F. Alber, S. Dokudovskaya, L. M. Veenhoff, W. Zhang, J. Kipper et al., Determining the architectures of macromolecular assemblies, Nature, vol.450, pp.683-694, 2007.

B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts et al., Molecular Biology of the Cell: Reference Edition, vol.1, 2008.

M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, 1987.

M. Barbieri, M. Chotalia, J. Fraser, L. Lavitas, J. Dostie et al., Complexity of chromatin folding is captured by the strings and binders switch model, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.16173-16178, 2012.

D. Baù, A. Sanyal, B. R. Lajoie, E. Capriotti, M. Byron et al., The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules, Nat. Struct. Mol. Biol, vol.18, pp.107-114, 2011.

A. S. Belmont, Visualizing chromosome dynamics with GFP, Trends Cell Biol, vol.11, pp.250-257, 2001.

H. Benoit and P. M. Doty, Light scattering from non-Gaussian chains, J. Phys. Chem, vol.57, pp.958-963, 1953.

A. B. Berger, G. G. Cabal, E. Fabre, T. Duong, H. Buc et al., High-resolution statistical mapping reveals gene territories in live yeast, Nat. Methods, vol.5, pp.1031-1037, 2008.

W. A. Bickmore and B. Van-steensel, Genome architecture: domain organization of interphase chromosomes, Cell, vol.152, pp.1270-1284, 2013.

M. Bohn, D. Heermann, and R. Van-driel, Random loop model for long polymers, Phys. Rev. E, vol.76, p.51805, 2007.

S. Boyle, The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells, Hum. Mol. Genet, vol.10, pp.211-219, 2001.

K. Bystricky, P. Heun, L. Gehlen, J. Langowski, and S. M. Gasser, Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques, Proc. Natl. Acad. Sci. U. S. A, vol.101, pp.16495-16500, 2004.

K. Bystricky, T. Laroche, G. Van-houwe, M. Blaszczyk, and S. M. Gasser, Chromosome looping in yeast: telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization, J. Cell Biol, vol.168, pp.375-387, 2005.

M. E. Cates and J. Deutsch, Conjectures on the statistics of ring polymers, J. Phys. France, vol.47, pp.2121-2128, 1986.
URL : https://hal.archives-ouvertes.fr/jpa-00210406

G. Cavalli, Chromosome kissing, Curr. Opin. Genet. Dev, vol.17, pp.443-450, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00191004

G. Cavalli and T. Misteli, Functional implications of genome topology, Nat. Struct. Mol. Biol, vol.20, pp.290-299, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00797832

P. R. Cook, The organization of replication and transcription, Science, vol.284, pp.1790-1795, 1999.

T. Cremer and C. Cremer, Chromosome territories, nuclear architecture and gene regulation in mammalian cells, Nat. Rev. Genet, vol.2, pp.292-301, 2001.

T. Cremer and M. Cremer, Chromosome territories, Cold Spring Harb. Perspect. Biol, vol.2, p.3889, 2010.

P. G. De-gennes, Scaling Concepts in Polymer Physics, 1979.

P. G. De-gennes, Reptation of a polymer chain in the presence of fixed obstacles, J. Chem. Phys, vol.55, p.572, 1971.

W. De-laat and J. Dekker, 3C-based technologies to study the shape of the genome, Methods, vol.58, pp.189-191, 2012.

E. De-wit and W. De-laat, A decade of 3C technologies: insights into nuclear organization, Genes Dev, vol.26, pp.11-24, 2012.

J. Dekker, M. A. Marti-renom, and L. A. Mirny, Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data, Nat. Rev. Genet, vol.14, pp.390-403, 2013.

J. Dekker, K. Rippe, M. Dekker, and N. Kleckner, Capturing chromosome conformation, Science, vol.295, pp.1306-1311, 2002.

D. Stefano, M. Rosa, A. Belcastro, V. Di-bernardo, D. Micheletti et al., Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19, PLoS Comput. Biol, vol.9, p.1003019, 2013.

J. R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li et al., Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.485, pp.376-380, 2012.

M. Doi and A. M. Edwards, The Theory of Polymer Dynamics, 1988.

J. Dostie and W. A. Bickmore, Chromosome organization in the nucleus-charting new territory across the Hi-Cs, Curr. Opin. Genet. Dev, vol.22, pp.125-131, 2012.

Z. Duan, M. Andronescu, K. Schutz, S. Mcilwain, Y. J. Kim et al., A three-dimensional model of the yeast genome, Nature, vol.465, pp.363-367, 2010.

