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Gene Regulation Info

Quantitative descriptions of gene regulation








  • Vainshtein Y., Rippe K. and Teif V.B. (2017). NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics 18, 158 | Open access article
  • Teif V.B., Mallm J.-P., Sharma T., Mark Welch D.B., Rippe K., Eils R., Langowski J., Olins A.L. and Olins D.E. (2017). Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. Nucleus | Open access article link will appear here | DOI: 10.1080/19491034.2017.1295201


  • Teif V.B and Cherstvy A.G. (2016). Chromatin and epigenetics: current biophysical views. AIMS Biophysics 3, 88-98 | Open access article | PDF
  • Teif V.B. (2016). Nucleosome positioning: resources and tools online. Briefings in Bioinformatics. 17, 745-757.  | Published version | PDF


  • Teif V.B., Kepper N., Yserentant K., Wedemann G., Rippe K. (2015). Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays. J. Phys.: Condens. Matter 27, 064110 | PDF |
  • Salih B., Teif V.B., Tripathi V., Trifonov E.N. (2015) Strong nucleosomes of mouse genome in recovered centromeric sequences. J. Biomol. Struct. Dynam. 33, 1164-1175 | Taylor & Francis Online | PDF |


  • Teif V.B., Beshnova D.A., Marth C., Vainshtein Y., Mallm J.-P., Höfer T. and Rippe K. (2014). Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Research. 24, 1285-1295 | Pubmed PDF | Icon for HighWire| Press release |
  • Beshnova D.A., Cherstvy A.G. Vainshtein Y. and Teif V.B. (2014). Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions. PLoS Comp. Biol. 10, e1003698 | PDF | Icon for Public Library of Science
  • Cherstvy A.G. and Teif V.B. (2014). Electrostatic effect of H1-histone protein binding on nucleosome repeat length. Phys. Biol. 11, 044001 | PDF |
  • Teif V.B. (2014). On the Sociology of Science 2.0. In "Opening Science: The Evolving Guide on How the Internet is Changing Research, Collaboration and Scholarly Publishing", Eds. S. Bartling, S. Friesike. Springer, 2014, IX, 335 p. 43 illus. | ISBN 978-3-319-00026-8 | Order book online |


  • Teif V.B., Erdel F., Beshnova D.A., Vainshtein Y., Mallm J.-P., Rippe K. (2013) Taking into account nucleosomes for predicting gene expression. Methods 62, 26-38 | Sciencedirect | PDF |
  • Schöpflin, R., Teif, V. B., Müller, O., Weinberg, C., Rippe, K. & Wedemann, G. (2013). Modeling nucleosome position distributions from experimental nucleosome positioning maps. Bioinformatics. 29, 2380-2386 | Pubmed | Full Text |
  • Cherstvy A.G. and Teif V.B. (2013) Structure-driven homology pairing of chromatin fibers: The role of electrostatics and protein bridging. J. Biol. Phys. 39, 363-385 | PDF |
  • Teif V.B., Beshnova D., Vainshtein Y., Höfer T., Rippe K. (2013). Developing a software suite to analyze the interplay between nucleosome arrangement, DNA methylation and tanscription factor binding. EMBnet.journal 19A, 39-40. | Abstract | PDF |
  • Teif V.B. (2013). Science 3.0: Corrections to the Science 2.0 paradigm. | ArXiv:1301.2522 |


  • Teif V. B., Shkrabkou A.V., Egorova V.P., Krot V.I. (2012). Nucleosomes in gene regulation: Theoretical approaches. Molecular Biology 46, 1-10. | PDF


  • Teif V. B. and Rippe K. (2011). Nucleosome mediated crosstalk between transcription factors. Phys. Biol. 8, 04400. | PubMed | PDF |
  • Teif V. B. and Bohinc K. (2011). Condensed DNA: condensing the concepts. Progr. Biophys. Mol. Biol. 105, 208-222. | PDF |
  • Längst G., Teif V. B. and Rippe K. (2011). Chromatin remodeling by translocation of nucleosomes. In “Genome organization and function in the cell nucleus”, Ed. K. Rippe, Wiley-VCH, Weinheim. P. 111-139. | 


