A. Amir, L. Gasieniec, and R. Shalom, Improved approximate common interval, Information Processing Letters, vol.103, issue.4, pp.142-149, 2007.
DOI : 10.1016/j.ipl.2007.03.006

A. Bergeron, C. Chauve, F. De-montgolfier, and M. Raffinot, Permutations, with Applications to Modular Decomposition of Graphs, ESA, pp.779-790, 2005.
DOI : 10.1137/060651331
URL : https://hal.archives-ouvertes.fr/hal-00159580

A. Bergeron, C. Chauve, and Y. Gingras, Bioinformatics Algorithms: Techniques and Applications, pp.177-202, 2008.

A. Bergeron, S. Corteel, and M. Raffinot, The Algorithmic of Gene Teams, WABI, pp.464-476, 2002.
DOI : 10.1007/3-540-45784-4_36

A. Bergeron and J. Stoye, On the Similarity of Sets of Permutations and Its Applications to Genome Comparison, Journal of Computational Biology, vol.13, issue.7, pp.1340-1354, 2006.
DOI : 10.1089/cmb.2006.13.1340

G. Blin, C. Chauve, G. Fertin, R. Rizzi, and S. Vialette, Comparing Genomes with Duplications: A Computational Complexity Point of View, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.4, pp.523-534, 2007.
DOI : 10.1109/TCBB.2007.1069
URL : https://hal.archives-ouvertes.fr/hal-00417720

S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye, Computation of Median Gene Clusters, Journal of Computational Biology, vol.16, issue.8, pp.1085-1099, 2009.
DOI : 10.1089/cmb.2009.0098

D. Che, G. Li, F. Mao, H. Wu, and Y. Xu, Detecting uber-operons in prokaryotic genomes, Nucleic Acids Research, vol.34, issue.8, pp.2418-2427, 2006.
DOI : 10.1093/nar/gkl294

G. Didier, T. Schmidt, J. Stoye, and D. Tsur, Character sets of strings, Journal of Discrete Algorithms, vol.5, issue.2, pp.330-340, 2007.
DOI : 10.1016/j.jda.2006.03.021

R. Downey and M. Fellows, Parameterized Complexity, 1999.
DOI : 10.1007/978-1-4612-0515-9
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.21.3797

M. Garey and D. Johnson, Computers and Intractability: A guide to the theory of NP-completeness, 1979.

R. Hoberman and D. Durand, The Incompatible Desiderata of Gene Cluster Properties, LNCS, vol.3678, pp.73-87, 2005.
DOI : 10.1007/11554714_7

K. Jahn, Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences, Journal of Computational Biology, vol.18, issue.9, pp.1255-1274, 2011.
DOI : 10.1089/cmb.2011.0132

J. H. Nadeau and B. A. Taylor, Lengths of chromosomal segments conserved since divergence of man and mouse., Proceedings of the National Academy of Sciences, vol.81, issue.3, pp.814-818, 1984.
DOI : 10.1073/pnas.81.3.814

C. Papadimitriou and M. Yannakakis, Optimization, approximation, and complexity classes, Journal of Computer and System Sciences, vol.43, issue.3, pp.425-440, 1991.
DOI : 10.1016/0022-0000(91)90023-X

S. Pasek, A. Bergeron, J. Risler, A. Louis, E. Ollivier et al., Identification of genomic features using microsyntenies of domains: Domain teams, Genome Research, vol.15, issue.6, pp.867-874, 2005.
DOI : 10.1101/gr.3638405

S. Rahmann and G. W. Klau, Integer Linear Programs for Discovering Approximate Gene Clusters, WABI, pp.298-309, 2006.
DOI : 10.1007/11851561_28

C. Simillion, K. Vandepoele, and Y. V. De-peer, Recent developments in computational approaches for uncovering genomic homology, BioEssays, vol.28, issue.11, pp.1225-1235, 2004.
DOI : 10.1002/bies.20127

T. Uno and M. Yagiura, Fast Algorithms to Enumerate All Common Intervals of Two Permutations, Algorithmica, vol.26, issue.2, pp.290-309, 2000.
DOI : 10.1007/s004539910014

X. Yang and S. Aluru, A Unified Model for Multi-genome Synteny and Gene Cluster Inference, 2009.

X. Yang and S. Aluru, An improved model for gene cluster inference, pp.190-195, 2010.