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Sequence Search and Comparative Genomic Analysis of SUMO-Activating Enzymes Using CoGe.

Carretero-Paulet L, Albert VA.

Methods Mol Biol. 2016;1450:261-72. doi: 10.1007/978-1-4939-3759-2_21.


Microsynteny and phylogenetic analysis of tandemly organised miRNA families across five members of Brassicaceae reveals complex retention and loss history.

Rathore P, Geeta R, Das S.

Plant Sci. 2016 Jun;247:35-48. doi: 10.1016/j.plantsci.2016.03.002. Epub 2016 Mar 10.


CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae species.

Chen H, Wang X.

Plant Physiol. 2013 Sep;163(1):354-62. doi: 10.1104/pp.113.219444. Epub 2013 Jul 29.


Comparative genomics reveals origin of MIR159A-MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae.

Anand S, Lal M, Das S.

Mol Genet Genomics. 2019 Jun;294(3):693-714. doi: 10.1007/s00438-019-01540-4. Epub 2019 Mar 6.


SynMap2 and SynMap3D: web-based whole-genome synteny browsers.

Haug-Baltzell A, Stephens SA, Davey S, Scheidegger CE, Lyons E.

Bioinformatics. 2017 Jul 15;33(14):2197-2198. doi: 10.1093/bioinformatics/btx144.


Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

Wang X, Wu J, Liang J, Cheng F, Wang X.

Database (Oxford). 2015 Nov 20;2015. pii: bav093. doi: 10.1093/database/bav093. Print 2015.


Comparative genomics in the Brassicaceae: a family-wide perspective.

Schranz ME, Song BH, Windsor AJ, Mitchell-Olds T.

Curr Opin Plant Biol. 2007 Apr;10(2):168-75. Epub 2007 Feb 14. Review.


The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers.

Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Kuelahoglu C, Bian C, Chen J, Fan G, Kaufmann K, Hall JC, Becker A, Bräutigam A, Weber AP, Shi C, Zheng Z, Li W, Lv M, Tao Y, Wang J, Zou H, Quan Z, Hibberd JM, Zhang G, Zhu XG, Xu X, Schranz ME.

Plant Cell. 2013 Aug;25(8):2813-30. doi: 10.1105/tpc.113.113480. Epub 2013 Aug 27.


A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae.

Hofberger JA, Nsibo DL, Govers F, Bouwmeester K, Schranz ME.

Genome Biol Evol. 2015 Jan 28;7(3):720-34. doi: 10.1093/gbe/evv020.


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.


Partial shotgun sequencing of the Boechera stricta genome reveals extensive microsynteny and promoter conservation with Arabidopsis.

Windsor AJ, Schranz ME, Formanová N, Gebauer-Jung S, Bishop JG, Schnabelrauch D, Kroymann J, Mitchell-Olds T.

Plant Physiol. 2006 Apr;140(4):1169-82.


Bolbase: a comprehensive genomics database for Brassica oleracea.

Yu J, Zhao M, Wang X, Tong C, Huang S, Tehrim S, Liu Y, Hua W, Liu S.

BMC Genomics. 2013 Sep 30;14:664. doi: 10.1186/1471-2164-14-664.


A segmental duplication in the common ancestor of Brassicaceae is responsible for the origin of the paralogs KCS6-KCS5, which are not shared with other angiosperms.

Singh S, Das S, Geeta R.

Mol Phylogenet Evol. 2018 Sep;126:331-345. doi: 10.1016/j.ympev.2018.04.018. Epub 2018 Apr 24.


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.


A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants.

Nelson AD, Forsythe ES, Devisetty UK, Clausen DS, Haug-Batzell AK, Meldrum AM, Frank MR, Lyons E, Beilstein MA.

G3 (Bethesda). 2016 Sep 8;6(9):2881-91. doi: 10.1534/g3.116.030338.


The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes.

Schranz ME, Lysak MA, Mitchell-Olds T.

Trends Plant Sci. 2006 Nov;11(11):535-42. Epub 2006 Oct 6. Review.


Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention.

Mandáková T, Li Z, Barker MS, Lysak MA.

Plant J. 2017 Jul;91(1):3-21. doi: 10.1111/tpj.13553. Epub 2017 May 11.


A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows JR, Höppner MP, Dainat J, Lantz H, Haas BJ, Grabherr MG.

BMC Bioinformatics. 2014 Jun 30;15:227. doi: 10.1186/1471-2105-15-227.


Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation.

Zhao T, Holmer R, de Bruijn S, Angenent GC, van den Burg HA, Schranz ME.

Plant Cell. 2017 Jun;29(6):1278-1292. doi: 10.1105/tpc.17.00312. Epub 2017 Jun 5.


Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids.

Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M.

Plant Physiol. 2008 Dec;148(4):1772-81. doi: 10.1104/pp.108.124867. Epub 2008 Oct 24.

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