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Items: 1 to 20 of 206

1.

Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne.

Ruttink T, Sterck L, Rohde A, Bendixen C, Rouzé P, Asp T, Van de Peer Y, Roldan-Ruiz I.

Plant Biotechnol J. 2013 Jun;11(5):605-17. doi: 10.1111/pbi.12051. Epub 2013 Feb 21.

2.

De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

Farrell JD, Byrne S, Paina C, Asp T.

PLoS One. 2014 Aug 15;9(8):e103567. doi: 10.1371/journal.pone.0103567. eCollection 2014.

3.

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote.

Liu S, Zhang Y, Zhou Z, Waldbieser G, Sun F, Lu J, Zhang J, Jiang Y, Zhang H, Wang X, Rajendran KV, Khoo L, Kucuktas H, Peatman E, Liu Z.

BMC Genomics. 2012 Nov 5;13:595. doi: 10.1186/1471-2164-13-595.

4.

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome.

Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK.

Am J Bot. 2012 Feb;99(2):186-92. doi: 10.3732/ajb.1100419. Epub 2012 Feb 1.

5.

A transcriptome map of perennial ryegrass (Lolium perenne L.).

Studer B, Byrne S, Nielsen RO, Panitz F, Bendixen C, Islam MS, Pfeifer M, Lübberstedt T, Asp T.

BMC Genomics. 2012 Apr 18;13:140. doi: 10.1186/1471-2164-13-140.

6.

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.

Ashrafi H, Hill T, Stoffel K, Kozik A, Yao J, Chin-Wo SR, Van Deynze A.

BMC Genomics. 2012 Oct 30;13:571. doi: 10.1186/1471-2164-13-571.

7.

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing.

Li X, Acharya A, Farmer AD, Crow JA, Bharti AK, Kramer RS, Wei Y, Han Y, Gou J, May GD, Monteros MJ, Brummer EC.

BMC Genomics. 2012 Oct 29;13:568. doi: 10.1186/1471-2164-13-568.

8.

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.

Iorizzo M, Senalik DA, Grzebelus D, Bowman M, Cavagnaro PF, Matvienko M, Ashrafi H, Van Deynze A, Simon PW.

BMC Genomics. 2011 Aug 2;12:389. doi: 10.1186/1471-2164-12-389.

9.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J.

BMC Bioinformatics. 2012 Jul 18;13:170. doi: 10.1186/1471-2105-13-170.

10.

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome.

Fraser BA, Weadick CJ, Janowitz I, Rodd FH, Hughes KA.

BMC Genomics. 2011 Apr 20;12:202. doi: 10.1186/1471-2164-12-202.

11.
12.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.

Milano I, Babbucci M, Panitz F, Ogden R, Nielsen RO, Taylor MI, Helyar SJ, Carvalho GR, Espiñeira M, Atanassova M, Tinti F, Maes GE, Patarnello T; FishPopTrace Consortium, Bargelloni L.

PLoS One. 2011;6(11):e28008. doi: 10.1371/journal.pone.0028008. Epub 2011 Nov 22.

14.

De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification.

Yates SA, Swain MT, Hegarty MJ, Chernukin I, Lowe M, Allison GG, Ruttink T, Abberton MT, Jenkins G, Skøt L.

BMC Genomics. 2014 Jun 9;15:453. doi: 10.1186/1471-2164-15-453.

15.

Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing.

Koepke T, Schaeffer S, Krishnan V, Jiwan D, Harper A, Whiting M, Oraguzie N, Dhingra A.

BMC Genomics. 2012 Jan 12;13:18. doi: 10.1186/1471-2164-13-18.

16.

Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa.

Scaglione D, Lanteri S, Acquadro A, Lai Z, Knapp SJ, Rieseberg L, Portis E.

Plant Biotechnol J. 2012 Oct;10(8):956-69. doi: 10.1111/j.1467-7652.2012.00725.x. Epub 2012 Jul 31.

17.

Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data.

Wong MM, Cannon CH, Wickneswari R.

BMC Genomics. 2012 Dec 24;13:726. doi: 10.1186/1471-2164-13-726.

18.

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).

Ferreira de Carvalho J, Poulain J, Da Silva C, Wincker P, Michon-Coudouel S, Dheilly A, Naquin D, Boutte J, Salmon A, Ainouche M.

Heredity (Edinb). 2013 Feb;110(2):181-93. doi: 10.1038/hdy.2012.76. Epub 2012 Nov 14.

19.

454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes.

Hook SE, Twine NA, Simpson SL, Spadaro DA, Moncuquet P, Wilkins MR.

Aquat Toxicol. 2014 Aug;153:73-88. doi: 10.1016/j.aquatox.2013.11.022. Epub 2013 Dec 12.

PMID:
24434169
20.

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.

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