Gene Regulation Info

Publications

2013:

• 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. | Advance Access Online | PDF |

• 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. | Advance Access Online | PDF |

• Schöpflin, R., Teif, V. B., Müller, O., Weinberg, C., Rippe, K. & Wedemann, G. (2013). Modeling nucleosome position distributions from experimental nucleosome positioning maps. Submitted.

• 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 |

2012:

• Teif V.B., Vainshtein Y., Caudron-Herger M., Mallm J.-P., Marth C., Höfer T., Rippe K. (2012). Genome-wide nucleosome positioning during embryonic stem cell development. Nature Struct. Mol. Biol. 19, 1185-92 | Pubmed | Bioquant press release | DKFZ press release | Full text online | PDF |

• Teif V. B. and Rippe K. (2012). Calculating transcription factor binding maps for chromatin. Brief. Bioinform. 13, 187-201 | Full text at Oxford University Press | PDF |

• 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 | 
  

2011:

• 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. | 

2010:

• 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 O_R operator of phage lambda. Nucleic Acids Res. 35, e80. 

• 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 |

• Teif V. B., Vorob’ev V. I. and Lando D. Y. (2002). A Single DNA chemical modification by cisplatin may cause long-range changes in protein binding to DNA. Results of computer modeling. Europ. J. Human Genet. 10, suppl. 1, 104.

• Teif V. B. and Lando D. Y. Conditions for DNA phase transition induced by ligand binding. Europ. J. Human Genet. 9 suppl. 1, 241 (2001).

• 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 |