Analysis of gene order evolution beyond single-copy genes

Methods in Molecular Biology

Volumn 855, Issue , 2012, Pages 397-429

  El Mabrouk, Nadia ^a   Sankoff, David ^b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Comparative genomics; Duplication; Gene family; Gene loss; Gene order; Rearrangement

Indexed keywords

ANIMAL; ARTICLE; GENE DUPLICATION; GENE ORDER; GENETICS; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; SYNTENY;

ANIMALS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE ORDER; GENOMICS; HUMANS; SYNTENY;

EID: 84859974254     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-582-4_15     Document Type: Article

References (138)

1. Watterson, G., Ewens, W., Hall, T., and Morgan, A. (1982) The chromosome inversion problem. Journal of Theoretical Biology, 99, 1-7. (Pubitemid 13209093)
2. Sankoff, D., G. Leduc, Antoine, N., Paquin, B., Lang, B., and Cedergren, R. (1992) Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences USA, 89, 6575-6579.
3. Ohno, S. (1970) Evolution by gene duplication. Springer.
4. Sanderson, M. and McMahon, M. (2007) Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evolutionary Biology, 7, S3.
5. Wapinski, I., Pfeffer, A., Friedman, N., and Regev, A. (2007) Natural history and evolutionary principles of gene duplication in fungi. Nature, 449, 54-61. (Pubitemid 47373776)
6. Hannenhalli, S. and Pevzner, P. A. (1995) Transforming men into mice (polynomial algorithm for genomic distance problem). Proceedings of the IEEE 36th Annual Symposium on Foundations of Computer Science, pp. 581-592.
7. Tesler, G. (2002) Efficient algorithms for multichromosomal genome rearrangements. Journal of Computer and System Sciences, 65, 587-609.
8. Bergeron, A., Mixtacki, J., and Stoye, J. (2006) A unifying view of genome rearrangements. Algorithms in Bioinformatics. WABI '06, vol. 4175 of Lecture Notes in Computer Science, pp. 163-173. (Pubitemid 44609667)
9. Bergeron, A., Mixtacki, J., and Stoye, J. (2009) A new linear time algorithm to compute the genomic distance via the double cut and join distance. Theoretical Computer Science, 410, 5300-5316.
10. Yancopoulos, S., Attie, O., and Friedberg, R. (2005) Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics, 21, 3340-3346. (Pubitemid 41222437)
11. Angibaud, S., Fertin, G., Rusu, I., and Vialette, S. (2007) A general framework for computing rearrangement distances between genomes with duplicates. Journal of Computational Biology, 14, 379-393. (Pubitemid 46911213)
12. Blin, G., Chauve, C., Fertin, G., Rizzi, R., and Vialette, S. (2007) Comparing genomes with duplications: a computational complexity point of view. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4, 523-534. (Pubitemid 350125876)
13. Chauve, C., Fertin, G., Rizzi, R., and Vialette, S. (2006) Genomes containing duplicates are hard to compare. Computational Science (ICCS 2006), vol. 3992 of Lecture Notes in Computer Science, pp. 783-790. (Pubitemid 44152585)
14. Hannenhalli, S. (1995) Polynomial-time algorithm for computing translocation distance between genomes. Galil, Z. and Ukkonen, E. (eds.), Combinatorial Pattern Matching. 6th Annual Symposium, vol. 937 of Lecture Notes in Computer Science, pp. 162-176, Springer.
15. Hannenhalli, S. and Pevzner, P. A. (1999) Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Journal of the ACM, 48, 1-27.
16. Bader, D., Moret, B., and Yan, M. (2001) A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. Journal of Computational Biology, 8, 483-491. (Pubitemid 33044073)
17. Bergeron, A., Mixtacki, J., and Stoye, J. (2004) Reversal distance without hurdles and fortresses. Sahinalp, S., Muthukrishnan, S., and Dogrusoz, U. (eds.), Combinatorial Pattern Matching '04, vol. 3109 of Lecture Notes in Computer Science, pp. 388-399.
