A. Sturtevant and C. Tan, The comparative genetics of Drosophila Pseudoobscura and Drosophila Melanogaster, Journal of Genetics, vol.34, pp.415-432, 1937.

G. Watterson, W. Ewens, T. Hall, and A. Morgan, The chromosome inversion problem, Journal of Theoretical Biology, vol.99, pp.1-7, 1982.

G. Fertin, A. Labarre, I. Rusu, E. Tannier, and S. Vialette, Combinatorics of genome rearrangements, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00416453

S. Hannenhalli and P. Pevzner, Transforming men into mice (polynomial algorithm for genomic distance problem), 36th Annual Symposium on Foundations of Computer Science, pp.581-592, 1995.

D. Bryant, The complexity of the breakpoint median problem, 1998.

G. Blin, C. Chauve, G. Fertin, R. Rizzi, and S. Vialette, Comparing Genomes with Duplications: a Computational Complexity Point of View, IEEE Transactions on Computational Biology and Bioinformatics, vol.4, pp.523-534, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00417720

A. Bergeron, J. Mixtacki, and J. Stoye, A Unifying View of Genome Rearrangements, Proceedings of WABI'06, pp.163-173, 2006.

S. Yancopoulos, O. Attie, and R. Friedberg, Efficient sorting of genomic permutations by translocation, inversion and block interchange, Bioinformatics, vol.21, pp.3340-3346, 2005.

E. Tannier and . Yeast, Ancestral Genome reconstruction: the possibilities of computational methods, Proceedings of RECOMB- CG'09, pp.1-12, 2009.

P. Feijao and J. Meidanis, SCJ: a breakpoint-like distance that simplifies several rearrangement problems, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, pp.1318-1329, 2011.
DOI : 10.1109/tcbb.2011.34

J. Ma, L. Zhang, B. Suh, B. Raney, R. Burhans et al., Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, pp.1557-1565, 2006.

D. Bertrand, Y. Gagnon, M. Blanchette, and N. El-mabrouk, Reconstruction of Ancestral Genome subject to Whole Genome Duplication, Speciation, Rearrangement and Loss, Proceedings of WABI'10, pp.78-89, 2010.

M. Muffato, A. Louis, C. Poisnel, and H. Crollius, Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes, Bioinformatics, vol.26, pp.1119-1121, 2010.

C. Chauve and E. Tannier, A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes, PLoS Computational Biology, vol.4, p.1000234, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00269397

J. Stoye and R. Wittler, A Unified Approach for Reconstructing Ancient Gene Clusters, IEEE/ACM Trans Comput Biol Bioinf, vol.6, issue.3, pp.387-400, 2009.

C. Chauve, H. Gavranovi?, A. Ouangraoua, and E. Tannier, Yeast ancestral genome reconstructions: the possibilities of computational methods II, Journal of Computational Biology, vol.17, pp.1097-1112, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00681091

B. Jones, A. Rajaraman, E. Tannier, and C. Chauve, ANGES: Reconstructing ANcestral GEnomeS maps, Bioinformatics, vol.18, 2012.
DOI : 10.1093/bioinformatics/bts457
URL : https://hal.archives-ouvertes.fr/hal-00733180

J. Ma, A. Ratan, B. Raney, B. Suh, L. Zhang et al., DUPCAR: reconstructing contiguous ancestral regions with duplications, Journal of Computational Biology, vol.15, pp.1007-1027, 2008.
DOI : 10.1089/cmb.2008.0069
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205822

S. Bérard, C. Gallien, B. Boussau, G. Szollosi, V. Daubin et al., Evolution of gene neighborhood within reconciled phylogenies, Bioinformatics, 2012.

R. Wittler, J. Ma?uch, M. Patterson, and J. Stoye, Consistency of sequence-based gene clusters, Journal of Computational Biology, vol.18, issue.9, pp.1023-1039, 2011.

C. Chauve, J. Ma?uch, M. Patterson, and R. Wittler, Tractability results for the Consecutive-Ones Property with multiplicity, Proceedings of CPM'11, pp.90-103, 2011.

M. Garey and D. Johnson, Computers and Intractability: A Guide to the Theory of NP-completeness W. H. Freeman & Co, 1979.

L. Lovasz and M. Plummer, Matching Theory, Annals of Discrete Mathematics North, vol.29, 1986.

A. Dessmark, A. Lingas, and O. Garrido, On Parallel Complexity of Maximum f-matching and the Degree Sequence Problem, Proceedings of the 19th International Symposium on Mathematical Foundations of Computer Science 1994 MFCS '94, pp.316-325, 1994.

S. Micali and V. Vazirani, An OV?E algorithm for finding maximum matching in general graphs, Proceedings of FOCS'80, pp.17-27, 1980.

I. Miklós and E. Tannier, Bayesian sampling of genomic rearrangement scenarios via double cut and join, Bioinformatics, vol.26, pp.3012-3019, 2010.

I. Miklós and E. Tannier, Approximating the number of double cut-an-join scenarios. Theoretical Computer Science, pp.30-40, 2011.

A. Darling, I. Miklós, and M. Ragan, Dynamics of genome rearrangement in bacterial populations, PLoS Genetics, vol.4, p.1000128, 2008.

P. Husemann and J. Stoye, Phylogenetic Comparative Assembly, Algorithms for Molecular Biology, vol.5, p.3, 2010.
DOI : 10.1186/1748-7188-5-3
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826331

M. Pop, Genome assembly reborn: recent computational challenges, Briefings in Bioinformatics, vol.10, pp.354-366, 2009.
DOI : 10.1093/bib/bbp026
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691937