3917 related articles for article (PubMed ID: 23845962)
1. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Haas BJ; Papanicolaou A; Yassour M; Grabherr M; Blood PD; Bowden J; Couger MB; Eccles D; Li B; Lieber M; MacManes MD; Ott M; Orvis J; Pochet N; Strozzi F; Weeks N; Westerman R; William T; Dewey CN; Henschel R; LeDuc RD; Friedman N; Regev A
Nat Protoc; 2013 Aug; 8(8):1494-512. PubMed ID: 23845962
[TBL] [Abstract][Full Text] [Related]
2. Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Grabherr MG; Haas BJ; Yassour M; Levin JZ; Thompson DA; Amit I; Adiconis X; Fan L; Raychowdhury R; Zeng Q; Chen Z; Mauceli E; Hacohen N; Gnirke A; Rhind N; di Palma F; Birren BW; Nusbaum C; Lindblad-Toh K; Friedman N; Regev A
Nat Biotechnol; 2011 May; 29(7):644-52. PubMed ID: 21572440
[TBL] [Abstract][Full Text] [Related]
3. Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis.
Wang S; Gribskov M
Bioinformatics; 2017 Feb; 33(3):327-333. PubMed ID: 28172640
[TBL] [Abstract][Full Text] [Related]
4. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
Li B; Dewey CN
BMC Bioinformatics; 2011 Aug; 12():323. PubMed ID: 21816040
[TBL] [Abstract][Full Text] [Related]
5. RNA-Seq in Nonmodel Organisms.
Chalifa-Caspi V
Methods Mol Biol; 2021; 2243():143-167. PubMed ID: 33606257
[TBL] [Abstract][Full Text] [Related]
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; 12 Suppl 14(Suppl 14):S2. PubMed ID: 22373417
[TBL] [Abstract][Full Text] [Related]
7. transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
Fallon TR; Čalounová T; Mokrejš M; Weng JK; Pluskal T
BMC Bioinformatics; 2023 Apr; 24(1):133. PubMed ID: 37016291
[TBL] [Abstract][Full Text] [Related]
8. De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies.
Thunders M; Cavanagh J; Li Y
Biol Res; 2017 Feb; 50(1):7. PubMed ID: 28241869
[TBL] [Abstract][Full Text] [Related]
9. EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
Chu HT; Hsiao WW; Chen JC; Yeh TJ; Tsai MH; Lin H; Liu YW; Lee SA; Chen CC; Tsao TT; Kao CY
Bioinformatics; 2013 Apr; 29(8):1004-10. PubMed ID: 23457040
[TBL] [Abstract][Full Text] [Related]
10. Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data.
Duan J; Xia C; Zhao G; Jia J; Kong X
BMC Genomics; 2012 Aug; 13():392. PubMed ID: 22891638
[TBL] [Abstract][Full Text] [Related]
11. De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes.
Chauhan P; Hansson B; Kraaijeveld K; de Knijff P; Svensson EI; Wellenreuther M
BMC Genomics; 2014 Sep; 15(1):808. PubMed ID: 25245033
[TBL] [Abstract][Full Text] [Related]
12. Evaluation of de novo transcriptome assemblies from RNA-Seq data.
Li B; Fillmore N; Bai Y; Collins M; Thomson JA; Stewart R; Dewey CN
Genome Biol; 2014 Dec; 15(12):553. PubMed ID: 25608678
[TBL] [Abstract][Full Text] [Related]
13. De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers.
Hölzer M; Marz M
Gigascience; 2019 May; 8(5):. PubMed ID: 31077315
[TBL] [Abstract][Full Text] [Related]
14. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J; Bruno VM; Fang Z; Meng X; Blow M; Zhang T; Sherlock G; Snyder M; Wang Z
BMC Genomics; 2010 Nov; 11():663. PubMed ID: 21106091
[TBL] [Abstract][Full Text] [Related]
15. 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; 17(Suppl 19):513. PubMed ID: 28155708
[TBL] [Abstract][Full Text] [Related]
16. Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.
Cerveau N; Jackson DJ
BMC Bioinformatics; 2016 Dec; 17(1):525. PubMed ID: 27938328
[TBL] [Abstract][Full Text] [Related]
17. Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq.
Lu B; Zeng Z; Shi T
Sci China Life Sci; 2013 Feb; 56(2):143-55. PubMed ID: 23393030
[TBL] [Abstract][Full Text] [Related]
18. FRAMA: from RNA-seq data to annotated mRNA assemblies.
Bens M; Sahm A; Groth M; Jahn N; Morhart M; Holtze S; Hildebrandt TB; Platzer M; Szafranski K
BMC Genomics; 2016 Jan; 17():54. PubMed ID: 26763976
[TBL] [Abstract][Full Text] [Related]
19. SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.
Johnson BK; Scholz MB; Teal TK; Abramovitch RB
BMC Bioinformatics; 2016 Feb; 17():66. PubMed ID: 26847232
[TBL] [Abstract][Full Text] [Related]
20. dbHT-Trans: An Efficient Tool for Filtering the Protein-Encoding Transcripts Assembled by RNA-Seq According to Search for Homologous Proteins.
Deng F; Chen SY
J Comput Biol; 2016 Jan; 23(1):1-9. PubMed ID: 26484655
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