18. Bafna, V. and Pevzner, P. A. (1998) Sorting by transpositions. SIAM Journal on Discrete Mathematics, 11, 224-240.
19. Hartman, T. (2003) A simpler 1.5-approximation algorithm for sorting by transpositions. R.Baeza-Yates, Chávez, E., and Crochemore, M. (eds.), Combinatorial Pattern Matching. 14th Annual Symposium., vol. 2676 of Lecture Notes in Computer Science, pp. 156-169.
20. Meidanis, J., Walter, M. E., and Dias, Z. (1997) Transposition distance between a permutation and its reverse. Baeza-Yates, R. (ed.), Proceedings of the Fourth South American Workshop on String Processing (WSP'97), pp. 70-79, Carleton University Press.
21. Walter, M. E., Dias, Z., and Meidanis, J. (1998) Reversal and transposition distance of linear chromosomes. Proceedings of String Processing and Information Retrieval: A South American Symposium (SPIRE'98), pp. 96-102.
22. Bergeron, A., Chauve, C., and Gingras, Y. (2008) Formal models of gene clusters. Mandoiu, I. and Zelikovsky, A. (eds.), Bioinformatics algorithms: techniques and applications, chap. 8, Wiley.
23. Bourque, G., Yacef, Y., and El-Mabrouk, N. (2005) Maximizing synteny blocks to identify ancestral homologs. Lecture Notes in Bioinformatics, vol. 3678 of RECOMB-CG, pp. 21-34, Springer.
24. Tatusov, R., Galperin, M., Natale, D., and Koonin, E. (2000) The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research, 28, 33-36. (Pubitemid 30047708)
25. Chen, F., Mackey, A., C.J. Stoeckert, J., and Roos, D. S. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Research, 34, D363-D368.
26. O'Brien, K., Remm, M., and Sonnhammer, E. (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. NucleicAcids Research, 33, D476-D480. (Pubitemid 40207918)
27. Lyons, E. and Freeling, M. (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal, 53, 661-673. (Pubitemid 351224693)
28. Murat, F., Xu, J., Tannier, E., Abrouk, M., uilhot, N., Pont, C., Messing, J., and Salse, J. (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Research, 20(11), 1545-1557.
29. Sankoff, D. (1999) Genome rearrangements with gene families. Bioinformatics, 15, 909-917.
30. Fu, Z., Chen, X., Vacic, V., Nan, P., Zhong, Y., and Jiang, T. (2007) MSOAR: A highthroughput ortholog assignment system based on genome rearrangement. Journal of Computational Biology, 14, 1160-1175. (Pubitemid 350100393)
31. Jiang, T. (2010) Some algorithmic challenges in genome-wide ortholog assignment. Journal of Computer Science and Technology, 25.
32. Shi, G. and Jiang, T. (2010) MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. BMC Bioinformatics, 11, 1160-1175. (Pubitemid 350100393)
33. Yancopoulos, S. and Friedberg, R. (2009) DCJ path formulation for genome transformations which include insertions, deletions, and duplications. Journal of Computational Biology, 16, 1311-1338.
34. Nadeau, J. and Taylor, B. (1984) Lengths of chromosomal segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences USA, 81, 814-818. (Pubitemid 14199035)
35. Sankoff, D., Parent, M., and Bryant, D. (2000) Accuracy and robustness of analyses based on numbers of genes in observed segments. Sankoff, D. and Nadeau, J. H. (eds.), Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and Evolution of Gene Families, pp. 299-306, Kluwer Academic.
36. Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. (2003) Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of theNationalAcademy of Sciences of theUnited States of America, 100, 11484-11489. (Pubitemid 37205962)
37. Pevzner, P. and Tesler, G. (2003) Genome rearrangements in mammalian evolution: Lessons from human and mouse genomic sequences. Genome Research, 13, 13-26.
