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Items: 1 to 20 of 161

1.

The aquatic animals' transcriptome resource for comparative functional analysis.

Chou CH, Huang HY, Huang WC, Hsu SD, Hsiao CD, Liu CY, Chen YH, Liu YC, Huang WY, Lee ML, Chen YC, Huang HD.

BMC Genomics. 2018 May 9;19(Suppl 2):103. doi: 10.1186/s12864-018-4463-x.

2.

PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms.

Gan RC, Chen TW, Wu TH, Huang PJ, Lee CC, Yeh YM, Chiu CH, Huang HD, Tang P.

BMC Bioinformatics. 2016 Dec 22;17(Suppl 19):513. doi: 10.1186/s12859-016-1366-1.

3.

Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis.

Wang S, Gribskov M.

Bioinformatics. 2017 Feb 1;33(3):327-333. doi: 10.1093/bioinformatics/btw625.

PMID:
28172640
4.

Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.

Mbandi SK, Hesse U, van Heusden P, Christoffels A.

BMC Bioinformatics. 2015 Feb 21;16:58. doi: 10.1186/s12859-015-0492-5.

5.

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome.

Visser EA, Wegrzyn JL, Steenkmap ET, Myburg AA, Naidoo S.

BMC Genomics. 2015 Dec 12;16:1057. doi: 10.1186/s12864-015-2277-7.

6.

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.

Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P.

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S2. doi: 10.1186/1471-2105-12-S14-S2.

7.

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.

Yang Y, Smith SA.

BMC Genomics. 2013 May 14;14:328. doi: 10.1186/1471-2164-14-328.

8.

Sequencing and de novo assembly of the Asian clam (Corbicula fluminea) transcriptome using the Illumina GAIIx method.

Chen H, Zha J, Liang X, Bu J, Wang M, Wang Z.

PLoS One. 2013 Nov 7;8(11):e79516. doi: 10.1371/journal.pone.0079516. eCollection 2013.

9.

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato.

Herraiz FJ, Blanca J, Ziarsolo P, Gramazio P, Plazas M, Anderson GJ, Prohens J, Vilanova S.

BMC Genomics. 2016 May 4;17:321. doi: 10.1186/s12864-016-2656-8.

10.

A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing.

Hoang NV, Furtado A, Mason PJ, Marquardt A, Kasirajan L, Thirugnanasambandam PP, Botha FC, Henry RJ.

BMC Genomics. 2017 May 22;18(1):395. doi: 10.1186/s12864-017-3757-8.

11.
12.

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J.

Bioinformatics. 2014 Jun 15;30(12):1660-6. doi: 10.1093/bioinformatics/btu077. Epub 2014 Feb 13.

PMID:
24532719
13.

Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus.

Rana SB, Zadlock FJ 4th, Zhang Z, Murphy WR, Bentivegna CS.

PLoS One. 2016 Apr 7;11(4):e0153104. doi: 10.1371/journal.pone.0153104. eCollection 2016.

14.

High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis.

Kim HA, Lim CJ, Kim S, Choe JK, Jo SH, Baek N, Kwon SY.

PLoS One. 2014 Mar 28;9(3):e92087. doi: 10.1371/journal.pone.0092087. eCollection 2014.

15.

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.

Riviere G, Klopp C, Ibouniyamine N, Huvet A, Boudry P, Favrel P.

BMC Bioinformatics. 2015 Dec 2;16:401. doi: 10.1186/s12859-015-0833-4.

16.

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database.

Blavet N, Charif D, Oger-Desfeux C, Marais GA, Widmer A.

BMC Genomics. 2011 Jul 26;12:376. doi: 10.1186/1471-2164-12-376.

17.

Multiple model species selection for transcriptomics analysis of non-model organisms.

Pai TW, Li KH, Yang CH, Hu CH, Lin HJ, Wang WD, Chen YR.

BMC Bioinformatics. 2018 Aug 13;19(Suppl 9):284. doi: 10.1186/s12859-018-2278-z.

18.

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.

19.

A high-quality annotated transcriptome of swine peripheral blood.

Liu H, Smith TPL, Nonneman DJ, Dekkers JCM, Tuggle CK.

BMC Genomics. 2017 Jun 24;18(1):479. doi: 10.1186/s12864-017-3863-7.

20.

RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development.

Torre S, Tattini M, Brunetti C, Fineschi S, Fini A, Ferrini F, Sebastiani F.

PLoS One. 2014 Nov 13;9(11):e112487. doi: 10.1371/journal.pone.0112487. eCollection 2014.

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