L. B. Edelman and P. Fraser, Transcription factories: genetic programming in three dimensions, Curr. Opin. Genet. Dev, vol.22, pp.110-114, 2012.

M. Eltsov, K. M. Maclellan, K. Maeshima, A. S. Frangakis, and J. Dubochet, Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ, Proc. Natl. Acad. Sci. U. S. A. 105, 19732. Flors, C, vol.95, pp.290-297, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00356712

J. Fraser, M. Rousseau, S. Shenker, M. A. Ferraiuolo, Y. Hayashizaki et al., Chromatin conformation signatures of cellular differentiation, Genome Biol, vol.10, p.37, 2009.

S. M. Gasser, Visualizing chromatin dynamics in interphase nuclei, Science, vol.296, pp.1412-1416, 2002.

L. R. Gehlen, G. Gruenert, M. B. Jones, C. D. Rodley, . Langowski et al., Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions, Nucleus, vol.3, issue.4, pp.370-383, 2012.

A. Y. Grosberg, S. K. Nechaev, and E. I. Shakhnovich, The role of topological constraints in the kinetics of collapse of macromolecules, J. Phys. France, vol.49, pp.2095-2100, 1988.
URL : https://hal.archives-ouvertes.fr/jpa-00210891

A. Y. Grosberg, Y. Rabin, S. Havlin, and A. Neer, Crumpled globule model of the three-dimensional structure of DNA, Europhys. Lett, vol.23, pp.373-378, 1993.

H. Yazdi, N. Guet, C. C. Johnson, R. C. Marko, and J. F. , Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions, Mol. Microbiol, vol.86, pp.1318-1333, 2012.

A. Halperin, On the collapse of multiblock copolymers, Macromolecules, vol.24, pp.1418-1419, 1991.

V. A. Harmandaris, D. Reith, N. F. Van-der-vegt, and K. Kremer, Comparison between coarse-graining models for polymer systems: two mapping schemes for polystyrene, Macromol. Chem. Phys, vol.208, pp.2109-2120, 2007.

P. Heun, T. Laroche, K. Shimada, P. Furrer, and S. M. Gasser, Chromosome dynamics in the yeast interphase nucleus, Science, vol.294, pp.2181-2186, 2001.

M. Hu, K. Deng, Z. Qin, J. Dixon, S. Selvaraj et al., Bayesian inference of spatial organizations of chromosomes, e1002893. Huang, K., 1987. Statistical Mechanics, vol.9, 2013.

J. N. Israelachvili, Intermolecular and Surface Forces (Google eBook), Revised third ed, 2011.

B. V. Iyer and G. Arya, Lattice animal model of chromosome organization, Phys. Rev. E, vol.86, p.11911, 2012.

D. A. Jackson, Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells, J. Cell Biol, vol.140, pp.1285-1295, 1998.

S. Jhunjhunwala, M. C. Van-zelm, M. M. Peak, S. Cutchin, R. Riblet et al., The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions, Cell, vol.133, pp.265-279, 2008.

S. Jun and B. Mulder, Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome, Proc. Natl. Acad. Sci. U. S. A, vol.103, pp.12388-12393, 2006.

R. Kalhor, H. Tjong, N. Jayathilaka, F. Alber, and L. Chen, Genome architectures revealed by tethered chromosome conformation capture and population-based modeling, Nat. Biotechnol, vol.30, pp.90-98, 2012.

A. Khokhlov and A. Grosberg, Statistical Physics of Macromolecules, 1994.

J. S. Kim, P. Pradhan, V. Backman, and I. Szleifer, The influence of chromosome density variations on the increase in nuclear disorder strength in carcinogenesis, Phys. Biol, vol.8, p.15004, 2011.

R. D. Kornberg, Chromatin structure: a repeating unit of histones and DNA, Science, vol.184, pp.868-871, 1974.

T. Kouzarides, Chromatin modifications and their function, Cell, vol.128, pp.693-705, 2007.

K. Kremer and G. S. Grest, Dynamics of entangled linear polymer melts: a moleculardynamics simulation, J. Chem. Phys, vol.92, pp.5057-5086, 1990.

G. Kreth, J. Finsterle, J. Von-hase, M. Cremer, and C. Cremer, Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code, Biophys. J, vol.86, pp.2803-2812, 2004.

E. Lieberman-aiden, N. L. Van-berkum, L. Williams, M. Imakaev, T. Ragoczy et al., Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, pp.289-293, 2009.

