Gene Regulation – Teif Lab

Publications

  1. Takahashi N., Pongor L., Agrawal S. P., Shtumpf M., Rajapakse V. N., Shafiei A., Schultz C. W., Kim S., Roame D., Carter P., Vilimas R., Nichols S., Desai P., Figg W. D. Sr, Bagheri M, Teif V. B.*, Thomas A.* (2024) Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor. bioRxiv 2024.06.02.597054 
  2. Tajmul Md, Bhatt D. N, Ruje L., Price E., Ji Y., Loukinov D., Teif V. B., Lobanenkov V. V., Pugacheva E. M (2024). CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation. bioRxiv 2024.09.25.614770.
  3. Shtumpf M., Jeong S., Bikova M., Mamayusupova H., Ruje L. and Teif V.B.* (2024) Aging clock based on nucleosome reorganisation derived from cell-free DNA. Aging Cell 23, e14100 | Open access article
  4. Jacob D.R., Guiblet W. M., Mamayusupova H., Shtumpf M., Ruje L., Ciuta I., Bikova M., Gretton S., Correa C., Dellow E., Agrawal S. P., Shafiei N., Drobysevskaja A., Armstrong C. M., Lam J. D. G., Vainshtein Y., Clarkson C. T., Thorn G. J., Sohn K., Madapura M. P., Chandrasekharan S., Brooke G.N., Klenova E., Zhurkin V. B*, Teif V. B.* (2024) Nucleosome reorganisation in breast cancer tissues. Clinical Epigenetics 16, 50 | Open access article
  5. Peng Y., Song W., Teif V.B, Ovcharenko I., Landsman D., Panchenko A.R. (2024) Detection of new pioneer transcription factors as cell-type specific nucleosome binders. eLife 13, RP88936 | Open access article 
  6. Gautam P., Ciuta I., Teif V. B.*, Sinha S. K.* (2024) Predicting p53-dependent cell transitions from thermodynamic models. Chem. Phys. 161, 135101 | Open access article.
  7. Piroeva K. V., McDonald C., Xanthopoulos C., Fox C., Clarkson C. T., Mallm J.-P., Vainshtein Y., Ruje L., Klett L. C., Stilgenbauer S., Mertens D., Kostareli E.,* Rippe K.* and Teif V. B.* (2023) Nucleosome repositioning in chronic lymphocytic leukaemia. Genome Research 33, 1649-1661 | Open access article.
  8. Shtumpf M., Piroeva K.V., Agrawal S.P., Jacob D.R., Teif V.B.* (2022). NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 131, 19-28 | open access article
  9. Thorn G.J., Clarkson C.T., Rademacher A., Mamayusupova H., Schotta G., Rippe K.* and Teif V.B.* (2022) DNA sequence-dependent formation of heterochromatin nanodomains. Nature Communications 13, 1861 | Open access article 
  10. Belokopytova P., Viesná E., Chiliński M., Qi Y., Salari H., Di Stefano M., Esposito A., Conte M., Chiariello A.M., Teif V.B., Plewczynski D., Zhang B., Jost D., Fishman V. (2022). 3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Res 50, W4–W12 | Open access article.
  11. Mohr A., Tianyuan C., Clarkson C.T., Brooke G.N, Teif V.B., Zwacka R.M. (2021). Fas-threshold signalling in MSCs causes tumour progression and metastasis. Cancer Letters 519, 63-77 | Open access article
  12. Hedley J.G., Teif V.B.* and Kornyshev A.A.* (2021) Nucleosome induced homology recognition in chromatin. J. Royal Soc. Interface 18, 20210147. | Open access article
  13. Cucinotta C.E.*, Martin B.J.E.*, Noé González M.*, Raman P.*, Teif V.B.*, Vlaming H.* 2021. Strength is in engagement: The rise of an online scientific community during the COVID‐19 pandemic. EMBO reports 22: e52612. | Open access article
  14. Teif V.B.,*, Gould T.J., Clarkson C.T., Boyd L., Antwi E.B., Ishaque N., Olins A.L. & Olins D.E.* (2020) Linker histone epitopes are hidden by in situ higher-order chromatin structure. Epigenetics and Chromatin 13, 26 | Open access article
  15. Teif V.B. (2020) Soft power of non-consensus protein-DNA binding. Biophys. J. 118, 1797-1798. | Open access article
  16. Antwi E.B., Olins A., Teif V.B., Bieg M., Bauer T., Gu Z., Brors B., Eils R., Olins D., Ishaque N. (2020) Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biology Open 9, bio044222. | Open access article
  17. 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 
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. Teif V.B.* and Cherstvy A.G. (2016). Chromatin and epigenetics: current biophysical views. AIMS Biophysics 3, 88-98 | Open access article
  25. Teif V.B.* (2016). Nucleosome positioning: resources and tools online. Briefings in Bioinformatics. 17, 745-757. | Open access article
  26. 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 |
  27. 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
  28. 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 | 
  29. 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
  30. Cherstvy A.G.* and Teif V.B. (2014). Electrostatic effect of H1-histone protein binding on nucleosome repeat length. Phys. Biol. 11, 044001 | PDF
  31. 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
  32. 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 |
  33. 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 |
  34. 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 |
  35. 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 |
  36. Teif V.B.* (2013). Science 3.0: Corrections to the Science 2.0 paradigm. | ArXiv:1301.2522 |
  37. 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 |
  38. Teif V. B.* and Rippe K. (2012). Calculating transcription factor binding maps for chromatin. Brief. Bioinform. 13, 187-201 | Open acces article
  39. 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 |  Article at publisher’s site
  40. Teif V. B.* and Rippe K.* (2011). Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers. Phys. Biol. 8, 04400. | *Co-corresponding authors | PubMed |  PDF |   Article at publisher’s site
  41. Teif V. B.* and Bohinc K.* (2011). Condensed DNA: condensing the concepts. Progr. Biophys. Mol. Biol. 105, 208-222. | *Co-corresponding authors |  PDF |  Article at publisher’s site
  42. 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
  43. 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
  44. 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
  45. Teif V. B.* and Rippe K. (2010). Statistical-mechanical lattice models for protein-DNA binding in chromatin. J. Phys.: Condens. Matter. 22, 414105 |  PDF |  Article at publisher’s site
  46. 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 |
  47. 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
  48. 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 | Article at publisher’s site
  49. 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
  50. Teif V. B.* (2005). Ligand-induced DNA condensation: choosing the model. Biophys. J. 89, 2574-2587.  Open access article
  51. 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)
  52. 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 |  Article at publisher’s site |
  53. 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 |
  54. Teif V. B. and Lando D. Y.* (2001) Calculation of DNA condensation caused by ligand adsorption. Molecular Biology 35, 117-119. |  PDF
  55. 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
  56. 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 |  Article at publisher’s site |