A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection (Q33751476)

29 July 2017

title

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection (English)

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29 July 2017

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29 July 2017

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29 July 2017

Daniel Teupser

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David Langenberger

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Jörg Hackermüller

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Christian Otto

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29 July 2017

Steve Hoffmann

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29 July 2017

Gero Doose

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29 July 2017

Sabina Christ

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29 July 2017

Manfred Kunz

series ordinal

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29 July 2017

Lesca M Holdt

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29 July 2017

publication date

10 February 2014

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29 July 2017

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29 July 2017

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29 July 2017

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29 July 2017

page(s)

R34

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Cell-type specific features of circular RNA expression

29 July 2017

cites work

1 reference

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Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks

14 July 2018

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Circular RNAs are a large class of animal RNAs with regulatory potency

14 July 2018

1 reference

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Natural RNA circles function as efficient microRNA sponges

14 July 2018

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Circular RNAs are abundant, conserved, and associated with ALU repeats

14 July 2018

1 reference

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14 July 2018

1 reference

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Landscape of transcription in human cells

14 July 2018

1 reference

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Novel domain combinations in proteins encoded by chimeric transcripts

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts

14 July 2018

1 reference

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The p53 isoforms are differentially modified by Mdm2.

14 July 2018

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Fast gapped-read alignment with Bowtie 2

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types

14 July 2018

1 reference

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SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

14 July 2018

1 reference

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Transcriptome-wide discovery of circular RNAs in Archaea

14 July 2018

1 reference

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Targeted RNA sequencing reveals the deep complexity of the human transcriptome

14 July 2018

1 reference

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Identification and characterization of a novel non-coding RNA involved in sperm maturation

14 July 2018

1 reference

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

14 July 2018

1 reference

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deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

A novel and well-defined benchmarking method for second generation read mapping

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Stearoyl CoA desaturase (SCD) facilitates proliferation of prostate cancer cells through enhancement of androgen receptor transactivation

14 July 2018

1 reference

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

14 July 2018

1 reference

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A global analysis of C. elegans trans-splicing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

First International p53 Isoforms Meeting: 'p53 isoforms through evolution: from identification to biological function'

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Integrative analysis of the melanoma transcriptome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Fast and SNP-tolerant detection of complex variants and splicing in short reads

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Implications of chimaeric non-co-linear transcripts

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

TopHat: discovering splice junctions with RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

ASTD: The Alternative Splicing and Transcript Diversity database

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Diverse splicing patterns of exonized Alu elements in human tissues

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Trans-splicing and operons

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

BLAT—The BLAST-Like Alignment Tool

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4056463

Circular intronic long noncoding RNAs

14 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FGB-2014-15-2-R34

21 January 2018

Identifiers

DOI

10.1186/GB-2014-15-2-R34

1 reference

Dimensions Publication ID

29 July 2017

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29 July 2017

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