K. Luger, M. L. Dechassa, and D. J. Tremethick, New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?, Nat. Rev. Mol. Cell Biol, vol.13, pp.436-447, 2012.

K. Maeshima, S. Hihara, and M. Eltsov, Chromatin structure: does the 30-nm fibre exist in vivo?, Curr. Opin. Cell Biol, vol.22, pp.291-297, 2010.

D. Marenduzzo, C. Micheletti, and P. R. Cook, Entropy-driven genome organization, Biophys. J, vol.90, pp.3712-3721, 2006.

Y. Markaki, D. Smeets, S. Fiedler, V. J. Schmid, L. Schermelleh et al., The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for stud, BioEssays, vol.34, pp.412-426, 2012.

J. F. Marko and E. D. Siggia, Stretching DNA. Macromolecules, vol.28, pp.8759-8770, 1995.

M. A. Marti-renom, L. A. Mirny, J. Mateos-langerak, M. Bohn, W. De-leeuw et al., Bridging the resolution gap in structural modeling of 3D genome organization, Proc. Natl. Acad. Sci. U. S. A, vol.7, p.3812, 2009.

K. Mekhail, J. Seebacher, S. P. Gygi, and D. Moazed, Role for perinuclear chromosome tethering in maintenance of genome stability, Nature, vol.456, pp.667-670, 2008.

D. Meluzzi and G. Arya, Recovering ensembles of chromatin conformations from contact probabilities, Nucleic Acids Res, vol.41, pp.63-75, 2013.

C. Micheletti, Comparing proteins by their internal dynamics: exploring structurefunction relationships beyond static structural alignments, Phys. Life Rev, vol.10, pp.1-26, 2012.

T. Misteli, Higher-order genome organization in human disease, Cold Spring Harb. Perspect. Biol, vol.2, p.794, 2010.

M. Müller, J. Wittmer, and M. Cates, Topological effects in ring polymers: a computer simulation study, Phys. Rev. E, vol.53, pp.5063-5074, 1996.

C. Münkel, R. Eils, S. Dietzel, D. Zink, C. Mehring et al., Compartmentalization of interphase chromosomes observed in simulation and experiment, J. Mol. Biol, vol.285, pp.1053-1065, 1999.

C. Münkel and J. Langowski, Chromosome structure predicted by a polymer model, Phys. Rev. E, vol.57, pp.5888-5896, 1998.

J. Ostashevsky, A polymer model for the structural organization of chromatin loops and minibands in interphase, Mol. Biol. Cell, vol.9, pp.3031-3040, 1998.

J. Pelletier, K. Halvorsen, B. Ha, R. Paparcone, S. J. Sandler et al., Physical manipulation of the Escherichia coli chromosome reveals its soft nature, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.2649-2656, 2012.

C. Possoz, I. Junier, and O. Espeli, Bacterial chromosome segregation, Front. Biosci, vol.17, pp.1020-1034, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01635952

W. Rieping, M. Habeck, and M. Nilges, Inferential structure determination, Science, vol.309, p.303, 2005.
DOI : 10.1126/science.1110428

K. Rippe, Making contacts on a nucleic acid polymer, Trends Biochem. Sci, vol.26, pp.733-740, 2001.
DOI : 10.1016/s0968-0004(01)01978-8

C. D. Rodley, F. Bertels, B. Jones, and J. M. O'sullivan, Global identification of yeast chromosome interactions using Genome conformation capture, Fungal Genet. Biol, vol.46, pp.879-886, 2009.

A. Rosa, N. B. Becker, and R. Everaers, Looping probabilities in model interphase chromosomes, Biophys. J, vol.98, pp.2410-2419, 2010.

A. Rosa and R. Everaers, Structure and dynamics of interphase chromosomes, PLoS Comput. Biol, vol.4, 2008.

J. Rouquette, C. Cremer, T. Cremer, and S. Fakan, Functional nuclear architecture studied by microscopy: present and future, Int. Rev. Cell Mol. Biol, vol.282, pp.1-90, 2010.
DOI : 10.1016/s1937-6448(10)82001-5

M. Rousseau, J. Fraser, M. A. Ferraiuolo, J. Dostie, and M. Blanchette, Threedimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling, BMC Bioinformat, vol.12, p.414, 2011.

M. Rubinstein and R. Colby, Polymer Physics, 2003.

R. K. Sachs, G. Van-den-engh, B. Trask, H. Yokota, and J. E. Hearst, A random-walk/ giant-loop model for interphase chromosomes, Proc. Natl. Acad. Sci. U. S. A, vol.92, pp.2710-2714, 1995.

