Vladimir B Teif

Summary

Affiliation: University of Heidelberg
Country: Germany

Publications

  1. doi request reprint Calculating transcription factor binding maps for chromatin
    Vladimir B Teif
    BioQuant and German Cancer Research Center DKFZ, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    Brief Bioinform 13:187-201. 2012
  2. pmc Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Nucleic Acids Res 37:5641-55. 2009
  3. doi request reprint Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    Phys Biol 8:044001. 2011
  4. doi request reprint Statistical-mechanical lattice models for protein-DNA binding in chromatin
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Phys Condens Matter 22:414105. 2010
  5. pmc A lattice model for transcription factor access to nucleosomal DNA
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Heidelberg, Germany
    Biophys J 99:2597-607. 2010
  6. doi request reprint Condensed DNA: condensing the concepts
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, Heidelberg, Germany
    Prog Biophys Mol Biol 105:208-22. 2011
  7. pmc Predicting gene-regulation functions: lessons from temperate bacteriophages
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Biophys J 98:1247-56. 2010
  8. doi request reprint Taking into account nucleosomes for predicting gene expression
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Methods 62:26-38. 2013
  9. ncbi request reprint Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, 69120 Heidelberg, Germany
    Genome Res 24:1285-95. 2014
  10. doi request reprint Modeling nucleosome position distributions from experimental nucleosome positioning maps
    Robert Schöpflin
    Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    Bioinformatics 29:2380-6. 2013

Collaborators

Detail Information

Publications12

  1. doi request reprint Calculating transcription factor binding maps for chromatin
    Vladimir B Teif
    BioQuant and German Cancer Research Center DKFZ, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    Brief Bioinform 13:187-201. 2012
    ..Strategies are discussed that could further facilitate calculations to allow computing genome-wide TF binding maps...
  2. pmc Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Nucleic Acids Res 37:5641-55. 2009
    ..Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality...
  3. doi request reprint Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    Phys Biol 8:044001. 2011
    ..In addition, the proposed model offers explanations for other distance-dependent effects at eukaryotic enhancers...
  4. doi request reprint Statistical-mechanical lattice models for protein-DNA binding in chromatin
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Phys Condens Matter 22:414105. 2010
    ..The results have a number of applications for quantitative models for the regulation of gene expression...
  5. pmc A lattice model for transcription factor access to nucleosomal DNA
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Heidelberg, Germany
    Biophys J 99:2597-607. 2010
    ..These findings indicate that partial unwrapping of DNA from the histone octamer needs to be taken into account in quantitative models of gene regulation in chromatin...
  6. doi request reprint Condensed DNA: condensing the concepts
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, Heidelberg, Germany
    Prog Biophys Mol Biol 105:208-22. 2011
    ..We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology...
  7. pmc Predicting gene-regulation functions: lessons from temperate bacteriophages
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Biophys J 98:1247-56. 2010
    ....
  8. doi request reprint Taking into account nucleosomes for predicting gene expression
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Methods 62:26-38. 2013
    ..We discuss strategies that address these issues to efficiently compute transcription factor binding in chromatin...
  9. ncbi request reprint Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, 69120 Heidelberg, Germany
    Genome Res 24:1285-95. 2014
    ..We rationalize this cell type-dependent targeting of CTCF with a quantitative biophysical model of competitive binding with the histone octamer, depending on the TET1, 5hmC, and 5mC state. ..
  10. doi request reprint Modeling nucleosome position distributions from experimental nucleosome positioning maps
    Robert Schöpflin
    Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    Bioinformatics 29:2380-6. 2013
    ..To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average...
  11. doi request reprint Genome-wide nucleosome positioning during embryonic stem cell development
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Nat Struct Mol Biol 19:1185-92. 2012
    ..Our results reveal regulatory mechanisms of cell differentiation that involve nucleosome repositioning...
  12. pmc Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions
    Daria A Beshnova
    Deutsches Krebsforschungszentrum DKFZ and BioQuant, Heidelberg, Germany
    PLoS Comput Biol 10:e1003698. 2014
    ....