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Results: 1 to 20 of 87

1.

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Kim D, Salzberg SL.

Genome Biol. 2011 Aug 11;12(8):R72. doi: 10.1186/gb-2011-12-8-r72.

PMID:
21835007
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.

PMID:
19289445
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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 27;4:75. doi: 10.1186/1755-8794-4-75.

PMID:
22032724
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

Carrara M, Beccuti M, Cavallo F, Donatelli S, Lazzarato F, Cordero F, Calogero RA.

BMC Bioinformatics. 2013;14 Suppl 7:S2. doi: 10.1186/1471-2105-14-S7-S2. Epub 2013 Apr 22.

PMID:
23815381
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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 15;14:193. doi: 10.1186/1471-2105-14-193.

PMID:
23768108
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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. doi: 10.1371/journal.pcbi.1001138. Epub 2011 May 19.

PMID:
21625565
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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. doi: 10.1371/journal.pcbi.1002464. Epub 2012 Apr 5.

PMID:
22496636
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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 1;29(13):i291-9. doi: 10.1093/bioinformatics/btt216.

PMID:
23812996
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27.

PMID:
20802226
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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 1;27(11):1481-8. doi: 10.1093/bioinformatics/btr184. Epub 2011 Apr 9.

PMID:
21478487
[PubMed - indexed for MEDLINE]
Free Article
11.

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.

Wu J, Zhang W, Huang S, He Z, Cheng Y, Wang J, Lam TW, Peng Z, Yiu SM.

Bioinformatics. 2013 Dec 1;29(23):2971-8. doi: 10.1093/bioinformatics/btt522. Epub 2013 Oct 11.

PMID:
24123671
[PubMed - indexed for MEDLINE]
12.

Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

Kangaspeska S, Hultsch S, Edgren H, Nicorici D, Murumägi A, Kallioniemi O.

PLoS One. 2012;7(10):e48745. doi: 10.1371/journal.pone.0048745. Epub 2012 Oct 31.

PMID:
23119097
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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 15;28(24):3232-9. doi: 10.1093/bioinformatics/bts617. Epub 2012 Oct 23.

PMID:
23093608
[PubMed - indexed for MEDLINE]
Free Article
14.

Fusion gene microarray reveals cancer type-specificity among fusion genes.

Løvf M, Thomassen GO, Bakken AC, Celestino R, Fioretos T, Lind GE, Lothe RA, Skotheim RI.

Genes Chromosomes Cancer. 2011 May;50(5):348-57. doi: 10.1002/gcc.20860. Epub 2011 Feb 8.

PMID:
21305644
[PubMed - indexed for MEDLINE]
15.

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 15;28(4):479-86. doi: 10.1093/bioinformatics/btr712. Epub 2012 Jan 4.

PMID:
22219203
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.

Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, Beesley AH.

PLoS One. 2012;7(6):e39987. doi: 10.1371/journal.pone.0039987. Epub 2012 Jun 27.

PMID:
22761941
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

CLASS: constrained transcript assembly of RNA-seq reads.

Song L, Florea L.

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.

PMID:
23734605
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Identification of fusion genes in breast cancer by paired-end RNA-sequencing.

Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, Rye IH, Nyberg S, Wolf M, Borresen-Dale AL, Kallioniemi O.

Genome Biol. 2011;12(1):R6. doi: 10.1186/gb-2011-12-1-r6. Epub 2011 Jan 19.

PMID:
21247443
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Dissect: detection and characterization of novel structural alterations in transcribed sequences.

Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC.

Bioinformatics. 2012 Jun 15;28(12):i179-87. doi: 10.1093/bioinformatics/bts214.

PMID:
22689759
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016.

PMID:
22383036
[PubMed - indexed for MEDLINE]
Free PMC Article

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