Gene Regulation – Teif Lab

Publications

2018:

  • Pavlaki I., Docquier F., Chernukhin I., Kita G., Gretton S., Clarkson C.T. , Teif V.B.*, Klenova E.* (2018) Poly(ADP-ribosyl)ation dependent changes in CTCF-chromatin binding and gene expression in breast cells. BBA Gene Regulatory Mechanisms (Accepted) | *Co-corresponding authors | bioRxiv preprint

2017:

  • 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 | *Co-corresponding authors | 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 8, 188-204 | *Co-corresponding authors | Open access article | PDF

2016:

  • 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

2015:

  • 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 | *Co-corresponding authors | Journal online | 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 |

2014:

  • 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 | *Co-corresponding authors | 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 |

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 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 |

2012:

https://i1.wp.com/www.nature.com/nsmb/images/journal_header_v3.jpg?resize=557%2C71

  • Teif V. B.* and Rippe K. (2012). Calculating transcription factor binding maps for chromatin. Brief. Bioinform. 13, 187-201 | Icon for Silverchair Information Systems | 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. | *Co-corresponding authors | PubMed | PDF |
  • Teif V. B.* and Bohinc K.* (2011). Condensed DNA: condensing the concepts. Progr. Biophys. Mol. Biol. 105, 208-222. | *Co-corresponding authors | 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 | *Co-corresponding authors | 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 | *Co-corresponding authors | 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.* 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 |