gatash, S.V. & Maleev, V.Y. “Conformational dynamics of a nucleic acid molecule over hydration-dehydration cycle:  A theoretical study,” Journal of Biomolecular Structure and Dynamics (1999), 16 (6): 1256.

Tolstorukov, M.Y., Gatash, S.V. & Maleev, V.Y. “Effect of hydration on conformational dynamics of nucleic acid molecule.  Spatially extended model,” Proceedings of the Conference on Physics of Biological Systems. Kiev, Ukraine (1998), p. 25.

Tolstorukov, M.Y., Gatash, S.V. & Maleev, V.Y. “Model of conformational transitions of nucleic acid molecule induced with changing relative humidity of the sample,”  Proceedings of the 2nd . Congress of Ukrainian Biophysical Society.  Kharkov, Ukraine (1998), p. 23 (in Ukrainian).

Tolstorukov, M.Y. “Mathematical model of the conformational transitions and nonlinear dynamics of the nucleic acid – water system,” In: Deuflhard, P. and Reich, S. (Eds):  2nd International Symposium: Algorithms for Macromolecular Modelling.  Berlin, Germany (1997), pp. 25-26.

Virnik, K.M. & Tolstorukov, M.Y. “Estimation of the diffusion coefficients of water bound to the DNA surface,” Proceedings of the 17th Discussion Conference:  Surface and Interfacial Phenomena in Macromolecular Systems.  Prague, Check Republic (1997), p. 5.

Virnik, K.M., Tolstorukov, M.Y. & Maleev, V.Y. “Diffusion of bound water molecules along fractal biopolymer surface,”  Proceedings of the 3rd International Conference:  The physical phenomena of condensed matter.  Kharkov, Ukraine (1997), p. 114 (in Russian).

Tolstorukov, M.Y., Gatash, S.V. & Maleev, V.Y. “The conformational transitions with hysteresis in the nucleic acid - water system,” Proceedings of the 3rd International Conference:  The Physical Phenomena of Condensed Matter.  Kharkov, Ukraine (1997), p. 115 (in Russian).

Tolstorukov, M.Y. & Gatash, S.V. “Self-organization and nonlinear dynamics of nucleic acid-water system,” Proceedings of the International Conference: Nonlinearity, Bifurcation, Chaos:  The Doors to the Future. Lodz, Poland (1996), pp. 231-234.