Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs (Q33823403)

29 July 2017

title

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs (English)

1 reference

29 July 2017

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1 reference

Vineet Bafna

5

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Olivier Harismendy

series ordinal

2

object named as

Olivier Harismendy

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29 July 2017

Marcus Kinsella

1

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29 July 2017

Masakazu Nakano

series ordinal

3

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29 July 2017

Kelly A Frazer

series ordinal

4

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29 July 2017

language of work or name

English

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publication date

16 February 2011

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29 July 2017

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29 July 2017

volume

27

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29 July 2017

issue

8

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29 July 2017

page(s)

1068-1075

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A probabilistic framework for aligning paired-end RNA-seq data

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Global and unbiased detection of splice junctions from RNA-seq data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Integrative analysis of the melanoma transcriptome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

RNA-Seq gene expression estimation with read mapping uncertainty

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Fusion genes and chromosome translocations in the common epithelial cancers

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Implications of chimaeric non-co-linear transcripts

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

RNA editing in human cancer: review

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Alternative splicing and biological heterogeneity in prostate cancer

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Chimeric transcript discovery by paired-end transcriptome sequencing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

TopHat: discovering splice junctions with RNA-Seq

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Transcriptome sequencing to detect gene fusions in cancer

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

RNA-Seq: a revolutionary tool for transcriptomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Mapping short DNA sequencing reads and calling variants using mapping quality scores

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Mapping and quantifying mammalian transcriptomes by RNA-Seq

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

EML4-ALK fusion lung cancer: a rare acquired event

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Alternative trans-splicing: a novel mode of pre-mRNA processing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Transcription-mediated gene fusion in the human genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

The transcriptional landscape of the mammalian genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

A spliced leader is present on a subset of mRNAs from the human parasite Schistosoma mansoni

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

The frequency and position of Alu repeats in cDNAs, as determined by database searching

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

A trans-spliced leader sequence on actin mRNA in C. elegans

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072550

Fused transcript of abl and bcr genes in chronic myelogenous leukaemia

29 October 2018

1 reference

12 December 2020

Evidence for trans splicing in trypanosomes

1 reference

12 December 2020

Is sequencing enlightenment ending the dark age of the transcriptome?

1 reference

12 December 2020

Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer

1 reference

12 December 2020

10.1093/BIOINFORMATICS/BTR085

Identifiers

DOI

1 reference

journals/bioinformatics/KinsellaHNFB11

29 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

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29 July 2017

1 reference