(Q36363386)

10 January 2018

title

ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data (English)

1 reference

10 January 2018

0 references

1 reference

You Li

1

1 reference

10 January 2018

Tayla B Heavican

2

1 reference

10 January 2018

Neetha N Vellichirammal

3

1 reference

10 January 2018

Javeed Iqbal

4

1 reference

10 January 2018

Chittibabu Guda

5

1 reference

10 January 2018

language of work or name

English

0 references

publication date

2 May 2017

1 reference

10 January 2018

published in

Nucleic Acids Research

1 reference

10 January 2018

volume

45

1 reference

10 January 2018

issue

13

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10 January 2018

page(s)

e120

1 reference

10 January 2018

Creative Commons Attribution-NonCommercial 4.0 International

copyright license

start time

2 May 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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28 June 2018

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RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas.

28 June 2018

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Chimeric RNAs generated by intergenic splicing in normal and cancer cells

28 June 2018

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28 June 2018

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The SMRT coregulator enhances growth of estrogen receptor-α-positive breast cancer cells by promotion of cell cycle progression and inhibition of apoptosis

28 June 2018

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Fusion genes in solid tumors: an emerging target for cancer diagnosis and treatment

28 June 2018

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State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

28 June 2018

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SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

28 June 2018

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Next-generation phylogenomics

28 June 2018

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The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma

28 June 2018

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New and continuing developments at PROSITE.

28 June 2018

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STAR: ultrafast universal RNA-seq aligner

28 June 2018

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Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Primer3--new capabilities and interfaces

28 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Improved survival in chronic myeloid leukemia since the introduction of imatinib therapy: a single-institution historical experience

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Putative tumour-suppressor gene DAB2 is frequently down regulated by promoter hypermethylation in nasopharyngeal carcinoma

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

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28 June 2018

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Fusion genes and chromosome translocations in the common epithelial cancers

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Chimeric transcript discovery by paired-end transcriptome sequencing

28 June 2018

1 reference

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28 June 2018

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Loss of the SMRT/NCoR2 corepressor correlates with JAG2 overexpression in multiple myeloma

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

An introduction to artificial neural networks in bioinformatics--application to complex microarray and mass spectrometry datasets in cancer studies

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

TopHat: discovering splice junctions with RNA-Seq

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Inhibition of MAPK-signaling pathway promotes the interaction of the corepressor SMRT with the human androgen receptor and mediates repression of prostate cancer cell growth in the presence of antiandrogens

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Transcriptome sequencing to detect gene fusions in cancer

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

The impact of translocations and gene fusions on cancer causation

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Galaxy: a platform for interactive large-scale genome analysis

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

The SANT domain: a unique histone-tail-binding module?

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

IkappaBalpha and p65 regulate the cytoplasmic shuttling of nuclear corepressors: cross-talk between Notch and NFkappaB pathways

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Post-transcriptional mechanisms in BCR/ABL leukemogenesis: role of shuttling RNA-binding proteins

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

The HUGO Gene Nomenclature Committee (HGNC).

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Fusion genes in leukemia: an emerging network

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

CGP 57148, a tyrosine kinase inhibitor, inhibits the growth of cells expressing BCR-ABL, TEL-ABL, and TEL-PDGFR fusion proteins

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Identification of common molecular subsequences

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Over- and under-representation of short oligonucleotides in DNA sequences

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Aberrant hypermethylation and reduced expression of disabled-2 promote the development of lung cancers.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Novel 5' fusion partners of ETV1 and ETV4 in prostate cancer

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Dynamic modeling of imatinib-treated chronic myeloid leukemia: functional insights and clinical implications.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

CD28 stimulation regulates its association with N-ethylmaleimide-sensitive fusion protein and other proteins involved in vesicle sorting

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

NK cell triggering by the human costimulatory molecules CD80 and CD86

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737728

Fusion of ETV6 with an intronic sequence of the BAZ2A gene in a paediatric pre-B acute lymphoblastic leukaemia with a cryptic chromosome 12 rearrangement

21 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28472320

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The minute chromosome (Phl) in chronic granulocytic leukemia

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28472320

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKX315

1 reference

10 January 2018

PMC publication ID

5737728

1 reference

10 January 2018

PubMed publication ID

28472320

1 reference

10 January 2018