193 related articles for article (PubMed ID: 25252653)
1. Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq.
Huang Y; Hu Y; Liu J
BMC Bioinformatics; 2014; 15 Suppl 9(Suppl 9):S3. PubMed ID: 25252653
[TBL] [Abstract][Full Text] [Related]
2. Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.
Seok J; Xu W; Jiang H; Davis RW; Xiao W
PLoS One; 2012; 7(2):e31440. PubMed ID: 22312447
[TBL] [Abstract][Full Text] [Related]
3. A robust method for transcript quantification with RNA-seq data.
Huang Y; Hu Y; Jones CD; MacLeod JN; Chiang DY; Liu Y; Prins JF; Liu J
J Comput Biol; 2013 Mar; 20(3):167-87. PubMed ID: 23461570
[TBL] [Abstract][Full Text] [Related]
4. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
Zhang R; Calixto CP; Tzioutziou NA; James AB; Simpson CG; Guo W; Marquez Y; Kalyna M; Patro R; Eyras E; Barta A; Nimmo HG; Brown JW
New Phytol; 2015 Oct; 208(1):96-101. PubMed ID: 26111100
[TBL] [Abstract][Full Text] [Related]
5. CLASS: constrained transcript assembly of RNA-seq reads.
Song L; Florea L
BMC Bioinformatics; 2013; 14 Suppl 5(Suppl 5):S14. PubMed ID: 23734605
[TBL] [Abstract][Full Text] [Related]
6. IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.
Kim H; Bi Y; Pal S; Gupta R; Davuluri RV
BMC Bioinformatics; 2011 Jul; 12():305. PubMed ID: 21794104
[TBL] [Abstract][Full Text] [Related]
7. TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.
Nariai N; Hirose O; Kojima K; Nagasaki M
Bioinformatics; 2013 Sep; 29(18):2292-9. PubMed ID: 23821651
[TBL] [Abstract][Full Text] [Related]
8. Ryūtō: network-flow based transcriptome reconstruction.
Gatter T; Stadler PF
BMC Bioinformatics; 2019 Apr; 20(1):190. PubMed ID: 30991937
[TBL] [Abstract][Full Text] [Related]
9. Visualization and analysis of RNA-Seq assembly graphs.
Nazarie FW; Shih B; Angus T; Barnett MW; Chen SH; Summers KM; Klein K; Faulkner GJ; Saini HK; Watson M; Dongen SV; Enright AJ; Freeman TC
Nucleic Acids Res; 2019 Aug; 47(14):7262-7275. PubMed ID: 31305886
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Turro E; Su SY; Gonçalves Â; Coin LJ; Richardson S; Lewin A
Genome Biol; 2011; 12(2):R13. PubMed ID: 21310039
[TBL] [Abstract][Full Text] [Related]
12. Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.
Mangul S; Caciula A; Al Seesi S; Brinza D; Mӑndoiu I; Zelikovsky A
BMC Genomics; 2014; 15 Suppl 5(Suppl 5):S7. PubMed ID: 25082147
[TBL] [Abstract][Full Text] [Related]
13. SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads.
Safikhani Z; Sadeghi M; Pezeshk H; Eslahchi C
Genomics; 2013; 102(5-6):507-14. PubMed ID: 24161398
[TBL] [Abstract][Full Text] [Related]
14. 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; 18(1):395. PubMed ID: 28532419
[TBL] [Abstract][Full Text] [Related]
15. A probabilistic framework for aligning paired-end RNA-seq data.
Hu Y; Wang K; He X; Chiang DY; Prins JF; Liu J
Bioinformatics; 2010 Aug; 26(16):1950-7. PubMed ID: 20576625
[TBL] [Abstract][Full Text] [Related]
16. JAGuaR: junction alignments to genome for RNA-seq reads.
Butterfield YS; Kreitzman M; Thiessen N; Corbett RD; Li Y; Pang J; Ma YP; Jones SJ; Birol İ
PLoS One; 2014; 9(7):e102398. PubMed ID: 25062255
[TBL] [Abstract][Full Text] [Related]
17. ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
Dao P; Numanagić I; Lin YY; Hach F; Karakoc E; Donmez N; Collins C; Eichler EE; Sahinalp SC
Bioinformatics; 2014 Mar; 30(5):644-51. PubMed ID: 24130305
[TBL] [Abstract][Full Text] [Related]
18. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.
Singh D; Orellana CF; Hu Y; Jones CD; Liu Y; Chiang DY; Liu J; Prins JF
Bioinformatics; 2011 Oct; 27(19):2633-40. PubMed ID: 21824971
[TBL] [Abstract][Full Text] [Related]
19. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.
Zhang R; Kuo R; Coulter M; Calixto CPG; Entizne JC; Guo W; Marquez Y; Milne L; Riegler S; Matsui A; Tanaka M; Harvey S; Gao Y; Wießner-Kroh T; Paniagua A; Crespi M; Denby K; Hur AB; Huq E; Jantsch M; Jarmolowski A; Koester T; Laubinger S; Li QQ; Gu L; Seki M; Staiger D; Sunkar R; Szweykowska-Kulinska Z; Tu SL; Wachter A; Waugh R; Xiong L; Zhang XN; Conesa A; Reddy ASN; Barta A; Kalyna M; Brown JWS
Genome Biol; 2022 Jul; 23(1):149. PubMed ID: 35799267
[TBL] [Abstract][Full Text] [Related]
20. Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing.
Orabi B; Xie N; McConeghy B; Dong X; Chauve C; Hach F
Nucleic Acids Res; 2023 Jan; 51(2):e11. PubMed ID: 36478271
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
