Students Staff

Academic Staff

Dr Vladimir Teif

Staff positionLecturer
Emailvteif@essex.ac.uk
Telephone01206 872121
Room3SW.6.18
Biography

2015 - current: Lecturer. University of Essex, School of Biological Sciences
2008 – 2015: German Cancer Research Center (DKFZ) and BioQuant, Heidelberg
      2011 – 2015: BIOMS Fellowship
      2009 – 2011: Fellow of the Cellnetworks Cluster of Excellence
      2008 – 2009: DKFZ Guest Scientist, Group of Prof. Karsten Rippe
2004 – 2008: Belarus National Academy of Sciences, Minsk, Belarus
      2009 – 2010: Senior Scientist
      2004 – 2008: Research Scientist

VISITING SCIENTIST POSITIONS:
02/2008 – 06/2008: University of California San Diego, (with Prof. Terence Hwa).
10/2007: DKFZ, Boehringer Ingelheim Short-Term Fellowship.
09/2007: International Center of Theoretical Physics, Trieste (UNESCO Fellow).
04/2007 – 05/2007, 11/2005 – 02/2006: Hebrew University, (FEBS Fellow).

HONORS:

  • 2017: Fellow of the Higher Education Academy, UK (FHEA)
  • 2011: BIOMS Fellowship, DKFZ and BioQuant, 2011-2015
  • 2009: German Excellence Cluster Cellnetworks Fellowship
  • 2009: DKFZ Guest Scientist Grant, DKFZ and BioQuant
  • 2008: CTBP Visiting Scientist Grant, University of California at San Diego
  • 2008: SFI Visiting Scientist Grant, Institute of Complex Systems, Santa Fe
  • 2007: Boehringer Ingelheim Short-Term Fellowship, DKFZ
  • 2007: UNESCO Visiting Scientist, International Center of Theoretical Physics
  • 2007: President’s Fellowship (top 100 young scientists of Belarus)
  • 2007: FEBS Short-Term Fellowship, Hebrew University, Jerusalem
  • 2006: Golda Meir Fellowship, Hebrew University, Jerusalem
  • 2004: Fellow of the Belarus National Academy of Sciences, 2004
  • 2002: INTAS Young Scientist Ph.D. Fellowship, CEA/Saclay, France

GRANTS

  • Wellcome Trust Seed Award, 2016. “Nucleosome repositioning as a mechanism for cell memory in cancer transitions”, PI. € 112,000.
  • @RAction grant, ANR (France), 2015. “Deciphering and modifying epigenetic mechanisms of stem cell development”, PI. € 870,000.
  • Merck grant "Chaire Junior Fondagen", 2015, PI. € 275,000
  • Sonata-BIS-4 grant, NCN (Poland), 2015, "Predicting differential transcription factor binding in chromatin", PI. € 500,000.
  • Intramural Grant of the German Cancer Research Center, 2012-2013, “Calculating transcription factor binding maps in chromatin”, PI. € 120,000.
  • Intramural Grant of the German Cancer Research Center, 2012-2013, “Developing a software suite for the analysis of epigenetic regulation from high-throughput sequencing data”, Co-PI, with Yevhen Vainshtein. € 20,000
  • Belarus National Foundation of Fundamental Research, Grant #B10M-060, “Investigation of chromatin rearrangements during gene regulation in tumor and normal tissues”, 2010-12, PI.
  • Belarusian Governmental Program “Bio-rational Pesticides-II”, “Study of synergistic effects of pesticide combinations using statistical analysis”, 2009-2010, co-PI.
  • Belarus National Foundation of Fundamental Research, Grant #B06M-127 “Biomolecular interactions with condensed DNA”, 2006-2008, PI.
  • Belarus National Foundation of Fundamental Research, #B02M-091 “Influence of anticancer and carcinogenic metal complexes on DNA condensation”, 2002-2004, PI.

Websitehttp://generegulation.info
Current research

Group members:

Vladimir Teif, PhD, FHEA

Graeme Thorn, PhD

Christopher Clarkson, MSc

Navid Shafiei (MSc student)

Alumni:

Dr Svetlana Gretton | Dr Ioanna Pavlaki | Tanvi Sharma | Joshua Burton

We are a small friendly group working on (1) biophysical modelling of epigenetic regulation in chromatin, (2) bioinformatics analysis of high-throughput sequencing data; and (3) sequencing experiments such as ChIP-seq. At the moment we are running several projects devoted to nucleosome positioning, chemical modifications of DNA and histones, and differential binding of proteins in chromatin during stem cell differentiation and cancer transitions.

If you are interested to join us please contact by email with your CV and a short cover letter, indicating how your skills fit to at least one of the directions outlined above.

Research interests
  • Modelling epigenetic regulation
  • Next Generation Sequencing
  • Biophysics of chromatin
  • DNA-protein binding
  • Cell differentiation
  • Cancer transition
  • Lattice models
  • AR/VR tools for education
Teaching responsibilities
  • BS222 Genome Science (Module supervisor)
  • BS312 Genome Bioinformatics
  • BS320 Human Molecular Genetics
  • BS304 Issues in Biomolecular Science
  • BS932 Advanced Cancer Biology
  • BS933 Practical Skills in Cancer Research

BSc and MSc research project supervision:

  • BS831 3rd Year BSc Research Projects
  • BS984 MSc Molecular Medicine
  • BS986 MSc Biotechnology

Advanced Ph.D. lectures and practical courses:

Publications

Automatically updated publications in Google Scholar | ORCID profile

2017

  • Pavlaki I., Docquier F., Chernukhin I., Teif V.B., Klenova E. (2017) Poly(ADP-ribosyl)ation dependent changes in CTCF-chromatin binding and gene expression in breast cells | bioRxiv preprint
  • Teif V.B. and Clarkson C.T. (2017) Nucleosome positioning. In "Encyclopedia of Bioinformatics and Computational Biology", Ed. S. Ranganathan, Elsevier | Author's manuscript
  • 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 | 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 | 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

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 |  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 | Pubmed PDFPress 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. | AbstractPDF |
  • Teif V.B. (2013). Science 3.0: Corrections to the Science 2.0 paradigm. | ArXiv:1301.2522 |

2012:

  • 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. | PubMedPDF
  • Teif V. B. and Bohinc K. (2011). Condensed DNA: condensing the concepts. Progr. Biophys. Mol. Biol. 105, 208-222. |  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 |  PDF
  • 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. | 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., Lando D. Y. On the cooperativity of metal ion binding to the bases of single-stranded DNA. Europ. J. Biochem. 271(1), 19 (2004). | Abstract
  • Teif V. B. (2003). On the cooperativity of metal ion binding to DNA. J. Biomol. Struct. Dynam. 20, 897-898. | Abstract
  • 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 |

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