Open Access
Issue
EPJ Nonlinear Biomed Phys
Volume 4, Number 1, December 2016
Article Number 2
Number of page(s) 15
DOI https://doi.org/10.1140/epjnbp/s40366-016-0029-5
Published online 05 May 2016
  1. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002; 295:1306–11.
  2. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289–93.
  3. Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7):1665–80.
  4. Dekker J, Misteli T. Long-range chromatin interactions. Cold Spring Harbor Perspect Biol. 2015; 7(10):019356.
  5. Ea V, Baudement MO, Lesne A, Forné T. Contribution of topological domains and loop formation to 3D chromatin organization. Genes. 2015; 6(3):734–50.
  6. Newman ME. The structure and function of complex networks. SIAM Rev. 2003; 45(2):167–256.
  7. Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU. Complex networks: Structure and dynamics. Phys Reports. 2006; 424(4):175–308.
  8. Di Paola L, De Ruvo M, Paci P, Santoni D, Giuliani A. Protein contact networks: an emerging paradigm in chemistry. Chem Rev. 2012; 113(3):1598–613.
  9. Lesne A, Riposo J, Roger P, Cournac A, Mozziconacci J. 3D genome reconstruction from chromosomal contacts. Nat Methods. 2014; 11(11):1141–3.
  10. Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J. Normalization of a chromosomal contact map. BMC Genomics. 2012; 13:436.
  11. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485(7398):376–80.
  12. Babaei S, Mahfouz A, Hulsman M, Lelieveldt BP, de Ridder J, Reinders M. Hi-C chromatin interaction networks predict co-expression in the mouse cortex. PLoS Comput Biol. 2015; 11(5):1004221.
  13. Singh Sandhu K, Li G, Sung WK, Ruan Y. Chromatin interaction networks and higher order architectures of eukaryotic genomes. J Cell Biochem. 2011; 112(9):2218–21.
  14. Sandhu KS, Li G, Poh HM, Quek YLK, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, Thalamuthu A, Sung WK, Ruan X, Fulwood MJ, Liu E, Csermely P, Ruan Y. Large-scale functional organization of long-range chromatin interaction networks. Cell Reports. 2012; 2(5):1207–19.
  15. Botta M, Haider S, Leung IX, Lio P, Mozziconacci J. Intra-and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol Syst Biol. 2010; 6(1):426.
  16. Hulsman M, Dimitrakopoulos C, de Ridder J. Scale-space measures for graph topology link protein network architecture to function. Bioinformatics. 2014; 30(12):237–45.
  17. Boulos R, Arneodo A, Jensen P, Audit B. Revealing long-range interconnected hubs in human chromatin interaction data using graph theory. Phys Rev Lett. 2013; 111(11):118102.
  18. Marbouty M, Cournac A, Flot JF, Marie-Nelly H, Mozziconacci J, Koszul R. Metagenomic chromosome conformation capture (meta3c) unveils the diversity of chromosome organization in microorganisms. Elife. 2014; 3:03318.
  19. Vendruscolo M, Kussell E, Domany E. Recovery of protein structure from contact maps. Folding Design. 1997; 2(5):295–306.
  20. Serra F, Di Stefano M, Spill YG, Cuartero Y, Goodstadt M, Baù D, Marti-Renom MA. Restraint-based three-dimensional modeling of genomes and genomic domains. FEBS Lett. 2015; 589(20):2987–95.
  21. Fraser J, Rousseau M, Shenker S, Ferraiuolo MA, Hayashizaki Y, Blanchette M, Dostie J. Chromatin conformation signatures of cellular differentiation. Genome Biol. 2009; 10:37.
  22. Hirata Y, Horai S, Aihara K. Reproduction of distance matrices and original time series from recurrence plots and their applications. Eur Phys J Special Topics. 2008; 164(1):13–22.
  23. Havel TF, Kuntz I, Crippen GM. The theory and practice of distance geometry. Bull Math Biol. 1983; 45:665–720.
  24. Torgerson WS. Multidimensional scaling: I. theory and method. Psychometrika. 1952; 17(4):401–19.
  25. Zhang Z, Li G, Toh KC, Sung WK. 3D chromosome modeling with semi-definite programming and hi-c data. J Comput Biol. 2013; 20(11):831–46.
  26. Varoquaux N, Ay F, Noble W, Vert JP. A statistical approach for inferring the three-dimensional structure of the genome. Bioinformatics. 2014; 30:26–33.
  27. Wickelmaier F, Vol. 46. An introduction to MDS. Denmark: Sound Quality Research Unit, Aalborg University; 2003.
  28. Sammon JW. A nonlinear mapping for data structure analysis. IEEE Trans Comput. 1969; 18(5):401–409.
  29. Kruskal JB. Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika. 1964; 29(1):1–27.
  30. Bécavin C, Tchitchek N, Mintsa-Eya C, Lesne A, Benecke A. Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition. Bioinformatics. 2011; 27(10):1413–21.

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