RNA-Seq mapping and detection of gene fusions with a suffix array algorithm (Q34229580)

31 July 2017

RNA-Seq mapping and detection of gene fusions with a suffix array algorithm (English)

1 reference

31 July 2017

0 references

1 reference

3

Milan Radovich

1 reference

31 July 2017

Onur Sakarya

1

1 reference

31 July 2017

Heinz Breu

2

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31 July 2017

Yongzhi Chen

4

1 reference

31 July 2017

Yulei N Wang

5

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31 July 2017

Catalin Barbacioru

6

1 reference

31 July 2017

Sowmi Utiramerur

7

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31 July 2017

Penn P Whitley

8

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31 July 2017

Joel P Brockman

9

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31 July 2017

Paolo Vatta

10

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31 July 2017

Zheng Zhang

11

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31 July 2017

Liviu Popescu

12

1 reference

31 July 2017

Matthew W Muller

13

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31 July 2017

Vidya Kudlingar

14

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31 July 2017

Nriti Garg

15

1 reference

31 July 2017

Chieh-Yuan Li

16

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31 July 2017

Benjamin S Kong

17

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31 July 2017

John P Bodeau

18

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31 July 2017

Robert C Nutter

19

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31 July 2017

Jian Gu

20

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31 July 2017

Kelli S Bramlett

21

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31 July 2017

Jeffrey K Ichikawa

22

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31 July 2017

Fiona C Hyland

23

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31 July 2017

Asim S Siddiqui

24

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31 July 2017

5 April 2012

1 reference

PLOS Computational Biology

31 July 2017

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31 July 2017

8

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31 July 2017

e1002464

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31 July 2017

4

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Creative Commons Attribution 4.0 International

31 July 2017

start time

5 April 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

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

6 July 2018

1 reference

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Estimation of alternative splicing isoform frequencies from RNA-Seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Transcriptional consequences of genomic structural aberrations in breast cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

De novo assembly and analysis of RNA-seq data.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Optimization of de novo transcriptome assembly from next-generation sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Integrative analysis of the melanoma transcriptome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

6 July 2018

Direct RNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Chimeric transcript discovery by paired-end transcriptome sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Circos: an information aesthetic for comparative genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

De novo transcriptome assembly with ABySS.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

mRNA-Seq whole-transcriptome analysis of a single cell

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

TopHat: discovering splice junctions with RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Transcriptome sequencing to detect gene fusions in cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Annotating genomes with massive-scale RNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

RNA-Seq: a revolutionary tool for transcriptomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Alternative isoform regulation in human tissue transcriptomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Optimal spliced alignments of short sequence reads

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Recurrent gene fusions in prostate cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Stem cell transcriptome profiling via massive-scale mRNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Mapping and quantifying mammalian transcriptomes by RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

The transcriptional landscape of the yeast genome defined by RNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

EML4-ALK fusion lung cancer: a rare acquired event

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Expression of variant TMPRSS2/ERG fusion messenger RNAs is associated with aggressive prostate cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Imatinib compared with interferon and low-dose cytarabine for newly diagnosed chronic-phase chronic myeloid leukemia

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Congenital mesoblastic nephroma t(12;15) is associated with ETV6-NTRK3 gene fusion: cytogenetic and molecular relationship to congenital (infantile) fibrosarcoma

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

A novel ETV6-NTRK3 gene fusion in congenital fibrosarcoma

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

Clinical significance of the BCR-ABL fusion gene in adult acute lymphoblastic leukemia: a Cancer and Leukemia Group B Study (8762)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3320572

MicroRNAs and cellular phenotypy

6 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002464

Evaluation of DNA microarray results with quantitative gene expression platforms

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002464

ERBB2, TBX2, RPS6KB1, and MYC alterations in breast tissues of BRCA1 and BRCA2 mutation carriers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002464

Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002464

Suffix Arrays: A New Method for On-Line String Searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002464

Analysis of molecular breakpoint and m-RNA transcripts in a prospective randomized trial of interferon in chronic myeloid leukaemia: no correlation with clinical features, cytogenetic response, duration of chronic phase, or survival

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22496636

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1002464

1 reference

journals/ploscb/SakaryaBRCWBUWBVZPMKGLKBNGBIHS12

31 July 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

31 July 2017

1 reference