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Items: 1 to 20 of 133

1.

Genome halving and double distance with losses.

Savard OT, Gagnon Y, Bertrand D, El-Mabrouk N.

J Comput Biol. 2011 Sep;18(9):1185-99. doi: 10.1089/cmb.2011.0136.

PMID:
21899424
2.

Restricted DCJ model: rearrangement problems with chromosome reincorporation.

Kováč J, Warren R, Braga MD, Stoye J.

J Comput Biol. 2011 Sep;18(9):1231-41. doi: 10.1089/cmb.2011.0116.

PMID:
21899428
3.

Genome aliquoting revisited.

Warren R, Sankoff D.

J Comput Biol. 2011 Sep;18(9):1065-75. doi: 10.1089/cmb.2011.0087.

PMID:
21899416
4.

Genome rearrangement with gene families.

Sankoff D.

Bioinformatics. 1999 Nov;15(11):909-17.

PMID:
10743557
5.

Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes.

Bérard S, Chateau A, Chauve C, Paul C, Tannier E.

J Comput Biol. 2009 Oct;16(10):1287-309. doi: 10.1089/cmb.2009.0088.

PMID:
19803733
6.

Theoretical and practical advances in genome halving.

Yin P, Hartemink AJ.

Bioinformatics. 2005 Apr 1;21(7):869-79. Epub 2004 Oct 28.

PMID:
15513986
7.

Genome halving with double cut and join.

Warren R, Sankoff D.

J Bioinform Comput Biol. 2009 Apr;7(2):357-71.

PMID:
19340920
8.

Double cut and join with insertions and deletions.

Braga MD, Willing E, Stoye J.

J Comput Biol. 2011 Sep;18(9):1167-84. doi: 10.1089/cmb.2011.0118.

PMID:
21899423
9.

A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes.

Lin Y, Moret BM.

J Comput Biol. 2011 Sep;18(9):1055-64. doi: 10.1089/cmb.2011.0098.

PMID:
21899415
10.

An exact solver for the DCJ median problem.

Zhang M, Arndt W, Tang J.

Pac Symp Biocomput. 2009:138-49.

11.

Gene loss under neighborhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome.

Zheng C, Kerr Wall P, Leebens-Mack J, DE Pamphilis C, Albert VA, Sankoff D.

J Bioinform Comput Biol. 2009 Jun;7(3):499-520.

PMID:
19507287
12.

The zero exemplar distance problem.

Jiang M.

J Comput Biol. 2011 Sep;18(9):1077-86. doi: 10.1089/cmb.2011.0097.

PMID:
21899417
13.

Genome rearrangement by the double cut and join operation.

Friedberg R, Darling AE, Yancopoulos S.

Methods Mol Biol. 2008;452:385-416. doi: 10.1007/978-1-60327-159-2_18. Review.

PMID:
18566774
14.

A simple algorithm to infer gene duplication and speciation events on a gene tree.

Zmasek CM, Eddy SR.

Bioinformatics. 2001 Sep;17(9):821-8.

PMID:
11590098
15.

DCJ path formulation for genome transformations which include insertions, deletions, and duplications.

Yancopoulos S, Friedberg R.

J Comput Biol. 2009 Oct;16(10):1311-38. doi: 10.1089/cmb.2009.0092.

PMID:
19803734
16.

A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions.

Bader M, Abouelhoda MI, Ohlebusch E.

BMC Bioinformatics. 2008 Dec 4;9:516. doi: 10.1186/1471-2105-9-516.

17.

Distance-based genome rearrangement phylogeny.

Wang LS, Warnow T, Moret BM, Jansen RK, Raubeson LA.

J Mol Evol. 2006 Oct;63(4):473-83. Epub 2006 Oct 4.

PMID:
17021931
18.

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
19.

On pairwise distances and median score of three genomes under DCJ.

Aganezov S Jr, Alekseyev MA.

BMC Bioinformatics. 2012;13 Suppl 19:S1. doi: 10.1186/1471-2105-13-S19-S1. Epub 2012 Dec 19.

20.

SCJ: a breakpoint-like distance that simplifies several rearrangement problems.

Feijão P, Meidanis J.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1318-29. doi: 10.1109/TCBB.2011.34.

PMID:
21339538

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