I. Sueki, K. Pili?ota, B. Gori, S. Tomiczek, . Müller et al., The oma orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic acids research, p.1158, 2014.

A. Bergeron, J. Mixtacki, and J. Stoye, A Unifying View of Genome Rearrangements, pp.163-173, 2006.
DOI : 10.1007/11851561_16
URL : http://www2.lifl.fr/SEQUOIA/MRI/20092010/articles/DCJBergeron.pdf

J. Peter, . Campbell, J. Philip, . Stephens, D. Erin et al., Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing, Nature genetics, issue.6, pp.40722-729, 2008.

E. V. Chambers, W. A. Bickmore, and C. A. Semple, Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci, PLoS Computational Biology, vol.4, issue.4, p.1003017, 2013.
DOI : 10.1371/journal.pcbi.1003017.s013
URL : https://doi.org/10.1371/journal.pcbi.1003017

C. Chauve, H. Gavranovic, A. Ouangraoua, and E. Tannier, Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II, Journal of Computational Biology, vol.17, issue.9, pp.1097-1112, 2010.
DOI : 10.1089/cmb.2010.0092
URL : https://hal.archives-ouvertes.fr/hal-00681091

T. Asif, . Chinwalla, L. Lisa, . Cook, D. Kimberly et al., Initial sequencing and comparative analysis of the mouse genome, Nature, issue.6915, pp.420520-562, 2002.

G. Cristina, . Ghiurcuta, M. Bernard, and . Moret, Evaluating synteny for improved comparative studies, Bioinformatics, vol.30, issue.12, pp.9-18, 2014.

J. Lander and . Dekker, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, issue.5950, pp.289-293, 2009.

H. Park and C. Jun, A simple and fast algorithm for K-medoids clustering, Expert Systems with Applications, vol.36, issue.2, pp.3336-3341, 2009.
DOI : 10.1016/j.eswa.2008.01.039

T. Sexton, E. Yaffe, E. Kenigsberg, F. Bantignies, B. Leblanc et al., Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome, Cell, vol.148, issue.3, pp.458-472, 2012.
DOI : 10.1016/j.cell.2012.01.010
URL : https://doi.org/10.1016/j.cell.2012.01.010

P. Simonaitis and K. M. Swenson, Finding local genome rearrangements, page To Appear, 2017.
DOI : 10.1186/s13015-018-0127-2
URL : https://almob.biomedcentral.com/track/pdf/10.1186/s13015-018-0127-2

M. Krister, P. Swenson, M. Simonaitis, and . Blanchette, Models and algorithms for genome rearrangement with positional constraints, Algorithms for Molecular Biology, vol.11, issue.1, p.13, 2016.

S. Amélie, C. Véron, C. Lemaitre, V. Gautier, M. Lacroix et al., Close 3d proximity of evolutionary breakpoints argues for the notion of spatial synteny, BMC genomics, vol.12, issue.1, p.303, 2011.

E. Yaffe and A. Tanay, Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nature Genetics, vol.464, issue.11, pp.1059-1065, 2011.
DOI : 10.1038/nature06008

S. Yancopoulos, O. Attie, and R. Friedberg, Efficient sorting of genomic permutations by translocation, inversion and block interchange, Bioinformatics, vol.99, issue.7, pp.3340-3346, 2005.
DOI : 10.1016/0022-5193(82)90384-8
URL : https://academic.oup.com/bioinformatics/article-pdf/21/16/3340/571439/bti535.pdf

X. Zeng, J. Matthew, J. Nesbitt, K. Pei, . Wang et al., OrthoCluster, Proceedings of the 11th international conference on Extending database technology Advances in database technology, EDBT '08, pp.656-667, 2008.
DOI : 10.1145/1353343.1353423

Y. Zhang, R. P. Mccord, Y. Ho, R. Bryan, . Lajoie et al., Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations, Cell, vol.148, issue.5, pp.148908-921, 2012.
DOI : 10.1016/j.cell.2012.02.002
URL : https://doi.org/10.1016/j.cell.2012.02.002