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Results: 1 to 20 of 99

1.

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration.

Looso M, Preussner J, Sousounis K, Bruckskotten M, Michel CS, Lignelli E, Reinhardt R, Höffner S, Krüger M, Tsonis PA, Borchardt T, Braun T.

Genome Biol. 2013 Feb 20;14(2):R16. doi: 10.1186/gb-2013-14-2-r16.

PMID:
23425577
[PubMed - in process]
Free PMC Article
2.

Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens.

Bruckskotten M, Looso M, Reinhardt R, Braun T, Borchardt T.

Nucleic Acids Res. 2012 Jan;40(Database issue):D895-900. doi: 10.1093/nar/gkr873. Epub 2011 Oct 27.

PMID:
22039101
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens.

Abdullayev I, Kirkham M, Björklund ÅK, Simon A, Sandberg R.

Exp Cell Res. 2013 May 1;319(8):1187-97. doi: 10.1016/j.yexcr.2013.02.013. Epub 2013 Feb 28.

PMID:
23454602
[PubMed - indexed for MEDLINE]
Free Article
4.

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.).

Li D, Deng Z, Qin B, Liu X, Men Z.

BMC Genomics. 2012 May 18;13:192. doi: 10.1186/1471-2164-13-192.

PMID:
22607098
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23110314
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23127152
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.

Hassan MA, Melo MB, Haas B, Jensen KD, Saeij JP.

BMC Genomics. 2012 Dec 12;13:696. doi: 10.1186/1471-2164-13-696.

PMID:
23231500
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.

Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Sánchez Alvarado A, Kempa S, Dieterich C, Rajewsky N, Chen W.

Genome Res. 2011 Jul;21(7):1193-200. doi: 10.1101/gr.113779.110. Epub 2011 May 2.

PMID:
21536722
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam].

Tao X, Gu YH, Wang HY, Zheng W, Li X, Zhao CW, Zhang YZ.

PLoS One. 2012;7(4):e36234. doi: 10.1371/journal.pone.0036234. Epub 2012 Apr 27.

PMID:
22558397
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome.

Su CL, Chao YT, Alex Chang YC, Chen WC, Chen CY, Lee AY, Hwa KT, Shih MC.

Plant Cell Physiol. 2011 Sep;52(9):1501-14. doi: 10.1093/pcp/pcr097. Epub 2011 Jul 19.

PMID:
21771864
[PubMed - indexed for MEDLINE]
11.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers.

Amin S, Prentis PJ, Gilding EK, Pavasovic A.

BMC Res Notes. 2014 Aug 1;7:488. doi: 10.1186/1756-0500-7-488.

PMID:
25084827
[PubMed - in process]
Free PMC Article
12.

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.

PMID:
21122097
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Software for pre-processing Illumina next-generation sequencing short read sequences.

Chen C, Khaleel SS, Huang H, Wu CH.

Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014.

PMID:
24955109
[PubMed]
Free PMC Article
14.

De novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome to identify putative genes involved in the aquatic adaptation and immune response.

Gui D, Jia K, Xia J, Yang L, Chen J, Wu Y, Yi M.

PLoS One. 2013 Aug 28;8(8):e72417. doi: 10.1371/journal.pone.0072417. eCollection 2013.

PMID:
24015242
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Development of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome.

Verma P, Shah N, Bhatia S.

Plant Biotechnol J. 2013 Sep;11(7):894-905. doi: 10.1111/pbi.12082. Epub 2013 Jun 13.

PMID:
23759076
[PubMed - indexed for MEDLINE]
16.
17.

A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.

Tulin S, Aguiar D, Istrail S, Smith J.

Evodevo. 2013 Jun 3;4:16. doi: 10.1186/2041-9139-4-16. eCollection 2013.

PMID:
23731568
[PubMed]
Free PMC Article
18.

Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress.

Bhardwaj J, Chauhan R, Swarnkar MK, Chahota RK, Singh AK, Shankar R, Yadav SK.

BMC Genomics. 2013 Sep 23;14:647. doi: 10.1186/1471-2164-14-647.

PMID:
24059455
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
25126744
[PubMed - in process]
Free PMC Article
20.

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
[PubMed - indexed for MEDLINE]

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