160 related articles for article (PubMed ID: 21478487)
1. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
McPherson A; Wu C; Hajirasouliha I; Hormozdiari F; Hach F; Lapuk A; Volik S; Shah S; Collins C; Sahinalp SC
Bioinformatics; 2011 Jun; 27(11):1481-8. PubMed ID: 21478487
[TBL] [Abstract][Full Text] [Related]
2. Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.
Benelli M; Pescucci C; Marseglia G; Severgnini M; Torricelli F; Magi A
Bioinformatics; 2012 Dec; 28(24):3232-9. PubMed ID: 23093608
[TBL] [Abstract][Full Text] [Related]
3. nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
McPherson A; Wu C; Wyatt AW; Shah S; Collins C; Sahinalp SC
Genome Res; 2012 Nov; 22(11):2250-61. PubMed ID: 22745232
[TBL] [Abstract][Full Text] [Related]
4. Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.
Abate F; Acquaviva A; Paciello G; Foti C; Ficarra E; Ferrarini A; Delledonne M; Iacobucci I; Soverini S; Martinelli G; Macii E
Bioinformatics; 2012 Aug; 28(16):2114-21. PubMed ID: 22711792
[TBL] [Abstract][Full Text] [Related]
5. Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification.
Hafstað V; Häkkinen J; Larsson M; Staaf J; Vallon-Christersson J; Persson H
BMC Genomics; 2023 Dec; 24(1):783. PubMed ID: 38110872
[TBL] [Abstract][Full Text] [Related]
6. INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Zhang J; White NM; Schmidt HK; Fulton RS; Tomlinson C; Warren WC; Wilson RK; Maher CA
Genome Res; 2016 Jan; 26(1):108-18. PubMed ID: 26556708
[TBL] [Abstract][Full Text] [Related]
7. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.
Liu S; Tsai WH; Ding Y; Chen R; Fang Z; Huo Z; Kim S; Ma T; Chang TY; Priedigkeit NM; Lee AV; Luo J; Wang HW; Chung IF; Tseng GC
Nucleic Acids Res; 2016 Mar; 44(5):e47. PubMed ID: 26582927
[TBL] [Abstract][Full Text] [Related]
8. InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.
Okonechnikov K; Imai-Matsushima A; Paul L; Seitz A; Meyer TF; Garcia-Alcalde F
PLoS One; 2016; 11(12):e0167417. PubMed ID: 27907167
[TBL] [Abstract][Full Text] [Related]
9. Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines.
Ha KC; Lalonde E; Li L; Cavallone L; Natrajan R; Lambros MB; Mitsopoulos C; Hakas J; Kozarewa I; Fenwick K; Lord CJ; Ashworth A; Vincent-Salomon A; Basik M; Reis-Filho JS; Majewski J; Foulkes WD
BMC Med Genomics; 2011 Oct; 4():75. PubMed ID: 22032724
[TBL] [Abstract][Full Text] [Related]
10. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Kinsella M; Harismendy O; Nakano M; Frazer KA; Bafna V
Bioinformatics; 2011 Apr; 27(8):1068-75. PubMed ID: 21330288
[TBL] [Abstract][Full Text] [Related]
11. FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.
Liu C; Ma J; Chang CJ; Zhou X
BMC Bioinformatics; 2013 Jun; 14():193. PubMed ID: 23768108
[TBL] [Abstract][Full Text] [Related]
12. Computational identification of micro-structural variations and their proteogenomic consequences in cancer.
Lin YY; Gawronski A; Hach F; Li S; Numanagic I; Sarrafi I; Mishra S; McPherson A; Collins CC; Radovich M; Tang H; Sahinalp SC
Bioinformatics; 2018 May; 34(10):1672-1681. PubMed ID: 29267878
[TBL] [Abstract][Full Text] [Related]
13. FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution.
Newman AM; Bratman SV; Stehr H; Lee LJ; Liu CL; Diehn M; Alizadeh AA
Bioinformatics; 2014 Dec; 30(23):3390-3. PubMed ID: 25143292
[TBL] [Abstract][Full Text] [Related]
14. Overview of Fusion Detection Strategies Using Next-Generation Sequencing.
Schröder J; Kumar A; Wong SQ
Methods Mol Biol; 2019; 1908():125-138. PubMed ID: 30649725
[TBL] [Abstract][Full Text] [Related]
15. Open-access synthetic spike-in mRNA-seq data for cancer gene fusions.
Tembe WD; Pond SJ; Legendre C; Chuang HY; Liang WS; Kim NE; Montel V; Wong S; McDaniel TK; Craig DW; Carpten JD
BMC Genomics; 2014 Sep; 15(1):824. PubMed ID: 25266161
[TBL] [Abstract][Full Text] [Related]
16. Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data.
Hoogstrate Y; Komor MA; Böttcher R; van Riet J; van de Werken HJG; van Lieshout S; Hoffmann R; van den Broek E; Bolijn AS; Dits N; Sie D; van der Meer D; Pepers F; Bangma CH; van Leenders GJLH; Smid M; French PJ; Martens JWM; van Workum W; van der Spek PJ; Janssen B; Caldenhoven E; Rausch C; de Jong M; Stubbs AP; Meijer GA; Fijneman RJA; Jenster GW
Gigascience; 2021 Dec; 10(12):. PubMed ID: 34891161
[TBL] [Abstract][Full Text] [Related]
17. SQUID: transcriptomic structural variation detection from RNA-seq.
Ma C; Shao M; Kingsford C
Genome Biol; 2018 Apr; 19(1):52. PubMed ID: 29650026
[TBL] [Abstract][Full Text] [Related]
18. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
McPherson A; Hormozdiari F; Zayed A; Giuliany R; Ha G; Sun MG; Griffith M; Heravi Moussavi A; Senz J; Melnyk N; Pacheco M; Marra MA; Hirst M; Nielsen TO; Sahinalp SC; Huntsman D; Shah SP
PLoS Comput Biol; 2011 May; 7(5):e1001138. PubMed ID: 21625565
[TBL] [Abstract][Full Text] [Related]
19. RNA-Seq mapping and detection of gene fusions with a suffix array algorithm.
Sakarya O; Breu H; Radovich M; Chen Y; Wang YN; Barbacioru C; Utiramerur S; Whitley PP; Brockman JP; Vatta P; Zhang Z; Popescu L; Muller MW; Kudlingar V; Garg N; Li CY; Kong BS; Bodeau JP; Nutter RC; Gu J; Bramlett KS; Ichikawa JK; Hyland FC; Siddiqui AS
PLoS Comput Biol; 2012; 8(4):e1002464. PubMed ID: 22496636
[TBL] [Abstract][Full Text] [Related]
20. FUSIM: a software tool for simulating fusion transcripts.
Bruno AE; Miecznikowski JC; Qin M; Wang J; Liu S
BMC Bioinformatics; 2013 Jan; 14():13. PubMed ID: 23323884
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]