38. Peng, Q., Alekseyev, M., Tesler, G., and Pevzner, P. (2009) Decoding synteny blocks and large-scale duplications in mammalian and plant genomes. Salzberg, S. and Warnow, T. (eds.), Algorithms in Bioinformatics, vol. 5724 of Lecture Notes in Computer Science, pp. 220-232.
39. Pham, S. and Pevzner, P. (2010) Drimm-synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics, 26, 2509-2516.
40. Durand, D. and Sankoff, D. (2003) Testing for gene clusters. Journal of Computational Biology, 10, 453-482.
41. Hoberman, R. and Durand, D. (2005) The incompatible desiderata of gene cluster properties. McLysaght, A. and Huson, D. (eds.), Comparative Genomics, vol. 3678 of Lecture Notes in Computer Science, pp. 73-87, Springer Berlin/Heidelberg.
42. Uno, T. and Yagiura, M. (2000) Fast algorithms to enumerate all common intervals of two permutations. Algorithmica, 26, 290-309.
43. Bergeron, A. and Stoye, J. (2003) On the similarity of sets of permutations and its applications to genome comparison. Journal of Computational Biology, 13, 1340-1354.
44. Heber, S. and Stoye, J. (2001) Finding all common intervals of k permutations. Amir, A. and Landau, G. M. (eds.), Combinatorial Pattern Matching. 12th Annual Symposium, vol. 2089 of Lecture Notes in Computer Science, pp. 207-218, Springer. (Pubitemid 33298875)
45. Landau, G., Parida, L., and Weimann, O. (2005) Gene proximity analysis across whole genomes via PQ trees. Journal of Computational Biology, 12, 1289-1306. (Pubitemid 44743644)
46. Bergeron, A., Corteel, S., and Raffinot, M. (2002) The algorithmic of gene teams. Guigó, R. and Gusfield, D. (eds.), Algorithms in Bioinformatics. Proceedings of WABI 2002, vol. 2452 of Lecture Notes in Computer Science, pp. 464-476, Springer.
47. Hoberman, R., Sankoff, D., and Durand, D. (2005) The statistical analysis of spatially clustered genes under the maximum gap criterion. Journal of Computational Biology, 12, 1083-1102. (Pubitemid 41580024)
48. Yang, Z. and Sankoff, D. (2010) Natural parameter values for generalized gene adjacency. Journal of Computational Biology, 17, 1113-1128.
49. Zhu, Q., Adam, Z., Choi, V., and Sankoff, D. (2009) Generalized gene adjacencies, graph bandwidth, and clusters in yeast evolution. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 6, 213-220.
50. Xu, X. and Sankoff, D. (2008) Tests for gene clusters satisfying the generalized adjacency criterion. Bazzan, A., Craven, M., and Martins, N. (eds.), Advances in Bioinformatics and Computational Biology, vol. 5167 of Lecture Notes in Computer Science, pp. 152-160, Springer Berlin/Heidelberg.
51. Li,W., Gu, Z.,Wang, H., and Nekrutenko, A. (2001) Evolutionary analysis of the human genome. Nature, 409, 847-849.
52. Wolfe, K. (2001) Yesterday's polyploids and the mystery of diploidization. Nature Reviews Genetics, 2, 333-341.
53. Blomme, T., Vandepoele, K., Bodt, S. D., Silmillion, C., Maere, S., and van de Peer, Y. (2006) The gain and loss of genes during 600 millions years of vertebrate evolution. Genome Biology, 7, R43.
54. Cotton, J. and Page, R. (2005) Rates and patterns of gene duplication and loss in the human genome. Proceedings of the Royal ociety of London. Series B, 272, 277-283.
55. Eichler, E. and Sankoff, D. (2003) Structural dynamics of eukaryotic chromosome evolution. Science, 301, 793-797. (Pubitemid 36962611)
56. Hahn, M., Han, M., and Han, S.-G. (2007) Gene family evolution across 12 drosophilia genomes. PLoS Genetics, 3:e197.
57. Lynch, M. and Conery, J. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
58. Gascuel, O., Bertrand, D., and Elemento, O. (2005) Reconstructing the duplication history of tandemly repeated sequences. Gascuel, O. (ed.), Mathematics of Evolution and Phylogeny, pp. 205-235, Oxford.
