Lorentz Center - The physics of genome folding and function from 20 Oct 2008 through 23 Oct 2008
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    The physics of genome folding and function
    from 20 Oct 2008 through 23 Oct 2008

 
Lorentz Center workshop: Physics of genome Folding and Function

Monday October 20

 

DNA/chromatin folding in the cell

chair: Roel van Driel

 

09.30     opening and format of the workshop

 

10.00     three introductory lectures

               thinking about DNA/chromatin folding [Roel van Driel]

               thermodynamics of polymer systems [Bela Mulder]

               macromolecular crowding in the cell [Ron Hancock]

 

12.15     lunch

 

13.15     introductory lecture (30 min each)

               polymer models [Dieter Heermann]

              

14.00     breakout session  A
identify the most important issues in the field and develop blue sky ideas and projects for addressing the issue of chromatin/DNA folding inside the nucleus/nucleoid

 

16.00     plenary discussion

 

17.30     wine and cheese party

 

 

Tuesday October 21

 

How is DNA/chromatin folded in the cell?

chair: Dieter Heermann

 

09.00     two introductory lectures (30 min each)

               how to measure DNA/chromatin folding in the cell [Job Dekker]

               modeling of DNA/chromatin folding [Helmut Schiessel]

 

11.00     breakout session  B
folding of DNA/chromatin at different length scales: multiple nucleosomes, genes/functional loci, complete chromosomes, nucleus/nucleoid

 

12.30     lunch

 

13.30     breakout session  B (cont.)

 

16.00     plenary discussion

 

 

Wednesday October 22

 

Relating models to biological structure and function

chair: Bela Mulder

 

09.00     two introductory lectures (30 min each)

               1D and 3D organization of genomes in relation to function [Nancy Kleckner]

               complicating matters: DNA/chromatin is not a simple polymer [Peter Cook]

11.00     breakout session  C

               1D and 3D genome structure and dynamics in relation to genome function

 

12.30     lunch

 

13.30     breakout session  C (cont.)

 

16.00     plenary discussion

 

17.30     decide on focus of last day workshop

 

19.00     Lorentz workshop dinner

 

 

Thursday October 23

 

Integrating ideas, concepts and scales

chair: Nancy Kleckner

 

09.00     integrating and focusing ideas of the past three days

               towards review papers and research programs

 

10.00     breakout session  D

               integrating ideas: contours of review papers and research programs

 

12.30     lunch

 

13.30     breakout session  D (cont.)

 

16.00     manuscripts and plans: the output of the workshop

 

18.00     closing

 

 

Aim and format Breakout Sessions

 

  • The Breakout Sessions are the core of the workshop. Here important new ideas will be generated.

 

  • The outcome of the breakout discussion of each group should be a combination of predictive quantitative modeling plus the critical biological approaches to test and develop model

 

  • Six groups of 6 participants with different expertise (physics, biology) will be formed. Each group will have available two rooms with computers and internet access.

 

  • In each Breakout Session all groups will concentrate on the same set of topics of that session. Doubtless, different groups will take different approaches and point of views.

 

  • In the plenary discussions the groups ‘compare notes’, sparking off novel insight in genome folding and function.

 

  • A Wiki will be set up for posting questions, ideas and presenting results and facilitating interactions between groups.

 

  • The last day will be devoted in integrating ideas, in part resulting in (reviews) papers and concrete research plans.

 

  • Among others, the Wiki will contain a face-book, stating the expertise of each participant.

 

 



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