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Results: 1 to 20 of 77

1.

Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study.

Bhutkar A, Gelbart WM, Smith TF.

Genome Biol. 2007;8(11):R236.

PMID:
17996033
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Techniques for multi-genome synteny analysis to overcome assembly limitations.

Bhutkar A, Russo S, Smith TF, Gelbart WM.

Genome Inform. 2006;17(2):152-61.

PMID:
17503388
[PubMed - indexed for MEDLINE]
3.

A mixture framework for inferring ancestral gene orders.

Zhang Y, Hu F, Tang J.

BMC Genomics. 2012;13 Suppl 1:S7. doi: 10.1186/1471-2164-13-S1-S7. Epub 2012 Jan 17.

PMID:
22369143
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes.

Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM.

Genetics. 2008 Jul;179(3):1657-80. doi: 10.1534/genetics.107.086108. Epub 2008 Jul 13.

PMID:
18622036
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes.

Zheng C, Sankoff D.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S9. doi: 10.1186/1471-2105-13-S10-S9.

PMID:
22759433
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Rearrangement phylogeny of genomes in contig form.

Muñoz A, Sankoff D.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):579-87. doi: 10.1109/TCBB.2010.66.

PMID:
20714028
[PubMed - indexed for MEDLINE]
7.

Recovering genome rearrangements in the mammalian phylogeny.

Zhao H, Bourque G.

Genome Res. 2009 May;19(5):934-42. doi: 10.1101/gr.086009.108.

PMID:
19411607
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Chromosomal elements evolve at different rates in the Drosophila genome.

González J, Ranz JM, Ruiz A.

Genetics. 2002 Jul;161(3):1137-54.

PMID:
12136017
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Descendants of whole genome duplication within gene order phylogeny.

Zheng C, Zhu Q, Sankoff D.

J Comput Biol. 2008 Oct;15(8):947-64. doi: 10.1089/cmb.2008.0118.

PMID:
18788908
[PubMed - indexed for MEDLINE]
10.

Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

Tuller T, Birin H, Kupiec M, Ruppin E.

J Comput Biol. 2010 Sep;17(9):1327-44. doi: 10.1089/cmb.2010.0112.

PMID:
20874411
[PubMed - indexed for MEDLINE]
11.

How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila.

Ranz JM, Casals F, Ruiz A.

Genome Res. 2001 Feb;11(2):230-9.

PMID:
11157786
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Genome-scale evolution: reconstructing gene orders in the ancestral species.

Bourque G, Pevzner PA.

Genome Res. 2002 Jan;12(1):26-36.

PMID:
11779828
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Genome-scale analysis of positionally relocated genes.

Bhutkar A, Russo SM, Smith TF, Gelbart WM.

Genome Res. 2007 Dec;17(12):1880-7. Epub 2007 Nov 7.

PMID:
17989252
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Advances in phylogeny reconstruction from gene order and content data.

Moret BM, Warnow T.

Methods Enzymol. 2005;395:673-700.

PMID:
15865990
[PubMed - indexed for MEDLINE]
15.

Ancestral animal genomes reconstruction.

Rascol VL, Pontarotti P, Levasseur A.

Curr Opin Immunol. 2007 Oct;19(5):542-6. Epub 2007 Aug 15. Review.

PMID:
17702562
[PubMed - indexed for MEDLINE]
16.

Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.

Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ.

Hum Genomics. 2003 Nov;1(1):30-40.

PMID:
15601531
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.

Rasmussen MD, Kellis M.

Genome Res. 2007 Dec;17(12):1932-42. Epub 2007 Nov 7.

PMID:
17989260
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The speciation history of the Drosophila nasuta complex.

Bachtrog D.

Genet Res. 2006 Aug;88(1):13-26.

PMID:
17014741
[PubMed - indexed for MEDLINE]
19.

Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives.

Machado CA, Kliman RM, Markert JA, Hey J.

Mol Biol Evol. 2002 Apr;19(4):472-88.

PMID:
11919289
[PubMed - indexed for MEDLINE]
Free Article
20.

A flexible ancestral genome reconstruction method based on gapped adjacencies.

Gagnon Y, Blanchette M, El-Mabrouk N.

BMC Bioinformatics. 2012;13 Suppl 19:S4. doi: 10.1186/1471-2105-13-S19-S4. Epub 2012 Dec 19.

PMID:
23281872
[PubMed - indexed for MEDLINE]
Free PMC Article

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