59. El-Mabrouk, N. and Sankoff, D. (2003) The reconstruction of doubled genomes. SIAM Journal on Computing, 32, 754-792.
60. Sankoff, D. (2001) Gene and genome duplication. Current Opinion in Genetics & Development, 11, 681-684. (Pubitemid 33000341)
61. Demuth, J., Bie, T. D., Stajich, J., Cristianini, N., and Hahn, M. (2006) The evolution of mammalian gene families. PLoS ONE, 1:e85.
62. Chen, K., Durand, D., and Farach-Colton, M. (2000) Notung: Dating gene duplications using gene family trees. Journal of Computational Biology, 7, 429-447.
63. Vernot, B., Stolzer, M., Goldman, A., and Durand, D. (2008) Reconciliation with nonbinary species trees. Journal of Computational Biology, 15, 981-1006.
64. Goodman, M., Czelusniak, J., Moore, G., Romero-Herrera, A., and Matsuda, G. (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology, 28, 132-163.
65. Hallett, M. T. and Lagergren, J. (2001) Efficient algorithms for lateral gene transfer problems. Proceedings of the Fifth Annual International Conference on Computational Biology (RECOMB'01), New York, pp. 149-156, ACM. (Pubitemid 32866153)
66. Chauve, C., Doyon, J.-P., and El-Mabrouk., N. (2008) Gene family evolution by duplication, speciation and loss. J. Comput. Biol., 15, 1043-1062. 426 N. El-Mabrouk and D. Sankoff
67. Chauve, C. and El-Mabrouk, N. (2009) New perspectives on gene family evolution: losses in reconciliation and a link with supertrees. Batzoglou, S. (ed.), Research in Molecular Biology (RECOMB 2009), vol. 5541 of Lecture Notes in Computer Science, pp. 46-58, Springer.
68. Gorecki, P. and Tiuryn., J. (2006) DLS-trees: a model of evolutionary scenarios. Theoretical Computer Science, 359, 378-399. (Pubitemid 44119080)
69. Arvestad, L., Berglung, A.-C., Lagergren, J., and Sennblad, B. (2004) Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. Gusfield, D. (ed.), RECOMB '04: Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, New York, pp. 326-335, ACM.
70. Ma, B., Li, M., and Zhang, L. (2000) From gene trees to species trees. SIAM Journal on Computing, 30, 729-752.
71. Page, R. (1994) Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology, 43, 58-77. (Pubitemid 24979624)
72. Guigó, R., Muchnik, I., and Smith, T. (1996) Reconstruction of ancient molecular phylogeny. Molecular Phylogenetics and Evolution, 6, 189-213. (Pubitemid 126320615)
73. Page, R. and Charleston, M. (1997) Reconciled trees and incongruent gene and species trees. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 37, 57-70.
74. Bonizzoni, P., Della Vedova, G., and Dondi, R. (2005) Reconciling a gene tree to a species tree under the duplication cost model. Theoretical Computer Science, 347, 36-53. (Pubitemid 41650210)
75. Durand, D., Haldórsson, B., and Vernot, B. (2006) A hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology, 13, 320-335.
76. Eulenstein, O., Mirkin, B., and Vingron, M. (1998) Duplication-based measures of difference between gene and species trees. Journal of Computational Biology, 5, 135-148. (Pubitemid 28153011)
77. Page., R. (1998) Genetree: comparing gene and species phylogenies using reconciled trees. Bioinformatics, 14, 819-820.
78. Zhang, L. (1997) On Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. Journal of Computational Biology, 4, 177-188.
79. Doyon, J.-P., Chauve, C., and Hamel., S. (2009) The space of gene tree/species tree reconciliations and parsimonious models. Journal of Computational Biology, 16, 1399-1418.
