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Detection of Genomic Structural Variants from Next-Generation Sequencing Data
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4479793
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26161383%20AND%20SRC:MED&resulttype=core&format=json
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19 February 2020
review article
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title
Detection of Genomic Structural Variants from Next-Generation Sequencing Data
(English)
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Europe PubMed Central
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4479793
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19 February 2020
author
Romina D'Aurizio
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2
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4479793
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19 February 2020
Alberto Magi
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3
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Europe PubMed Central
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4479793
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26161383%20AND%20SRC:MED&resulttype=core&format=json
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19 February 2020
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Lorenzo Tattini
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4479793
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19 February 2020
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25 June 2015
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4479793
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19 February 2020
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Frontiers in Bioengineering and Biotechnology
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Europe PubMed Central
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4479793
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26161383%20AND%20SRC:MED&resulttype=core&format=json
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19 February 2020
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3
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Europe PubMed Central
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4479793
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19 February 2020
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19 February 2020
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Simultaneous structural variation discovery among multiple paired-end sequenced genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 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
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Overview of DNA sequencing strategies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Nanopore sensors for nucleic acid analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Assemblathon 1: a competitive assessment of de novo short read assembly methods
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
CREST maps somatic structural variation in cancer genomes with base-pair resolution.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Landscape of next-generation sequencing technologies.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Genome structural variation discovery and genotyping
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Quake: quality-aware detection and correction of sequencing errors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Limitations of next-generation genome sequence assembly
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
A window into third-generation sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
rSW-seq: algorithm for detection of copy number alterations in deep sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
mrsFAST: a cache-oblivious algorithm for short-read mapping.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Efficient construction of an assembly string graph using the FM-index
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
A shifting level model algorithm that identifies aberrations in array-CGH data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Personalized copy number and segmental duplication maps using next-generation sequencing.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Copy number variation in human health, disease, and evolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
A geometric approach for classification and comparison of structural variants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Evaluation of next generation sequencing platforms for population targeted sequencing studies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
High-resolution mapping of copy-number alterations with massively parallel sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
A faster circular binary segmentation algorithm for the analysis of array CGH data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
An initial map of insertion and deletion (INDEL) variation in the human genome.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
The phusion assembler
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
Assembly of microarrays for genome-wide measurement of DNA copy number
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
29 September 2017
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
CLEVER: clique-enumerating variant finder
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
Detecting copy number variation with mated short reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
Sensitive and accurate detection of copy number variants using read depth of coverage
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
The fragment assembly string graph
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
2 June 2018
Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
27 November 2018
De novo detection of copy number variation by co-assembly.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
27 November 2018
PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
27 November 2018
MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4479793
retrieved
27 November 2018
Identifiers
DOI
10.3389/FBIOE.2015.00092
2 references
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3428091
stated in
Europe PubMed Central
PMCID
4479793
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26161383%20AND%20SRC:MED&resulttype=core&format=json
retrieved
19 February 2020
OpenCitations bibliographic resource ID
3428091
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3428091
PMCID
4479793
2 references
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3428091
stated in
Europe PubMed Central
PMCID
4479793
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26161383%20AND%20SRC:MED&resulttype=core&format=json
retrieved
19 February 2020
PubMed ID
26161383
2 references
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3428091
stated in
Europe PubMed Central
PMCID
4479793
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26161383%20AND%20SRC:MED&resulttype=core&format=json
retrieved
19 February 2020
ResearchGate publication ID
279223060
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