Publications

  1. Clarkson C.T., Deeks E.A., Samarista R., Mamayusupova H., Zhurkin V.B.*, Teif V.B.* (2019) CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Res 47, 11181-11196. |  Open access article 
  2. Antwi E.B., Olins A., Teif V.B., Bieg M., Bauer T., Gu Z., Brors B., Eils R., Olins D., Ishaque N. (2019) Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. bioRxiv preprint.
  3. Wiehle L., Thorn G.J., Raddatz G., Clarkson C.T., Rippe K., Lyko F., Breiling A.*, Teif V.B.* (2019) DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Research 29, 750-761 | Open access article  | Journal Cover
  4. Mallm J.-P., Iskar M., Ishaque N., Klett L.C., Kugler S.J., Muino J.M., Teif V.B., Poos A.M., Großmann S., Erdel F., Tavernari D., Koser S.D., Schumacher S., Brors B., König R., Remondini D., Vingron M., Stilgenbauer S., Lichter P., Zapatka M., Mertens D.*, Rippe K.* (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Syst Biol 15, e8339 | Open access article | Journal Cover
  5. Teif V.B.* and Clarkson C.T. (2019) Nucleosome Positioning. In Encyclopedia of Bioinformatics and Computational Biology (Ed.: S. Ranganathan, M. Gribskov, K. Nakai, and C. Schönbach), vol. 2, pp. 308–317. Oxford: Academic Press |Published version |  Authors’ manuscript
  6. 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. Biochim Biophys Acta (BBA) – Gene Regulatory Mechanisms 1861, 718-730 | *Co-corresponding authors | Open access article
  7. 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
  8. 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
  9. Teif V.B.* and Cherstvy A.G. (2016). Chromatin and epigenetics: current biophysical views. AIMS Biophysics 3, 88-98 | Open access article
  10. Teif V.B.* (2016). Nucleosome positioning: resources and tools online. Briefings in Bioinformatics. 17, 745-757. | Open access article
  11. 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 |
  12. 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 OnlinePDF
  13. 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 | Open access article | Press release
  14. 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 | Open access article
  15. Cherstvy A.G.* and Teif V.B. (2014). Electrostatic effect of H1-histone protein binding on nucleosome repeat length. Phys. Biol. 11, 044001 | PDF
  16. 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 | Open access book
  17. 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 |
  18. 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 |
  19. 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 |
  20. 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. | AbstractPDF |
  21. Teif V.B.* (2013). Science 3.0: Corrections to the Science 2.0 paradigm. | ArXiv:1301.2522 |
  22. 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 | *Co-corresponding authors | Pubmed | Bioquant press release | DKFZ press release | Full text online PDF |
  23. Teif V. B.* and Rippe K. (2012). Calculating transcription factor binding maps for chromatin. Brief. Bioinform. 13, 187-201 | Open acces article
  24. Teif V. B.*, Shkrabkou A.V., Egorova V.P., Krot V.I. (2012). Nucleosomes in gene regulation: Theoretical approaches. Molecular Biology 46, 1-10. | PDFArticle at publisher’s site
  25. Teif V. B.* and Rippe K.* (2011). Nucleosome mediated crosstalk between transcription factors. Phys. Biol. 8, 04400. | *Co-corresponding authors | PubMedPDF |   Article at publisher’s site
  26. Teif V. B.* and Bohinc K.* (2011). Condensed DNA: condensing the concepts. Progr. Biophys. Mol. Biol. 105, 208-222. | *Co-corresponding authors |  PDFArticle at publisher’s site
  27. 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. |  Book online
  28. 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 | Open access article
  29. Teif V. B.* (2010). Predicting gene-regulation functions: Lessons from temperate bacteriophages. Biophys. J. 98, 1247-1256 |  Open access article Highlighted in an interview in the Genome Technology Magazine
  30. Teif V. B.* and Rippe K. (2010). Statistical-mechanical lattice models for protein-DNA binding in chromatin. J. Phys.: Condens. Matter. 22, 414105 |  PDFArticle at publisher’s site
  31. 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 |
  32. 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 | Open access article
  33. 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. | PubMedPDF | Article at publisher’s site
  34. 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. |  Open access article
  35. Teif V. B.* (2005). Ligand-induced DNA condensation: choosing the model. Biophys. J. 89, 2574-2587.  Open access article
  36. 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 (In Russian)
  37. 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. .|  PDFArticle at publisher’s site |
  38. 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 | Article at publisher’s site |
  39. Teif V. B. and Lando D. Y.* (2001) Calculation of DNA condensation caused by ligand adsorption. Molecular Biology 35, 117-119. |  PDF
  40. 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
  41. 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. |  PDFArticle at publisher’s site |