, NCBI: Complete Microbial Genomes

M. Huynen and P. Bork, Measuring genome evolution, Proc Natl Acad Sci, vol.95, pp.5849-5856, 1998.

E. Koonin and Y. Wolf, Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world, Nucl Acids Res, vol.36, pp.6688-6719, 2008.

T. Itoh, K. Takemoto, H. Mori, and T. Gojobori, Evolutionary Instability of Operon Structures Disclosed by Sequence Comparisons of Complete Microbial Genomes, Mol Biol Evol, vol.16, pp.332-346, 1999.

T. Dandekar, B. Snel, M. Huynen, and P. , Conservation of gene order: A fingerprint of proteins that physically interact, Trends Biochem Sci, vol.23, pp.324-328, 1998.

G. Tesler, GRIMM: genome rearrangements web server, Bioinformatics, vol.18, issue.3, pp.492-493, 2002.

A. Sinha and J. Meller, Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms, BMC Bioinformatics, vol.8, p.82, 2007.

T. Uno and M. Yagiura, Fast Algorithms to Enumerate All Common Intervals of Two Permutations, p.26, 2000.

S. Heber and J. Stoye, Algorithms for Finding Gene Clusters, WABI: International Workshop on Algorithms in Bioinformatics, 2001.

G. Didier, Common intervals of two sequences, Algorithms in Bioinformatics Proceedings, vol.2812, pp.17-24, 2003.

A. Bergeron, S. Corteel, and M. Raffinot, The Algorithmic of Gene Teams, WABI: International Workshop on Algorithms in Bioinformatics, vol.2452, pp.464-476, 2002.

X. He and M. Goldwasser, Identifying Conserved Gene Clusters in the Presence of Homology Families, J Comput Biol, vol.12, issue.6, pp.638-656, 2005.

S. Pasek, A. Bergeron, J. Risler, A. Louis, E. Ollivier et al., Identification of genomic features using microsyntenies of domains: Domain teams

, Genome Res, vol.15, issue.6, pp.867-874, 2005.

S. Kim, J. H. Choi, and J. Yang, Gene Teams with Relaxed Proximity Constraint. IEEE Computational Systems Bioinformatics Conference (CSB 2005) 2005, pp.44-55

X. Ling, X. He, D. Xin, and J. Han, Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison, J Comput Biol, vol.15, issue.6, pp.593-609, 2008.

X. Ling, X. He, and D. Xin, Detecting gene clusters under evolutionary constraint in a large number of genomes, Bioinformatics, vol.25, issue.5, pp.571-577, 2009.

F. Boyer, A. Morgat, L. Labarre, J. Pothier, and A. Viari, Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data, Bioinformatics, vol.21, issue.23, pp.4209-4215, 2005.

P. Calabrese and S. Chakravarty, Vision T: Fast identification and statistical evaluation of segmental homologies in comparative maps, ISMB (Supplement of Bioinformatics), vol.19, pp.74-80, 2003.

B. Haas, A. Delcher, J. Wortman, and S. Salzberg, DAGchainer: a tool for mining segmental genome duplications and synteny, Bioinformatics, vol.20, issue.18, pp.3643-3646, 2004.

X. Wang, X. Shi, Z. Li, Q. Zhu, L. Kong et al., Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice, BMC Bioinformatics, vol.7, p.447, 2006.

C. Rödelsperger and C. Dieterich, Syntenator: multiple gene order alignments with a gene-specific scoring function, Algorithms for Molecular Biology, vol.3, p.14, 2008.

C. Rödelsperger and C. Dieterich, CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes, PloS one, vol.5, p.8861, 2010.

Y. P. Denielou, F. Boyer, A. Viari, and M. F. Sagot, Multiple Alignment of Biological Networks: A Flexible Approach. CPM: 20th Symposium on Combinatorial Pattern Matching, vol.5577, pp.263-273, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00845384

H. Ogata, W. Fujibuchi, S. Goto, and M. Kanehisa, A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters, Nucl Acids Res, vol.28, issue.20, pp.4021-4028, 2000.

M. Kalaev, V. Bafna, and R. Sharan, Fast and Accurate Alignment of Multiple Protein Networks, International Conference on Research in Computational Molecular Biology RECOMB, vol.4955, pp.246-256, 2008.

C. Simillion, K. Vandepoele, Y. Saeys, and Y. Van-de-peer, Building genomic profiles for uncovering segmental homology in the twilight zone

, Genome Res, vol.14, issue.6, pp.1095-1106, 2004.

M. Remm, C. Storm, and E. Sonnhammer, Automatic clustering of orthologs and in-paralogs from pairwise species comparisons, J Mol Biol, vol.314, pp.1041-1052, 2001.

A. Altenhoff and C. Dessimoz, Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods, PloS Comput Biol, vol.5, p.1000262, 2009.

M. Habib, C. Paul, and M. Raffinot, Maximal Common Connected Sets of Interval Graphs, CPM: 15th Symposium on Combinatorial Pattern Matching, vol.3109, pp.347-358, 2004.
URL : https://hal.archives-ouvertes.fr/lirmm-00108787

K. Vandepoele, Y. Saeys, C. Simillion, J. Raes, and Y. Van-de-peer, The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice, Genome Res, vol.12, issue.11, pp.1792-1801, 2002.

C. Simillion, K. Janssens, and L. Sterck, Van de Peer Y: i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles, Bioinformatics, vol.24, pp.127-128, 2008.

K. Cho, W. Lim, R. Math, A. Islam, S. Hong et al., Comparative analysis of the glg operons of Pectobacterium chrysanthemi PY35 and other prokaryotes, J Mol Evol, vol.67, pp.1-12, 2008.

M. Montero, G. Almagro, G. Eydallin, A. Viale, F. Muñoz et al., Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression, Biochem J, vol.433, pp.107-117, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00547994

S. Lin, R. Hanson, and J. Cronan, Biotin synthesis begins by hijacking the fatty acid synthetic pathway, Nat Chem Biol, vol.6, issue.9, pp.682-688, 2010.

D. Rodionov, A. Mironov, and M. Gelfand, Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea, Genome Res, vol.12, issue.10, pp.1507-1516, 2002.

F. Lemoine, O. Lespinet, and B. Labedan, Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data, BMC Evol Biol, vol.7, p.237, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00194466

G. Gonnet, M. Hallett, C. Korostensky, and L. Bernardin, Darwin v. 2:0: an interpreted computer language for the biosciences, Bioinformatics, vol.16, pp.101-103, 2000.

. Deniélou, Bacterial syntenies: an exact approach with gene quorum, BMC Bioinformatics, vol.12, p.193, 2011.