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Protocols

FusionSeq specifications

Information


Unique identifier OMICS_01351
Name FusionSeq
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 0.6.1
Stability Stable
Requirements
bowtie, Blat, GSL, BIOS, GD library, ROOT, Homo Sapiens Reference Genome
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Mark Rubin
  • person_outline FusionSeq Team

Additional information


http://info.gersteinlab.org/FusionSeq_FAQ

Publication for FusionSeq

FusionSeq citations

 (9)
library_books

De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion gene transcripts of potential functional significance

2017
BMC Med Genomics
PMCID: 5575902
PMID: 28851357
DOI: 10.1186/s12920-017-0289-7

[…] genes that may be drivers of breast cancer onset and/or progression []., currently available computational methods for chimeric transcript discovery such as tophat-fusion [], snowshoeftd [] and fusionseq [], typically rely upon reference genome mapping of short (50–75 bp) paired-end reads generated by the sequencing of both ends (5′- and 3′-) of an rna or cdna fragment. while these methods […]

library_books

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

2016
Nucleic Acids Res
PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] further dissemination., in recent years, there has been a remarkably concerted effort to develop algorithms and tools for identifying gene fusions from sequencing data. the first dedicated software, fusionseq, was published in 2010 (); by the end of 2012, 15 other tools had been released. at present, we find 30 different methods for identifying gene fusions () (table ), with the contenders […]

library_books

Divergent clonal evolution of castration resistant neuroendocrine prostate cancer

2016
Nat Med
PMCID: 4777652
PMID: 26855148
DOI: 10.1038/nm.4045

[…] levels, respectively. if erg fusion was detected at either dna, mrna, or protein level, the sample was considered positive. for other non-canonical and canonical fusion transcript detection, fusionseq was employed as previously described., to assess cyld deletion in tissues, we developed a dual-color fish assay consisting of a locus specific probe (rp11-327f22) plus reference probe […]

library_books

Functional characterization of BC039389 GATM and KLK4 KRSP1 chimeric read through transcripts which are up regulated in renal cell cancer

2015
BMC Genomics
PMCID: 4422297
PMID: 25888189
DOI: 10.1186/s12864-015-1446-z

[…] expression patterns or functions in general, and in oncogenesis in particular, are poorly understood., we used paired-end rna-seq and a specifically designed computational data analysis pipeline (fusionseq) to nominate read-through events in a small discovery set of renal cell carcinomas (rcc) and confirmed them in a larger validation cohort., 324 read-through events were called overall; […]

library_books

Fusion Transcript Discovery in Formalin Fixed Paraffin Embedded Human Breast Cancer Tissues Reveals a Link to Tumor Progression

2014
PLoS One
PMCID: 3984112
PMID: 24727804
DOI: 10.1371/journal.pone.0094202

[…] transcript. recently published fusions detected using rna-seq data have displayed this discrete expression pattern at acceptor fusion junction sites , . multiple bioinformatics approaches including fusionseq , defuse and tophat-fusion have used expression data in their pipelines and all these methods rely on the analysis of an individual subject. the cohort-based approach described […]

library_books

NTRK1 Fusion in Glioblastoma Multiforme

2014
PLoS One
PMCID: 3960150
PMID: 24647444
DOI: 10.1371/journal.pone.0091940

[…] or progression of the fusion-bearing gbms., to search for novel gene fusions in gbm, we analyzed paired-end rna-seq data of 162 gbm patients, available through tcga . a subset of modules from the fusionseq pipeline was adopted to score potential fusions based on the number of “discordant read pairs.” the discordant read pairs are paired-end reads whose 5′ and 3′ reads map to different genes, […]


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FusionSeq institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA; Department of Urology, Weill Cornell Medical College, New York, NY, USA; Prognosys Biosciences, Inc., La Jolla, CA, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Computer Science, Yale University, New Haven, CT, USA
FusionSeq funding source(s)
Supported by the ‘Yale University Biomedical High-Performance Computing Center’ and NIH grant no. RR19895, a National Cancer Institute grant R01CA125612, a National Human Genome Research Institute grant 5R44HG004237, the Prostate Cancer Foundation, and the Breslin Foundation.

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