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Comparative genomics III: Synteny Hierarchies and Gene clusters

The following are the algorithmic papers in this area. Apart from that, many papers on applications of gene clusters and statistical properties exist, but are not listed here.

  1. T. Uno and M. Yagiura. Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26(2):290-309, 2000.
  2. S. Heber and J. Stoye. Finding all common intervals of k permutations. In A. Amir and G. Landau, editors, Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching, CPM 2001, volume 2089 of LNCS, pages 207-218, Berlin, 2001. Springer Verlag.
  3. S. Heber and J. Stoye. Algorithms for finding gene clusters. In O. Gascuel and B. Moret, editors,Proceedings of the First International Workshop on Algorithms in Bioinformatics, WABI 2001, volume 2149 of LNCS, pages 252-263, Berlin, 2001. Springer Verlag.
  4. G. Didier, T. Schmidt, J. Stoye, D. Tsur. Character Sets of Strings. J. Discr. Alg. 5(2):330-340, 2007.
  5. A. Bergeron, S. Corteel, and M. Raffinot. The algorithmic of gene teams. In R. Guigó and D. Gusfield,editors, Proceedings of the Second International Workshop on Algorithms in Bioinformatics, WABI 2002, volume 2452 of LNCS, pages 464-476, Berlin, 2002. Springer Verlag.
  6. N. Luc, J.-L. Risler, A. Bergeron, and M. Raffinot. Gene teams: a new formalization of gene clusters for comparative genomics. Comp. Biol. Chem. 27:59-67, 2003.
  7. T. Schmidt and J. Stoye. Quadratic time algorithms for finding common intervals in two and more sequences. In S. C. Sahinalp, S. Muthukrishnan, and U. Dogrusoz, editors, Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching, CPM 2004, volume 3109 of LNCS, pages 347-358, Berlin, 2004. Springer Verlag.
  8. X. He and M. H. Goldwasser. Identifying conserved gene clusters in the presence of homology families. J. Comp. Biol. 12(6):638-656, 2005.
  9. G. M. Landau, L. Parida, and O. Weimann. Gene proximity analysis across whole genomes via PQ tree. J. Comp. Biol. 12(10):1289–1306, 2005.
  10. A. Bergeron, C. Chauve, F. de Montgolfier, and M. Raffinot. Computing common intervals of K permutations, with applications to modular decomposition of graphs. SIAM J. Discrete Mathematics 22(3):1022–1039, 2008.
  11. S. Böcker, K. Jahn, J. Mixtacki, J. Stoye. Computation of Median Gene Clusters. J. Comp. Biol. 16(8):1085-1099, 2009.
  12. F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, S. Böcker. Swiftly Computing Center Strings. BMC Bioinformatics 12:106, 2011.
  13. D. Doerr, J. Stoye, S. Böcker, K. Jahn. Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings. BMC Genomics 15(Suppl. 6): S2, 2014.