580 related articles for article (PubMed ID: 21824971)
1. 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]
2. Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.
Brooks MJ; Rajasimha HK; Roger JE; Swaroop A
Mol Vis; 2011; 17():3034-54. PubMed ID: 22162623
[TBL] [Abstract][Full Text] [Related]
3. DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Hu Y; Huang Y; Du Y; Orellana CF; Singh D; Johnson AR; Monroy A; Kuan PF; Hammond SM; Makowski L; Randell SH; Chiang DY; Hayes DN; Jones C; Liu Y; Prins JF; Liu J
Nucleic Acids Res; 2013 Jan; 41(2):e39. PubMed ID: 23155066
[TBL] [Abstract][Full Text] [Related]
4. GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment.
Zhang Z; Huang S; Wang J; Zhang X; Pardo Manuel de Villena F; McMillan L; Wang W
Bioinformatics; 2013 Jul; 29(13):i291-9. PubMed ID: 23812996
[TBL] [Abstract][Full Text] [Related]
5. Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.
LeGault LH; Dewey CN
Bioinformatics; 2013 Sep; 29(18):2300-10. PubMed ID: 23846746
[TBL] [Abstract][Full Text] [Related]
6. PennDiff: detecting differential alternative splicing and transcription by RNA sequencing.
Hu Y; Lin J; Hu J; Hu G; Wang K; Zhang H; Reilly MP; Li M
Bioinformatics; 2018 Jul; 34(14):2384-2391. PubMed ID: 29474557
[TBL] [Abstract][Full Text] [Related]
7. Accurate inference of isoforms from multiple sample RNA-Seq data.
Tasnim M; Ma S; Yang EW; Jiang T; Li W
BMC Genomics; 2015; 16 Suppl 2(Suppl 2):S15. PubMed ID: 25708199
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
Li W; Jiang T
Bioinformatics; 2012 Nov; 28(22):2914-21. PubMed ID: 23060617
[TBL] [Abstract][Full Text] [Related]
10. CIDANE: comprehensive isoform discovery and abundance estimation.
Canzar S; Andreotti S; Weese D; Reinert K; Klau GW
Genome Biol; 2016 Jan; 17():16. PubMed ID: 26831908
[TBL] [Abstract][Full Text] [Related]
11. RNA-Skim: a rapid method for RNA-Seq quantification at transcript level.
Zhang Z; Wang W
Bioinformatics; 2014 Jun; 30(12):i283-i292. PubMed ID: 24931995
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. 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]
14. ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
Denti L; Rizzi R; Beretta S; Vedova GD; Previtali M; Bonizzoni P
BMC Bioinformatics; 2018 Nov; 19(1):444. PubMed ID: 30458725
[TBL] [Abstract][Full Text] [Related]
15. Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).
Sturgill D; Malone JH; Sun X; Smith HE; Rabinow L; Samson ML; Oliver B
BMC Bioinformatics; 2013 Nov; 14():320. PubMed ID: 24209455
[TBL] [Abstract][Full Text] [Related]
16. Identifying differentially spliced genes from two groups of RNA-seq samples.
Wang W; Qin Z; Feng Z; Wang X; Zhang X
Gene; 2013 Apr; 518(1):164-70. PubMed ID: 23228854
[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. 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]
19. 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]
20. Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching.
Rehrauer H; Opitz L; Tan G; Sieverling L; Schlapbach R
BMC Bioinformatics; 2013 Dec; 14():370. PubMed ID: 24365034
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