80. Page, R. and Cotton, J. (2002) Vertebrate phylogenomics: reconciled trees and gene duplications. Pacific Symposium on Biocomputing, pp. 536-547.
81. Zmasek, C. M. and Eddy, S. R. (2001) A simple algorithm to infer gene duplication and speciiation events on a gene tree. Bioinformatics, 17, 821-828. (Pubitemid 32970480)
82. Hallett, M. and Lagergren, J. (2000) New algorithms for the duplication-loss model. Shamir, R., Miyano, S., Istrail, S., Pevzner, P., and Waterman, M. S. (eds.), Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, New York, pp. 138-146, RECOMB, ACM.
83. Hahn, M. (2007) Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology, 8.
84. Chang, W. and Eulenstein, O. (2006) Reconciling gene trees with apparent polytomies. Chen, D. and Lee, D. T. (eds.), Proceedings of the 12th Conference on Computing and Combinatorics (COCOON), vol. 4112 of Lecture Notes in Computer Science, pp. 235-244. (Pubitemid 44531975)
85. Doroftei, A. and El-Mabrouk, N. (2011) Removing noice from gene trees. Algorithms in Bioinformatics, vol. 6833 of Lecture Notes in Computer Science, pp. 76-91.
86. Shoja, V. and Zhang, L. (2006) A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat. Molecular Biology and Evolution, 23, 2134-2141. (Pubitemid 44536822)
87. Glusman, G., Yanai, I., Rubin, I., and Lancet, D. (2001) The complete human olfactory subgenome. Genome Research, 11, 685-702.
88. LaRue, R., Jonsson, S., Silverstein, K., Lajoie, M., Bertrand, D., El-Mabrouk, N., Hötzel, I., Andresdottir, V., Smith, T., and Harris, R. (2008) The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals. BMC Molecular Biology, 9, 104.
89. Arden, B., Clark, S., Kabelitz, D., and Mak, T. (1995) Human T-cell receptor variable gene segment families. Immunogenetics, 42, 455-500. (Pubitemid 26025063)
90. Shannon, M., Hamilton, A., Gordon, L., Branscomb, E., and Stubbs, L. (2003) Differential expansion of zinc finger transcription factor loci in homologous human and mouse gene clusters. Genome Research, 13, 1097-1110. (Pubitemid 36764190)
91. Song, G., Zhang, L., Vinar, T., and Miller, W. (2009) Inferring the recent duplication history of a gene cluster. Ciccarelli, F. and Miklós, I. (eds.), Comparative Genomics, vol. 5817 of Lecture Notes in Computer Science, Springer.
92. Schwartz, S., Kent,W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D., and Miller, W. (2003) Human-mouse alignments with blastz. Genome Research, 13, 103-107.
93. Zhang, Y., Song, G., Hsu, C., and Miller, W. (2009) Simultaneous history reconstruction for complex gene clusters in multiple species. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 162-173.
94. Zhang, Y., Song, G., Vinar, T., Green, E., Siepel, A., and Miller,W. (2008) Reconstructing the evolutionary history of complex human gene clusters. M. Vingron and L. Wong (eds.), Research in Computational Molecular Biology. (RECOMB 2008), vol. 4955 of Lecture Notes in Computer Science, pp. 29-49, Springer.
95. Vinar?, T., Brejová, B., Song, G., and Siepel, A. (2010) Reconstructing histories of complex gene clusters on a phylogeny. Journal of Computational Biology, 17, 1267-1269.
