493 related articles for article (PubMed ID: 26831908)
1. 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]
2. Information transduction capacity reduces the uncertainties in annotation-free isoform discovery and quantification.
Deng Y; Bao F; Yang Y; Ji X; Du M; Zhang Z; Wang M; Dai Q
Nucleic Acids Res; 2017 Sep; 45(15):e143. PubMed ID: 28911101
[TBL] [Abstract][Full Text] [Related]
3. Using BRIE to Detect and Analyze Splicing Isoforms in scRNA-Seq Data.
Huang Y; Sanguinetti G
Methods Mol Biol; 2019; 1935():175-185. PubMed ID: 30758827
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. 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]
6. Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.
Zhang W; Chang JW; Lin L; Minn K; Wu B; Chien J; Yong J; Zheng H; Kuang R
PLoS Comput Biol; 2015 Dec; 11(12):e1004465. PubMed ID: 26699225
[TBL] [Abstract][Full Text] [Related]
7. rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data.
Shi Y; Chinnaiyan AM; Jiang H
Bioinformatics; 2015 Jul; 31(13):2222-4. PubMed ID: 25717189
[TBL] [Abstract][Full Text] [Related]
8. Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE.
Andreotti S; Canzar S
Methods Mol Biol; 2019; 1870():199-208. PubMed ID: 30539557
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. 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]
11. 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]
12. SNPlice: variants that modulate Intron retention from RNA-sequencing data.
Mudvari P; Movassagh M; Kowsari K; Seyfi A; Kokkinaki M; Edwards NJ; Golestaneh N; Horvath A
Bioinformatics; 2015 Apr; 31(8):1191-8. PubMed ID: 25481010
[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. 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]
15. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Pertea M; Kim D; Pertea GM; Leek JT; Salzberg SL
Nat Protoc; 2016 Sep; 11(9):1650-67. PubMed ID: 27560171
[TBL] [Abstract][Full Text] [Related]
16. TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs.
Liu J; Yu T; Jiang T; Li G
Genome Biol; 2016 Oct; 17(1):213. PubMed ID: 27760567
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Trapnell C; Williams BA; Pertea G; Mortazavi A; Kwan G; van Baren MJ; Salzberg SL; Wold BJ; Pachter L
Nat Biotechnol; 2010 May; 28(5):511-5. PubMed ID: 20436464
[TBL] [Abstract][Full Text] [Related]
19. TopHat: discovering splice junctions with RNA-Seq.
Trapnell C; Pachter L; Salzberg SL
Bioinformatics; 2009 May; 25(9):1105-11. PubMed ID: 19289445
[TBL] [Abstract][Full Text] [Related]
20. BRIE: transcriptome-wide splicing quantification in single cells.
Huang Y; Sanguinetti G
Genome Biol; 2017 Jun; 18(1):123. PubMed ID: 28655331
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]