185 related articles for article (PubMed ID: 21079731)
1. HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data.
Dimon MT; Sorber K; DeRisi JL
PLoS One; 2010 Nov; 5(11):e13875. PubMed ID: 21079731
[TBL] [Abstract][Full Text] [Related]
2. Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.
Bai Y; Kinne J; Donham B; Jiang F; Ding L; Hassler JR; Kaufman RJ
BMC Genomics; 2016 Aug; 17 Suppl 7(Suppl 7):503. PubMed ID: 27556805
[TBL] [Abstract][Full Text] [Related]
3. PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
Zhang Y; Lameijer EW; 't Hoen PA; Ning Z; Slagboom PE; Ye K
Bioinformatics; 2012 Feb; 28(4):479-86. PubMed ID: 22219203
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
Wang K; Singh D; Zeng Z; Coleman SJ; Huang Y; Savich GL; He X; Mieczkowski P; Grimm SA; Perou CM; MacLeod JN; Chiang DY; Prins JF; Liu J
Nucleic Acids Res; 2010 Oct; 38(18):e178. PubMed ID: 20802226
[TBL] [Abstract][Full Text] [Related]
6. RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.
Sorber K; Dimon MT; DeRisi JL
Nucleic Acids Res; 2011 May; 39(9):3820-35. PubMed ID: 21245033
[TBL] [Abstract][Full Text] [Related]
7. Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.
Mapleson D; Venturini L; Kaithakottil G; Swarbreck D
Gigascience; 2018 Dec; 7(12):. PubMed ID: 30418570
[TBL] [Abstract][Full Text] [Related]
8. LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.
Levin L; Bar-Yaacov D; Bouskila A; Chorev M; Carmel L; Mishmar D
PLoS One; 2015; 10(11):e0143329. PubMed ID: 26606265
[TBL] [Abstract][Full Text] [Related]
9. PASTA: splice junction identification from RNA-sequencing data.
Tang S; Riva A
BMC Bioinformatics; 2013 Apr; 14():116. PubMed ID: 23557086
[TBL] [Abstract][Full Text] [Related]
10. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes.
Stein S; Lu ZX; Bahrami-Samani E; Park JW; Xing Y
Nucleic Acids Res; 2015 Dec; 43(22):10612-22. PubMed ID: 26578562
[TBL] [Abstract][Full Text] [Related]
11. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.
Nellore A; Jaffe AE; Fortin JP; Alquicira-Hernández J; Collado-Torres L; Wang S; Phillips RA; Karbhari N; Hansen KD; Langmead B; Leek JT
Genome Biol; 2016 Dec; 17(1):266. PubMed ID: 28038678
[TBL] [Abstract][Full Text] [Related]
12. SpliceVec: Distributed feature representations for splice junction prediction.
Dutta A; Dubey T; Singh KK; Anand A
Comput Biol Chem; 2018 Jun; 74():434-441. PubMed ID: 29580738
[TBL] [Abstract][Full Text] [Related]
13. Two-pass alignment improves novel splice junction quantification.
Veeneman BA; Shukla S; Dhanasekaran SM; Chinnaiyan AM; Nesvizhskii AI
Bioinformatics; 2016 Jan; 32(1):43-9. PubMed ID: 26519505
[TBL] [Abstract][Full Text] [Related]
14. Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach.
Zhang Y; Liu X; MacLeod J; Liu J
BMC Genomics; 2018 Dec; 19(1):971. PubMed ID: 30591034
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. iMapSplice: Alleviating reference bias through personalized RNA-seq alignment.
Liu X; MacLeod JN; Liu J
PLoS One; 2018; 13(8):e0201554. PubMed ID: 30096157
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. 2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.
Parker MT; Knop K; Barton GJ; Simpson GG
Genome Biol; 2021 Mar; 22(1):72. PubMed ID: 33648554
[TBL] [Abstract][Full Text] [Related]
19. IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data.
Bai Y; Ji S; Wang Y
BMC Genomics; 2015; 16 Suppl 2(Suppl 2):S9. PubMed ID: 25707295
[TBL] [Abstract][Full Text] [Related]
20. Supersplat--spliced RNA-seq alignment.
Bryant DW; Shen R; Priest HD; Wong WK; Mockler TC
Bioinformatics; 2010 Jun; 26(12):1500-5. PubMed ID: 20410051
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