96. Fitch, W. (1977) Phylogenies constrained by cross-over process as illustrated by human hemoglobins and a thirteen-cycle, eleven amino-acid repeat in human apolipoprotein A-I. Genetics, 86, 623-644. (Pubitemid 8164243)
97. Bertrand, D. and Gascuel, O. (2005) Topological rearrangements and local search method for tandem duplication trees. IEEE/ ACM Transactions on Computational iology and Bioinformatics, 2, 15-28. (Pubitemid 40750754)
98. Elemento, O., Gascuel, O., and Lefranc, M.-P. (2002) Reconstructing the duplication history of tandemly repeated genes. Molecular Biology and Evolution, 19, 278-288. (Pubitemid 34184599)
99. Tang, M., Waterman, M., and Yooseph, S. (2001) Zinc finger gene clusters and tandem gene duplication. Research in Molecular Biology (RECOMB 2001), pp. 297-304. (Pubitemid 32866174)
100. Zhang, L., Ma, B., Wang, L., and Xu, Y. (2003) Greedy method for inferring tandem duplication history. Bioinformatics, 19,1497-1504. (Pubitemid 37038865)
101. Chaudhuri, K., Chen, K., Mihaescu, R., and Rao, S. (2006) On the tandem duplicationrandomloss model of genome rearrangement. SODA.
102. Lajoie, M., Bertrand, D., El-Mabrouk, N., and Gascuel, O. (2007) Duplication and inversion history of a tandemly repeated genes family. Journal of Computational Biology, 14, 462-478. (Pubitemid 46911219)
103. Bertrand, D., Lajoie, M., and El-Mabrouk, N. (2008) Inferring ancestral gene orders for a family of tandemly arrayed genes. Journal of Computational Biology, 15, 1063-1077.
104. Lajoie, M., Bertrand, D., and El-Mabrouk, N. (2009) Inferring the evolutionary history of gene clusters from phylogenetic and gene order data. Molecular Biology and Evolution, 27, 761-772.
105. Sankoff, D. and Blanchette, M. (1997) The median problem for break-points in comparative genomics. Jiang, T. and Lee, D. (eds.), Computing and Combinatorics, Proceeedings of COCOON '97, Berlin, pp. 251-263, no. 1276 in Lecture Notes in Computer Science, Springer. (Pubitemid 127110291)
106. Cosner, M., Jansen, R., Moret, B., Raubeson, L., Wang, L.-S., Warnow, T., and Wyman, S. (2000) An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. D.Sankoff and Nadeau, J. (eds.), Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, pp. 99-121, Kluwer Academic Publishers.
107. HPCwire (2000) Grappa runs in a record time. 9, 47.
108. Siepel, A. (2001) Exact Algorithms for the Reversal Median Problem. Master's thesis, University of New Mexico.
109. Caprara, A. (2001) On the practical solution of the reversal median problem. Gascuel, O. and Moret, B. (eds.), Algorithms in Bioinformatics (WABI). First International Workshop, vol. 2149 of Lecture Notes in Computer Science, pp. 238-251, Springer. (Pubitemid 33322586)
110. Bourque, G. and Pevzner, P. (2002) Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Research, 12, 26-36. (Pubitemid 34065587)
111. Moret, B., Wang, L., Warnow, T., and Wyman, S. (2001) New approaches for reconstructing phylogenies from gene order data. Bioinformatics, 17, S165-S173. (Pubitemid 33793507)
112. Tannier, E., Zheng, C., and Sankoff, D. (2009) Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics, 10.
113. Adam, Z. and Sankoff, D. (2010) A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances. Journal of Computational Biology, 17, 1299-1314.
114. Xu, A. (2009) A fast and exact algorithm for the median of three problem: a graph decomposition approach. Journal of Computational Biology, 16, 1369-1381.
115. Zheng, C. (2010) Pathgroups, a dynamic data structure for genome reconstruction problems. Bioinformatics, 26, 1587-1594.
116. Zheng, C. and Sankoff, D. (2011) On the Pathgroups approach to rapid small phylogeny. BMC Bioinformatics, 12, S4.
117. Sankoff, D. and Blanchette, M. (1998) Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology, 5, 555-570. (Pubitemid 28436301)
118. Chauve, C., Gavranovic, H., Ouangraoua, A., and Tannier, E. (2008) Yeast ancestral genome reconstructions: the possibilities of computational methods. PloS Computational Biology, 4, e1000234.
