Guided genome halving: Provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces Cerevisiae

Pacific Symposium on Biocomputing 2010, PSB 2010

Volumn , Issue , 2010, Pages 21-30

  Gavranović, Haris ^a   Tannier, Eric ^b  

^a UNIVERSITY OF SARAJEVO   (Bosnia and Herzegovina)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANCESTRAL GENOMES; GENE ORDERS; GENOME DUPLICATION; LOWER BOUNDS; OPTIMAL SOLUTIONS; SUBGRAPHS;

COMBINATORIAL OPTIMIZATION; HEURISTIC ALGORITHMS; OPTIMAL SYSTEMS; YEAST;

GENES;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; FUNGAL GENOME; GENE DUPLICATION; GENETICS; MOLECULAR EVOLUTION; SACCHAROMYCES CEREVISIAE; YEAST;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, FUNGAL; MODELS, GENETIC; SACCHAROMYCES CEREVISIAE; YEASTS;

EID: 78049464436     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. Alekseyev MA, Pevzner PA (2008) Colored de Bruijn graphs and the genome halving problem, IEEE/ACM Transactions on Computational Biology and Bioinformatics 4:98-107
2. Alekseyev MA, Pevzner PA (2009) Breakpoint graphs and Ancestral Genome Reconstruction, Genome Research 19(5):943-57
3. Bergeron A. Mixtacki J, Stove J (2006) A unifying view of genome rearrangments, Proceedings of WABI'06, Springer, Lecture Notes in Computer Science 4175:163-173
4. Byrne KP, Wolfe KH (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Research 15(10):1456-61
5. El-Mabrouk N, Sankoff D (2003) The reconstruction of doubled genomes, SIAM Journal of Computing 32:754-792
6. Mixtacki J (2008) Genome Halving under DCJ Revisited Proceedings of COCOON'08, Springer, Lecture Notes in Computer Science 5092:276-286
7. Fertin G, Labarre A, Rusu I, Tannier E, Vialette S (2009) Combinatorics of Genome Rearrangements, MIT press
8. Gordon JL, Byrne KP, Wolfe KH (2009) Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome, PLoS Genetics 5(5): e1000485
9. Sankoff D (2009) Reconstructing the History of Yeast Genomes, PLoS Genet 5(5): e1000483
10. Seoighe C, Wolfe KH (1998) Extent of genomic rearrangement after genome duplication in yeast, Proc Natl Acad Sci U S A. 95(8):4447-52
11. Swenson KM, Arndt W, Tang J, Moret BME (2008) Phylogenetic reconstruction from complete gene orders of whole genomes, Proceedings of APBC'08, Imperial College Press, Advances in Bioinformatics and Computational Biology 6:241-250
12. Tannier E (2009) Yeast ancestral genome recontruction: the possibilities of automatic methods, Proceedings of RECOMB Comparative Genomics'09, Springer, Lecture Notes in Bioinformatics 5817:1-12
13. Tannier E, Zheng C, Sankoff D (2009) Multichromosomal Median and Halving Problems under Different Genomic Distances, BMC Bioinformatics 10:120
14. Warren R, Sankoff D (2009) Genome aliquoting with double cut and join, BMC Bioinformatics, 10(Suppl 1):S2
15. Xu AW (2008) A Fast and Exact Algorithm for the Median of Three Problem-A Graph Decomposition Approach, Proceedings of Recomb-Comparative Genomics'08, Springer, Lecture Notes in Bioinformatics 5267:184-197
16. Yancopoulos S, Attie O, Friedberg R (2005) Efficient sorting of genomic permutations by translocation, inversion and block interchange, Bioinformatics 21:3340-3346
17. Zhao H and Bourque G (2009) Recovering genome rearrangements in the mammalian phylogeny, Genome Research 19:934-942
18. Zheng C, Zhu Q, Sankoff D (2006) Genome halving with an outgroup, Evolutionary Bioinformatics 2:319-326
19. Zheng C, Zhu Q, Adam Z, Sankoff D (2008) Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes, Bioinformatics 24(13):i96-104