A. Bergeron, C. Chauve, F. De-montgolfier, and M. Raffinot, Permutations, with Applications to Modular Decomposition of Graphs, SIAM Journal on Discrete Mathematics, vol.22, issue.3, pp.1022-1039, 2008.
DOI : 10.1137/060651331

URL : https://hal.archives-ouvertes.fr/hal-00159580

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

A. Bergeron, Y. Gingras, and C. Chauve, Formal Models of Gene Clusters, Bioinformatics Algorithms: Techniques and Applications, chapter 8, pp.177-202, 2008.
DOI : 10.1002/9780470253441.ch8

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, Proceedings of RECOMB 2008, pp.331-345, 2008.

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

X. He and M. H. Goldwasser, Identifying Conserved Gene Clusters in the Presence of Homology Families, Journal of Computational Biology, vol.12, issue.6, pp.638-656, 2005.
DOI : 10.1089/cmb.2005.12.638

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

U. Kurzik-dumke and A. Zengerle, Identification of a novel Drosophila melanogaster gene, angel, a member of a nested gene cluster at locus 59F4,5, Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, vol.1308, issue.3, pp.1308177-181, 1996.
DOI : 10.1016/0167-4781(96)00108-X

G. M. Landau, L. Parida, and O. Weimann, Using PQ Trees for Comparative Genomics, Proceedings of CPM 2005, pp.128-143, 2005.
DOI : 10.1007/11496656_12

S. Ohno, Evolution by gene duplication, 1970.
DOI : 10.1007/978-3-642-86659-3

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

T. Schmidt and J. Stoye, Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences, Proceedings of CPM 2004, pp.347-358, 2004.
DOI : 10.1007/978-3-540-27801-6_26

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

M. Zhang and H. W. Leong, Gene Team Tree: A Compact Representation of All Gene Teams, Proceedings of Recomb-CG 2008, pp.100-112, 2008.
DOI : 10.1007/978-3-540-87989-3_8