Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 76

1.

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.

2.

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.

3.

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.

4.

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W.

Bioinformatics. 2011 Jul 15;27(14):1922-8. doi: 10.1093/bioinformatics/btr310. Epub 2011 May 18.

PMID:
21593131
5.

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 15;28(16):2114-21. doi: 10.1093/bioinformatics/bts334. Epub 2012 Jun 17.

PMID:
22711792
6.

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery.

Piazza R, Pirola A, Spinelli R, Valletta S, Redaelli S, Magistroni V, Gambacorti-Passerini C.

Nucleic Acids Res. 2012 Sep;40(16):e123. doi: 10.1093/nar/gks394. Epub 2012 May 8.

7.

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.

8.

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
9.

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.

Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.

Nucleic Acids Res. 2011 Aug;39(15):e100. doi: 10.1093/nar/gkr362. Epub 2011 May 27.

10.

FUSIM: a software tool for simulating fusion transcripts.

Bruno AE, Miecznikowski JC, Qin M, Wang J, Liu S.

BMC Bioinformatics. 2013 Jan 16;14:13. doi: 10.1186/1471-2105-14-13.

11.

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Wang L, Feng Z, Wang X, Wang X, Zhang X.

Bioinformatics. 2010 Jan 1;26(1):136-8. doi: 10.1093/bioinformatics/btp612. Epub 2009 Oct 24.

PMID:
19855105
12.

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.

13.

State-of-the-art fusion-finder algorithms sensitivity and specificity.

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

Biomed Res Int. 2013;2013:340620. doi: 10.1155/2013/340620. Epub 2013 Feb 17.

14.

Novel software package for cross-platform transcriptome analysis (CPTRA).

Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. doi: 10.1186/1471-2105-10-S11-S16.

15.

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
16.

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.

Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF.

Bioinformatics. 2013 Mar 1;29(5):649-51. doi: 10.1093/bioinformatics/btt011. Epub 2013 Jan 12.

17.

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 Dec 1;11(12):e0167417. doi: 10.1371/journal.pone.0167417. eCollection 2016.

18.

ChimeraScan: a tool for identifying chimeric transcription in sequencing data.

Iyer MK, Chinnaiyan AM, Maher CA.

Bioinformatics. 2011 Oct 15;27(20):2903-4. doi: 10.1093/bioinformatics/btr467. Epub 2011 Aug 11.

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

20.

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. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10.

Supplemental Content

Support Center