756 related articles for article (PubMed ID: 22998089)
1. Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.
Vijay N; Poelstra JW; Künstner A; Wolf JB
Mol Ecol; 2013 Feb; 22(3):620-34. PubMed ID: 22998089
[TBL] [Abstract][Full Text] [Related]
2. 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]
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. Challenges and advances for transcriptome assembly in non-model species.
Ungaro A; Pech N; Martin JF; McCairns RJS; Mévy JP; Chappaz R; Gilles A
PLoS One; 2017; 12(9):e0185020. PubMed ID: 28931057
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. Transcript Profiling Using Long-Read Sequencing Technologies.
Bayega A; Wang YC; Oikonomopoulos S; Djambazian H; Fahiminiya S; Ragoussis J
Methods Mol Biol; 2018; 1783():121-147. PubMed ID: 29767360
[TBL] [Abstract][Full Text] [Related]
7. RNA-Seq for transcriptome analysis in non-model plants.
Garg R; Jain M
Methods Mol Biol; 2013; 1069():43-58. PubMed ID: 23996307
[TBL] [Abstract][Full Text] [Related]
8. Detection and quantification of alternative splicing variants using RNA-seq.
Bryant DW; Priest HD; Mockler TC
Methods Mol Biol; 2012; 883():97-110. PubMed ID: 22589127
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. 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; 30(12):1660-6. PubMed ID: 24532719
[TBL] [Abstract][Full Text] [Related]
11. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence.
Góngora-Castillo E; Buell CR
Nat Prod Rep; 2013 Apr; 30(4):490-500. PubMed ID: 23377493
[TBL] [Abstract][Full Text] [Related]
12. RNA-Seq: revelation of the messengers.
Van Verk MC; Hickman R; Pieterse CM; Van Wees SC
Trends Plant Sci; 2013 Apr; 18(4):175-9. PubMed ID: 23481128
[TBL] [Abstract][Full Text] [Related]
13. De Novo Plant Transcriptome Assembly and Annotation Using Illumina RNA-Seq Reads.
Kerr SC; Gaiti F; Tanurdzic M
Methods Mol Biol; 2019; 1933():265-275. PubMed ID: 30945191
[TBL] [Abstract][Full Text] [Related]
14. 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; 16():1057. PubMed ID: 26652261
[TBL] [Abstract][Full Text] [Related]
15. Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.
Mangul S; Caciula A; Glebova O; Mandoiu I; Zelikovsky A
In Silico Biol; 2011-2012; 11(5-6):251-61. PubMed ID: 23202426
[TBL] [Abstract][Full Text] [Related]
16. Designing a transcriptome next-generation sequencing project for a nonmodel plant species.
Strickler SR; Bombarely A; Mueller LA
Am J Bot; 2012 Feb; 99(2):257-66. PubMed ID: 22268224
[TBL] [Abstract][Full Text] [Related]
17. Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C(3) and C(4) species.
Bräutigam A; Mullick T; Schliesky S; Weber AP
J Exp Bot; 2011 May; 62(9):3093-102. PubMed ID: 21398430
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Comparison of Gene Expression Profiles in Nonmodel Eukaryotic Organisms with RNA-Seq.
Cheng H; Wang Y; Sun MA
Methods Mol Biol; 2018; 1751():3-16. PubMed ID: 29508286
[TBL] [Abstract][Full Text] [Related]
20. Reference-free transcriptome assembly in non-model animals from next-generation sequencing data.
Cahais V; Gayral P; Tsagkogeorga G; Melo-Ferreira J; Ballenghien M; Weinert L; Chiari Y; Belkhir K; Ranwez V; Galtier N
Mol Ecol Resour; 2012 Sep; 12(5):834-45. PubMed ID: 22540679
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
