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Items: 1 to 20 of 29

1.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, Flutre T, Pelegrin C, Ohyanagi H, Seidel M, Giacomoni F, Reichstadt M, Alaux M, Gicquello E, Legeai F, Cerutti L, Numa H, Tanaka T, Mayer K, Itoh T, Quesneville H, Feuillet C.

Front Plant Sci. 2012 Jan 31;3:5. doi: 10.3389/fpls.2012.00005. eCollection 2012.

2.

Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa.

Pazos-Navarro M, Dabauza M, Correal E, Hanson K, Teakle N, Real D, Nelson MN.

BMC Genet. 2011 Dec 15;12:104. doi: 10.1186/1471-2156-12-104.

3.

Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers.

Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X.

BMC Genomics. 2011 Sep 19;12:451. doi: 10.1186/1471-2164-12-451.

4.

Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels.

Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J.

BMC Genomics. 2011 Mar 14;12:148. doi: 10.1186/1471-2164-12-148.

5.

Forest tree genomics: growing resources and applications.

Neale DB, Kremer A.

Nat Rev Genet. 2011 Feb;12(2):111-22. doi: 10.1038/nrg2931. Review.

PMID:
21245829
6.

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum).

Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA.

BMC Genomics. 2011 Jan 13;12:30. doi: 10.1186/1471-2164-12-30.

7.

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.

Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA.

BMC Genomics. 2010 Dec 1;11:681. doi: 10.1186/1471-2164-11-681.

8.

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.

Ueno S, Le Provost G, Léger V, Klopp C, Noirot C, Frigerio JM, Salin F, Salse J, Abrouk M, Murat F, Brendel O, Derory J, Abadie P, Léger P, Cabane C, Barré A, de Daruvar A, Couloux A, Wincker P, Reviron MP, Kremer A, Plomion C.

BMC Genomics. 2010 Nov 23;11:650. doi: 10.1186/1471-2164-11-650.

9.

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.

Durand J, Bodénès C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herrán A, Ikaran Z, Cabané C, Ueno S, Alberto F, Dumoulin PY, Guichoux E, de Daruvar A, Kremer A, Plomion C.

BMC Genomics. 2010 Oct 15;11:570. doi: 10.1186/1471-2164-11-570.

10.

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery.

Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA.

BMC Genomics. 2010 Mar 16;11:180. doi: 10.1186/1471-2164-11-180.

11.

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx.

Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV.

BMC Genomics. 2009 May 12;10:219. doi: 10.1186/1471-2164-10-219.

12.

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection.

Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE.

BMC Plant Biol. 2009 May 9;9:51. doi: 10.1186/1471-2229-9-51.

13.

Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don.

Li X, Wu HX, Dillon SK, Southerton SG.

BMC Genomics. 2009 Jan 21;10:41. doi: 10.1186/1471-2164-10-41.

14.

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome.

Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M.

BMC Genomics. 2008 Jun 30;9:312. doi: 10.1186/1471-2164-9-312.

15.

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH.

Mol Ecol. 2008 Apr;17(7):1636-47. doi: 10.1111/j.1365-294X.2008.03666.x. Epub 2008 Feb 5.

PMID:
18266620
16.

KAAS: an automatic genome annotation and pathway reconstruction server.

Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5. Epub 2007 May 25.

17.

Efficient secondary database driven annotation using model organism sequences.

Faria-Campos AC, Campos SV, Prosdocimi F, Franco GC, Franco GR, Ortega JM.

In Silico Biol. 2006;6(5):363-72.

PMID:
17274765
18.

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

Kohany O, Gentles AJ, Hankus L, Jurka J.

BMC Bioinformatics. 2006 Oct 25;7:474.

19.
20.

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.

Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J.

BMC Genomics. 2005 Oct 19;6:144.

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