Program

Monday, June 22, 2015

Time Event  
1:30 pm - 2:00 pm Welcome and conference aims - Ralf Everaers, Sarah Harris And Cedric Vaillant  
2:00 pm - 3:45 pm Genomics beyond sequencing – the need for Physical Genomics  
14:00 - 15:00 › Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans + Does the physical organisation of the genome within the nucleus matter : the big picture - Peter Meister, Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern  
15:00 - 15:45 › What Hi-C can and cannot tell us about functional genomic architecture. - Thomas Sexton, Institut de Génétique et de Biologie Moléculaire et Cellulaire  
3:45 pm - 4:15 pm Coffee break  
4:15 pm - 6:15 pm Genomics beyond sequencing – the need for Physical Genomics  
16:15 - 17:00 › Topological aspects of chromosome folding - Angelo Rosa, Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies  
17:00 - 17:45 › The large-scale hierarchical features of chromatin spatial organization - Mario Nicodemi, Dipartimento di Fisica, Universita' di Napoli "Federico II"  
17:45 - 18:15 › Exploring long-range contacts between topological domains (TADs) in ES cells and neurons - Dorothee Kraemer, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine  
6:15 pm - 7:15 pm Discussion session - Whole group  

Tuesday, June 23, 2015

Time Event  
9:00 am - 9:45 am The need for Physical Genomics – continued  
09:00 - 09:45 › Loop extrusion as a mechanism of chromosome condensation - Leonid Mirny, Massachusetts Institute of Technology  
9:45 am - 10:15 am Coffee break  
10:15 am - 12:30 pm The need for Physical Genomics – continued  
10:15 - 11:00 › Chromatin Hydrodynamics - Yitzhak Rabin, Department of Physics, Bar-Ilan University  
11:00 - 11:45 › Differential chromosome conformations and dynamics in living cells - Kerstin Bystricky, University of Toulouse  
11:45 - 12:30 › Diversity of chromosome organization in microorganisms - Romain Koszul, Regulation spatiale des genomes, Departement Genomes et Genetique  
12:30 pm - 2:00 pm Lunch  
2:00 pm - 3:30 pm Restraint-based modeling of the 3d folding  
14:00 - 14:45 › The 3D colors of chromatin - Julien Mozziconacci, UPMC  
14:45 - 15:30 › Timing in the nucleus: replication domains and graph theory - Benjamin Audit, Laboratoire de Physique de l'ENS Lyon  
3:30 pm - 4:00 pm Coffee break  
4:00 pm - 5:30 pm Restraint-based modeling of the 3d folding  
16:00 - 16:45 › Determining 3D structures of whole, individual genomes using single-cell Hi-C - Tim Stevens, MRC Laboratory of Molecular Biology  
16:45 - 17:30 › Colocalization of coregulated genes: A steered molecular dynamics study of Human Chromosome 19 - Marco Di Stefano, Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies  
5:30 pm - 6:00 pm Poster Pitches - 1 slide/2 mins per poster  
6:00 pm - 7:00 pm Poster session - with nibbles and drinks  

Wednesday, June 24, 2015

Time Event  
9:00 am - 9:45 am The specific sequence- and epigenetic state-dependent folding of chromosomes  
09:00 - 09:45 › Nucleosome-positioning & Long-range contacts at Topological boundaries - Olivier Cuvier, Laboratoire de biologie moléculaire eucaryote du CNRS  
9:45 am - 10:15 am Coffee break  
10:15 am - 12:15 pm The specific sequence- and epigenetic state-dependent folding of chromosomes  
10:15 - 11:00 › Structural organization of human replication timing domains - alain arneodo, Laboratoire de Physique de l'ENS Lyon  
11:00 - 11:30 › The Chromosome as a topological device for conversion of energy into information - Georgi Muskhelishvili, School of Engineering and Science [Bremen]  
11:30 - 12:00 › Topologically associating domain boundaries serve as hitchhiking platforms for the Drosophila dosage compensation complex - Fidel Ramirez, The Max Planck Institute of Immunobiology and Epigenetics  
12:00 pm - 2:00 pm Lunch  
2:00 pm - 3:15 pm Epigenetic regulation of chromosome folding  
14:00 - 14:45 › Epigenomics in 4D: modeling the dynamic coupling between epigenome and chromatin organization - Daniel Jost, Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble  
14:45 - 15:15 › Epigenetics switches chromosomes from polymer to copolymer physics - Jean-Marc Victor, Université Pierre et Marie Curie - Paris 6  
3:15 pm - 4:15 pm Discussion session - Small groups - 10 groups of 5 participants.  
4:15 pm - 4:45 pm Coffee break  
4:45 pm - 6:45 pm Feedback from small group discussion - A representative from each small group gives a 10min talk summarising the discussion  
7:30 pm - 11:00 pm Social dinner  

Thursday, June 25, 2015

Time Event  
9:00 am - 9:45 am Supercoiling, DNA, Chromatin  
09:00 - 09:45 › DNA Looping Across Length Scales: Computational Modeling and its Application to Cre Site-specific Recombination - Stephen Levene, University of Texas at Dallas [Richardson]  
9:45 am - 10:15 am Coffee break  
10:15 am - 12:15 pm Supercoiling, DNA, Chromatin  
10:15 - 11:00 › Possible role of DNA supercoiling in formation of topological domains - Andrzej Stasiak, Center for Integrative Genomics - Institute of Bioinformatics, Génopode  
11:00 - 11:30 › Transcription and supercoiling : torsion-mediated interaction between adjacent genes - Sam Meyer, INSA Lyon  
11:30 - 12:15 › Modeling effects of nucleosome positioning in short and long chromatin fibers - Gero Wedemann, University of Applied Sciences Stralsund  
12:15 pm - 2:00 pm Lunch  
2:00 pm - 4:15 pm Supercoiling, DNA, Chromatin  
14:00 - 14:45 › Chromatin dynamics studied by molecular dynamics simulations and single-molecule FRET - Jörg Langowski, Dept. Biophysics of Macromolecules, German Cancer Research Center  
14:45 - 15:30 › DNA segregation in E. coli: the role of chromosome structuring - Ivan Junier, Laboratoire Adaptation et Pathogénie des Microorganismes  
3:30 pm - 4:00 pm Coffee break  
4:00 pm - 5:00 pm Discussion  
5:00 pm - 6:15 pm Poster session - with nibbles and drinks  

Friday, June 26, 2015

Time Event  
9:00 am - 9:45 am Multiscale DNA modelling - from QM to coarse grained simulations  
09:00 - 09:45 › The Sequence-Dependent Statistical Mechanics of DNA - John Maddocks, Ecole Polytechnique Fédérale de Lausanne  
9:45 am - 10:15 am Coffee break  
10:15 am - 11:30 am Multiscale DNA modelling - from QM to coarse grained simulations  
10:15 - 10:45 › Simulating the interaction of sequence and writhing in nucleic acids - Christian Matek, University of Oxford (UK)  
10:45 - 11:30 › DNA and its environment: a close look at ion binding - Richard Lavery, Bases Moléculaires et Structurales des Systèmes Infectieux  
11:30 am - 1:00 pm Summary and close  
  
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