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Items: 1 to 20 of 641


A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.

Kurtz S, Narechania A, Stein JC, Ware D.

BMC Genomics. 2008 Oct 31;9:517. doi: 10.1186/1471-2164-9-517.


Sequence composition, organization, and evolution of the core Triticeae genome.

Li W, Zhang P, Fellers JP, Friebe B, Gill BS.

Plant J. 2004 Nov;40(4):500-11.


Transposable element annotation of the rice genome.

Juretic N, Bureau TE, Bruskiewich RM.

Bioinformatics. 2004 Jan 22;20(2):155-60.


Analysis of common k-mers for whole genome sequences using SSB-tree.

Choi JH, Cho HG.

Genome Inform. 2002;13:30-41.


Genome-wide characterization of long terminal repeat -retrotransposons in apple reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons.

Sun HY, Dai HY, Zhao GL, Ma Y, Ou CQ, Li H, Li LG, Zhang ZH.

J Integr Plant Biol. 2008 Sep;50(9):1130-9. doi: 10.1111/j.1744-7909.2008.00717.x.


Maize genome sequencing by methylation filtration.

Palmer LE, Rabinowicz PD, O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR.

Science. 2003 Dec 19;302(5653):2115-7.


Enrichment of gene-coding sequences in maize by genome filtration.

Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J.

Science. 2003 Dec 19;302(5653):2118-20.


In-depth view of structure, activity, and evolution of rice chromosome 10.

Rice Chromosome 10 Sequencing Consortium.

Science. 2003 Jun 6;300(5625):1566-9. Erratum in: Science. 2003 Sep 5;301(5638):1327.


JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

BMC Bioinformatics. 2006 Nov 23;7:513.


The maize genome as a model for efficient sequence analysis of large plant genomes.

Rabinowicz PD, Bennetzen JL.

Curr Opin Plant Biol. 2006 Apr;9(2):149-56. Epub 2006 Feb 3. Review.


Rice transposable elements are characterized by various methylation environments in the genome.

Takata M, Kiyohara A, Takasu A, Kishima Y, Ohtsubo H, Sano Y.

BMC Genomics. 2007 Dec 20;8:469.


Evidence-based gene predictions in plant genomes.

Liang C, Mao L, Ware D, Stein L.

Genome Res. 2009 Oct;19(10):1912-23. doi: 10.1101/gr.088997.108. Epub 2009 Jun 18.


A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica.

Oki N, Yano K, Okumoto Y, Tsukiyama T, Teraishi M, Tanisaka T.

Genes Genet Syst. 2008 Aug;83(4):321-9.


Computational prediction and molecular confirmation of Helitron transposons in the maize genome.

Du C, Caronna J, He L, Dooner HK.

BMC Genomics. 2008 Jan 28;9:51. doi: 10.1186/1471-2164-9-51.


A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley.

Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N.

Plant J. 2009 Sep;59(5):712-22. doi: 10.1111/j.1365-313X.2009.03911.x. Epub 2009 May 12.


The TIGR Maize Database.

Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D771-6.


Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome.

Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, McCombie WR, Martienssen RA.

Nat Genet. 1999 Nov;23(3):305-8.


Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.

Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR.

Plant Physiol. 2001 Mar;125(3):1166-74.


How to usefully compare homologous plant genes and chromosomes as DNA sequences.

Lyons E, Freeling M.

Plant J. 2008 Feb;53(4):661-73. doi: 10.1111/j.1365-313X.2007.03326.x. Review.

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