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34 results
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Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities.
Teif VB, Rippe K. Teif VB, et al. Nucleic Acids Res. 2009 Sep;37(17):5641-55. doi: 10.1093/nar/gkp610. Epub 2009 Jul 22. Nucleic Acids Res. 2009. PMID: 19625488 Free PMC article.
General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.
Teif VB. Teif VB. Nucleic Acids Res. 2007;35(11):e80. doi: 10.1093/nar/gkm268. Epub 2007 May 25. Nucleic Acids Res. 2007. PMID: 17526526 Free PMC article.
Predicting gene-regulation functions: lessons from temperate bacteriophages.
Teif VB. Teif VB. Biophys J. 2010 Apr 7;98(7):1247-56. doi: 10.1016/j.bpj.2009.11.046. Biophys J. 2010. PMID: 20371324 Free PMC article.
Condensed DNA: condensing the concepts.
Teif VB, Bohinc K. Teif VB, et al. Prog Biophys Mol Biol. 2011 May;105(3):208-22. doi: 10.1016/j.pbiomolbio.2010.07.002. Epub 2010 Jul 16. Prog Biophys Mol Biol. 2011. PMID: 20638406 Review.
A lattice model for transcription factor access to nucleosomal DNA.
Teif VB, Ettig R, Rippe K. Teif VB, et al. Biophys J. 2010 Oct 20;99(8):2597-607. doi: 10.1016/j.bpj.2010.08.019. Biophys J. 2010. PMID: 20959101 Free PMC article.
Statistical-mechanical lattice models for protein-DNA binding in chromatin.
Teif VB, Rippe K. Teif VB, et al. J Phys Condens Matter. 2010 Oct 20;22(41):414105. doi: 10.1088/0953-8984/22/41/414105. Epub 2010 Sep 30. J Phys Condens Matter. 2010. PMID: 21386588
Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers.
Teif VB, Rippe K. Teif VB, et al. Phys Biol. 2011 Aug;8(4):044001. doi: 10.1088/1478-3975/8/4/044001. Epub 2011 Jun 10. Phys Biol. 2011. PMID: 21666293
Calculating transcription factor binding maps for chromatin.
Teif VB, Rippe K. Teif VB, et al. Brief Bioinform. 2012 Mar;13(2):187-201. doi: 10.1093/bib/bbr037. Epub 2011 Jul 6. Brief Bioinform. 2012. PMID: 21737419
Genome-wide nucleosome positioning during embryonic stem cell development.
Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K. Teif VB, et al. Nat Struct Mol Biol. 2012 Nov;19(11):1185-92. doi: 10.1038/nsmb.2419. Epub 2012 Oct 21. Nat Struct Mol Biol. 2012. PMID: 23085715
Taking into account nucleosomes for predicting gene expression.
Teif VB, Erdel F, Beshnova DA, Vainshtein Y, Mallm JP, Rippe K. Teif VB, et al. Methods. 2013 Jul 15;62(1):26-38. doi: 10.1016/j.ymeth.2013.03.011. Epub 2013 Mar 21. Methods. 2013. PMID: 23523656 Review.
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