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Items: 1 to 20 of 97

1.

Fractionation, rearrangement and subgenome dominance.

Sankoff D, Zheng C.

Bioinformatics. 2012 Sep 15;28(18):i402-i408. doi: 10.1093/bioinformatics/bts392.

2.

A consolidation algorithm for genomes fractionated after higher order polyploidization.

Jahn K, Zheng C, Kováč J, Sankoff D.

BMC Bioinformatics. 2012;13 Suppl 19:S8. doi: 10.1186/1471-2105-13-S19-S8. Epub 2012 Dec 19.

3.

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.

Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH.

Nucleic Acids Res. 2012 Apr;40(7):e49. doi: 10.1093/nar/gkr1293. Epub 2012 Jan 4.

4.

Synteny of Prunus and other model plant species.

Jung S, Jiwan D, Cho I, Lee T, Abbott A, Sosinski B, Main D.

BMC Genomics. 2009 Feb 10;10:76. doi: 10.1186/1471-2164-10-76.

5.

Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.

6.

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.

Berlin S, Lagercrantz U, von Arnold S, Ost T, Rönnberg-Wästljung AC.

BMC Genomics. 2010 Feb 23;11:129. doi: 10.1186/1471-2164-11-129.

7.

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.

8.

Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level.

Gehrmann T, Reinders MJ.

Bioinformatics. 2015 Nov 1;31(21):3437-44. doi: 10.1093/bioinformatics/btv389. Epub 2015 Jun 27.

9.

Genome rearrangement with gene families.

Sankoff D.

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

PMID:
10743557
10.

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
11.

Two evolutionarily distinct classes of paleopolyploidy.

Garsmeur O, Schnable JC, Almeida A, Jourda C, D'Hont A, Freeling M.

Mol Biol Evol. 2014 Feb;31(2):448-54. doi: 10.1093/molbev/mst230. Epub 2013 Dec 1.

PMID:
24296661
12.

Synteny and comparative analysis of miRNA retention, conservation, and structure across Brassicaceae reveals lineage- and sub-genome-specific changes.

Jain A, Das S.

Funct Integr Genomics. 2016 May;16(3):253-68. doi: 10.1007/s10142-016-0484-1. Epub 2016 Feb 12.

PMID:
26873704
13.

Practical halving; the Nelumbo nucifera evidence on early eudicot evolution.

Zheng C, Sankoff D.

Comput Biol Chem. 2014 Jun;50:75-81. doi: 10.1016/j.compbiolchem.2014.01.010. Epub 2014 Jan 26.

PMID:
24525373
14.

Expression divergence of cellulose synthase (CesA) genes after a recent whole genome duplication event in Populus.

Takata N, Taniguchi T.

Planta. 2015 Jan;241(1):29-42. doi: 10.1007/s00425-014-2217-9. Epub 2014 Dec 9.

PMID:
25486888
15.

Fractionation of synteny in a genomic region containing tandemly duplicated genes across glycine max, Medicago truncatula, and Arabidopsis thaliana.

Schlueter JA, Scheffler BE, Jackson S, Shoemaker RC.

J Hered. 2008 Jul-Aug;99(4):390-5. doi: 10.1093/jhered/esn010. Epub 2008 Mar 2.

PMID:
18316321
16.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).

Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D.

Science. 2006 Sep 15;313(5793):1596-604.

17.

[Chromosome synteny of the A genome of two evolutionary wheat lines].

Dobrovol'skaia OB, Sourdille P, Bernard M, Salina EA.

Genetika. 2009 Nov;45(11):1548-55. Russian.

PMID:
20058801
18.

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.

19.

MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T.

J Comput Biol. 2007 Nov;14(9):1160-75.

PMID:
17990975
20.

Pathgroups, a dynamic data structure for genome reconstruction problems.

Zheng C.

Bioinformatics. 2010 Jul 1;26(13):1587-94. doi: 10.1093/bioinformatics/btq255. Epub 2010 May 18.

PMID:
20483815

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