R. D. Schram, G. T. Barkema, and H. Schiessel, On the stability of fractal globules, J. Chem. Phys, vol.138, p.224901, 2013.

J. Shimada and H. Yamakawa, Ring-closure probabilities for twisted wormlike chains. Application to DNA, Macromolecules, vol.17, pp.689-698, 1984.
DOI : 10.1021/ma00134a028

J. L. Sikorav and G. Jannink, Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model, Biophys. J, vol.66, pp.827-837, 1994.

D. W. Sumners and S. G. Whittington, Knots in self-avoiding walks, J. Phys. A Math. Genet, vol.21, pp.1689-1694, 1988.
DOI : 10.1088/0305-4470/21/7/030

A. Taddei, H. Schober, and S. M. Gasser, The budding yeast nucleus, Cold Spring Harb. Perspect. Biol, vol.2, p.612, 2010.
DOI : 10.1101/cshperspect.a000612

URL : http://cshperspectives.cshlp.org/content/2/8/a000612.full.pdf

H. Tanizawa, O. Iwasaki, A. Tanaka, J. R. Capizzi, P. Wickramasinghe et al., Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation, Nucleic Acids Res, vol.38, pp.8164-8177, 2010.

P. Thérizols, T. Duong, B. Dujon, C. Zimmer, and E. Fabre, Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres, Proc. Natl. Acad. Sci. U. S. A, vol.107, 2010.

H. Tjong, K. Gong, L. Chen, and F. Alber, Physical tethering and volume exclusion determine higher-order genome organization in budding yeast, Genome Res, vol.22, pp.1295-1305, 2012.

N. Toan, D. Marenduzzo, P. Cook, and C. Micheletti, Depletion effects and loop formation in self-avoiding polymers, Phys. Rev. Lett, vol.97, p.178302, 2006.

N. Tokuda, T. P. Terada, and M. Sasai, Dynamical modeling of three-dimensional genome organization in interphase budding yeast, Biophys. J, vol.102, pp.296-304, 2012.

N. Uchida, G. S. Grest, and R. Everaers, Viscoelasticity and primitive path analysis of entangled polymer liquids: from F-actin to polyethylene, J. Chem. Phys, vol.128, p.44902, 2008.

M. A. Umbarger, E. Toro, M. A. Wright, G. J. Porreca, D. Bau et al., The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation, Mol. Cell, vol.44, pp.252-264, 2011.

E. J. Van-rensburg and N. Madras, A nonlocal Monte Carlo algorithm for lattice trees, J. Phys. A Math. Genet, vol.25, pp.303-333, 1992.

C. Vanderzande, T. Vettorel, A. Y. Grosberg, and K. Kremer, Statistics of polymer rings in the melt: a numerical simulation study, Phys. Biol, vol.6, p.25013, 1998.

P. H. Viollier, M. Thanbichler, P. T. Mcgrath, L. West, M. Meewan et al., Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication, Proc. Natl. Acad. Sci. U. S. A, vol.101, pp.9257-9262, 2004.

X. Wang, P. Montero-llopis, and D. Z. Rudner, Organization and segregation of bacterial chromosomes, Nat. Rev. Genet, vol.14, pp.191-203, 2013.

P. A. Wiggins, K. C. Cheveralls, J. S. Martin, R. Lintner, and J. Kondev, Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament, Proc. Natl. Acad. Sci. U. S. A, vol.107, pp.4991-4995, 2010.

H. Wong, H. Marie-nelly, S. Herbert, P. Carrivain, H. Blanc et al., A predictive computational model of the dynamic 3D interphase yeast nucleus, Curr. Biol, vol.22, pp.1881-1890, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01420017

E. Yaffe and A. Tanay, Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nat. Genet, vol.43, pp.1059-1065, 2011.

A. M. Yoffe, P. Prinsen, A. Gopal, C. M. Knobler, W. M. Gelbart et al., Predicting the sizes of large RNA molecules, Proc. Natl. Acad. Sci. U. S. A, vol.105, pp.16153-16158, 2008.

H. Yokota, G. Van-den-engh, J. E. Hearst, R. K. Sachs, and B. J. Trask, Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus, J. Cell Biol, vol.130, pp.1239-1249, 1995.

Y. Zhang and D. W. Heermann, Loops determine the mechanical properties of mitotic chromosomes, PLoS One, vol.6, 2011.

C. Zimmer and E. Fabre, Principles of chromosomal organization: lessons from yeast, J. Cell Biol, vol.192, pp.723-733, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-02079552