Croissants & Coffee Seminars

From DNA to Cell Function: Regulatory Networks & Imaging

The seminars take place every three or four weeks on Friday 10 am in the in the Bioquant, seminar room 042 or 043 on the
ground floor. They are intended to bring together people from the Bioquant and the Bioquant network that
share common research interests on the topic "From DNA to Cell Function: Regulatory Networks & Imaging"

Friday, Feb 13, 2009, 10 am, BIOQUANT seminar room 044

Speaker: Vladimir Teif (DKFZ Guest Scientist, Institute of Bioorganic Chemistry, Belarus National Academy of Sciences)

Title: Predicting gene regulation in chromatin from statistical-mechanical descriptions using DNA lattice models

From a given set of molecular players and rules of their interaction and enzymatic activites, Nature is able to "calculate" the transcription level for each gene. How to play this biological game on a man-made computer is a challenging question. Classical molecular biology explores the mechanistic details of transcription and translation, while the emerging field of systems biology tends to quantify gene expression on a larger scale without accounting for the physical details of macromolecular interactions. Here we will discuss an intermediate approach to bridge the fields by developing a statistical-mechanical description of functional interactions of DNA, transcription factors, and architectural proteins, and connecting these binding events to larger-scale decisions on gene expression. An introduction to the lattice models will be followed by examples of applications of this approach to bacteriophages. Finally, we will proceed to lattice models for gene regulation in chromatin, where the positions of nucleosomes are determined both by the intrinsic affinities of the histone octamer to a given DNA sequence and by the ATP-dependent activity of nucleosome translocation complexes referred to as chromatin remodelers.


The "Croissant & Coffee Seminars" schedule/features are:

  • check-in from 10:00 to 10:15 in seminar room 042 on the ground floor and get your croissant & coffee (or tea)
  • bring your own cup
  • the seminar starts at 10:15
  • seminars should include an informal presentation of interesting stuff (also unfinished work in progress is wellcome)
  • seminars should provide the opportunity for plenty of discussions during the seminar. To have sufficient time for that the presentation itself should take no longer than 40 minutes
  • we finish no later than 11:15 o’clock no matter how interesting it is (everybody is wellcome to continue the discussions somewhere else...)

If you have suggestions for seminar speakers (also graduate students and post-docs) or if you want to be added/removed to/from the seminar mailing list please e-mail to Karsten Rippe.


Previous seminars

Friday October 25, 2007

Malte Wachsmuth: Measuring diffusion, binding and multimerization of proteins in the nucleus by fluoresence fluctuation microscopy

Friday, December 7, 2007

Hans Engelhardt: Optical microscopy beyond the diffraction limit

Friday, March 7, 2008

Thomas Höfer: Mathematical modeling of cellular processes

Friday, April 4, 2008

Dirk-Peter Herten: Future perspectives of single-molecule spectroscopy

Friday, April 11, 2008

Martijn Luijsterburg: Dynamic in vivo interactions of repair factors with UV-damaged DNA

Friday, May 9, 2008

Hauke Busch: Using Gene Network Dynamics to Obtain a Bird's Eye View on Cellular Decision


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