119. Murat, F., Xu, J.H., Tannier, E., Abrouk, M., Guilhot, N., Pont, C., Messing, J., and Salse, J. (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Research, 20(11):1545-1557.
120. Gavranovic, H., Chauve, C., Salse, J., and Tannier, E. (2011)Mapping ancestral genomes with massive gene loss: A matrix sandwich problem. Bioinformatics, 27:i257-i265.
121. Muffato, M., Louis, A., Poisnel, C.E. and Crollius, R. (2011) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics, 26(8):1119-1121.
122. Fulkerson, D. and Gross, O. (1965) Incidence matricesand interval graphs. Pac. J. Math., 15, 835-855.
123. Blanc, G., Hokamp, K., and Wolfe, K. (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Research, 13, 137-144. (Pubitemid 36575763)
124. Bowers, J., Chapman, B., Rong, J., and Paterson, A. (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature, 422, 433-438. (Pubitemid 36411396)
125. Salse, J., Bolot, S., Throude, M., Jouffe, V., Piegu, B., Quraishi, U., Calcagno, T., Cooke, R., Delseny, M., and Feuillet, C. (2008) Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. The Plant Cell, 20, 11-24. (Pubitemid 352844030)
126. Soltis,D.,Albert,V., Leebens-Mack, J., Bell, C., Paterson, A., Zheng, C., Sankoff, D., dePamphilis, C., Wall, P., and Soltis, P. (2009) Polyploidy and angiosperm diversification. American Journal of Botany, 96, 336-348.
127. Zheng, C., Zhu, Q., and Sankoff, D. (2008) Descendants of whole genome duplication within gene order phylogeny. Journal of Computational Biology, 15, 947-964.
128. Alekseyev,M. and Pevzner, P. (2007) Colored de Bruijn graphs and the genome halving problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4, 98-107. (Pubitemid 46375819)
129. Mixtacki, J. (2008) Genome halving under DCJ revisited. Hu, X. and Wang, J. (eds.), Computing and Combinatorics (COCOON). Seventeenth Annual Conference, vol. 5092 of Lecture Notes in Computer Science, pp. 276-286, Springer.
130. Warren, R. and Sankoff, D. (2009) Genome halving with double cut and join. Journal of Bioinformatics and Computational Biology, 7, 357-371.
131. Gagnon, Y., Tremblay-Savard, O., Bertrand, D., and El-Mabrouk, N. (2010) Advances on genome duplication distances. Tannier, E. (ed.), Comparative Genomics (RECOMB CG '10), vol. 6398 of Lecture Notes in Computer Science, pp. 25-38.
132. Sankoff, D., Zheng, C.,Wall, P., dePamphilis, C., Leebens-Mack, J., and Albert, V. (2009) Towards improved reconstruction of ancestral gene order in angiosperm phylogeny. Journal of Computational Biology, 16, 1353-67.
133. Gavranovic, H. and Tannier, E. (2010) Guided genome halving: probably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae. Pacific Symposium on Biocomputing, vol. 15, pp. 21-30.
134. Zheng, C., Zhu, Q., Adam, Z., and Sankoff, D. (2008) Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. Bioinformatics, 24, i96-i104. (Pubitemid 351911662)
135. Gordon, J., Byrne, K., and Wolfe, K. (2009) Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PloS Genetics, 5, e1000485.
136. Warren, R. and Sankoff, D. (2010) Genome aliquoting revisited. Tannier, E. (ed.), Comparative Genomics (RECOMB CG). Eighth Annual Workshop, vol. 6398 of Lecture Notes in Computer Science, pp. 1-12, Springer.
137. Fertin, G., Labarre, A., Rusu, I., Tannier, E., and Vialette, S. (2009) Combinatorics of genome rearrangements. The MIT Press.
138. Tremblay-Savard, O., Bertrand, D., and El- Mabrouk, N. (2011) Evolution of orthologous tandemly arrayed gene clusters. BMC Bioinformatics, 12(Suppl 9), S2.