Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (Q21284304)

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English	Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives	scientific article

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scholarly article

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Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (English)

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object named as

Quan Wang

3

author given names

Quan

author last names

Wang

1 reference

Dimensions Publication ID

20 August 2022

object named as

Qingguo Wang

2

author given names

Qingguo

author last names

Wang

1 reference

Dimensions Publication ID

20 August 2022

object named as

Min Zhao

1

author given names

Min

author last names

Zhao

1 reference

Dimensions Publication ID

20 August 2022

4

object named as

Peilin Jia

author given names

Peilin

author last names

Jia

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Dimensions Publication ID

20 August 2022

5

object named as

Zhongming Zhao

author given names

Zhongming

author last names

Zhao

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Dimensions Publication ID

20 August 2022

language of work or name

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publication date

2013

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BMC Bioinformatics

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14 Suppl 11

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Suppl 11

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S1

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copyright license

Creative Commons Attribution 2.0 Generic

1 September 2013

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April 2022 Public Data File from Crossref

copyright status

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describes a project that uses

massive parallel sequencing

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based on heuristic

inferred from title

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Mapping copy number variation by population-scale genome sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Exome sequencing identifies the cause of a mendelian disorder

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Accurate whole human genome sequencing using reversible terminator chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Paired-end mapping reveals extensive structural variation in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Global variation in copy number in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Sequencing technologies - the next generation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Identification of common molecular subsequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Detection of large-scale variation in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

Large-scale copy number polymorphism in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

19 March 2017

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

7 April 2017

The landscape of somatic copy-number alteration across human cancers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

7 April 2017

Next-generation DNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

7 April 2017

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

7 April 2017

Circular binary segmentation for the analysis of array-based DNA copy number data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

7 April 2017

Advances in understanding cancer genomes through second-generation sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

10 May 2017

CNVeM: copy number variation detection using uncertainty of read mapping

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Statistical challenges associated with detecting copy number variations with next-generation sequencing.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

A regression model for estimating DNA copy number applied to capture sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Copy number variation detection and genotyping from exome sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

CONTRA: copy number analysis for targeted resequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

An integrative probabilistic model for identification of structural variation in sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Read count approach for DNA copy number variants detection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Simultaneous structural variation discovery among multiple paired-end sequenced genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Identification of genomic indels and structural variations using split reads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Field guide to next-generation DNA sequencers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Accurate and exact CNV identification from targeted high-throughput sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Genome structural variation discovery and genotyping

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

A window into third-generation sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

rSW-seq: algorithm for detection of copy number alterations in deep sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

mrsFAST: a cache-oblivious algorithm for short-read mapping.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

FRT-seq: amplification-free, strand-specific transcriptome sequencing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Computational methods for discovering structural variation with next-generation sequencing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Personalized copy number and segmental duplication maps using next-generation sequencing.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

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12 September 2017

A geometric approach for classification and comparison of structural variants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

High-resolution mapping of copy-number alterations with massively parallel sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Methods and strategies for analyzing copy number variation using DNA microarrays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Accurate and reliable high-throughput detection of copy number variation in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Copy number variation: new insights in genome diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

Assembly of microarrays for genome-wide measurement of DNA copy number

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

12 September 2017

De novo assembly and genotyping of variants using colored de Bruijn graphs

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

27 September 2017

Detecting copy number variation with mated short reads

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

30 May 2018

Sensitive and accurate detection of copy number variants using read depth of coverage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

30 May 2018

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

30 May 2018

Challenges for CNV interpretation in clinical molecular karyotyping: lessons learned from a 1001 sample experience

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https://api.crossref.org/works/10.1186%2F1471-2105-14-S11-S1

21 January 2018

De novo detection of copy number variation by co-assembly.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

29 November 2018

MSB: a mean-shift-based approach for the analysis of structural variation in the genome

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3846878

29 November 2018

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10.1186/1471-2105-14-S11-S1

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Consolidated OpenCitations Corpus – April 2017

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journals/bmcbi/ZhaoWWJZ13

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DBLP Dataset 2021-01-02

28 January 2021

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Consolidated OpenCitations Corpus – April 2017

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