  • Teif V. B., Ettig R. and Rippe K. (2010). A lattice model for transcription factor access to nucleosomal DNA. Biophys. J. 99, 2597-2607 | PDF
  • Teif V. B. (2010). Predicting gene-regulation functions: Lessons from temperate bacteriophages. Biophys. J. 98, 1247-1256 |

--->Highlighted in an interview in the Genome Technology Magazine

  • Teif V. B. and Rippe K. (2010). Statistical-mechanical lattice models for protein-DNA binding in chromatin. J. Phys.: Condens. Matter. 22, 414105 | PDF |
  • Teif V. B., Harries D., Lando D.Y. and Ben-Shaul A. (2010). Matrix formalism for sequence-specific polymer binding to multicomponent lipid membranes. In “Membrane-active peptides: methods and results on structure and function", Ed. M. Castanho, International University Line, La Jolla. | PDF |

2009 and earlier:

  • Teif V. B. and Rippe K. (2009). Predicting nucleosome positions on the DNA: combining intrinsic affinities and remodeler activities. Nucleic Acids Res. 37, 5641-5655. | PubMed | PDF | Supplementary Materials |
  • Teif V. B., Harries D., Lando D. Y. and Ben-Shaul A. (2008). Matrix formalism for site-specific binding of unstructured proteins to multicomponent lipid membranes. J. Pept. Sci. 14, 368-373. | PubMed | PDF | Supplementary computer program |
  • Teif V. B. (2007). General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: Application to OR operator of phage lambda. Nucleic Acids Res. 35, e80. Click here to read Click here to read
  • Teif V. B. (2005). Ligand-induced DNA condensation: choosing the model. Biophys. J. 89, 2574-2587.
  • Teif V. B., Lando D. Y. On the cooperativity of metal ion binding to the bases of single-stranded DNA. Europ. J. Biochem. 271(1), 19 (2004). | Abstract
  • Teif V. B. (2003). On the cooperativity of metal ion binding to DNA. J. Biomol. Struct. Dynam. 20, 897-898. | Abstract
  • Teif V. B. and Lando D. Y. (2003) DNA condensation caused by ligand binding. In “Bioregulators: investigation and application”, Minsk, “Technoprint”. P. 116-128. | PDF (Rus)
  • Teif V.B. and Lando D.Y. (2002). Modeling of DNA Condensation and Decondensation Caused by Ligand Binding. J. Biomol Struct Dynam. 20, 215-222. .| PDF | Full Text |
  • Teif V. B., Haroutunian S. H., Vorob'ev V. I. and Lando D. Y. (2002) Short-range interactions and size of ligands bound to DNA strongly influence adsorptive phase transition caused by long-range interactions. J. Biomol. Struct. Dynam. 19, 1103-1110.| PDF | Full Text at Taylor & Francis Online |
  • Teif V. B. and Lando D. Y. (2001) Calculation of DNA condensation caused by ligand adsorption. Molecular Biology 35, 117-119. | PDF
  • Teif V. B. and Lando D. Y. (2001) DNA condensation caused by ligand binding may serve as a sensor. Sensor Technology 2001, ed. M. Elwenspoek, Kluver, Dordrecht, P. 155-160. | PDF
  • Teif V. B., Vorob’ev V. I., Lando D. Y. (2001). Calculation of DNA condensation caused by ligand binding using a two-state model. J. Biomol. Struct. Dynam. 18, 908-909. | Abstract |
  • Lando D. Y. and Teif V. B. (2000) Long-range interactions between ligands bound to a DNA molecule give rise to adsorption with the character of phase transition of the first kind. J. Biomol. Struct. Dynam. 17, 903-911. | PDF | | Full Text at Taylor & Francis Online |