-
1
-
-
79951970227
-
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
-
Abyzov, A. et al. (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res., 21, 974-33.
-
(2011)
Genome Res.
, vol.21
, pp. 974-1033
-
-
Abyzov, A.1
-
2
-
-
79954672317
-
Genome structural variation discovery and genotyping
-
Alkan, C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363-33.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 363-433
-
-
Alkan, C.1
-
3
-
-
70349556543
-
Personalized copy number and segmental duplication maps using next-generation sequencing
-
Alkan, C. et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41, 1061-33.
-
(2009)
Nat. Genet.
, vol.41
, pp. 1061-2043
-
-
Alkan, C.1
-
4
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
Aird, D. et al. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol., 12, R18.
-
(2011)
Genome Biol.
, vol.12
-
-
Aird, D.1
-
5
-
-
84861548193
-
Summarizing and correction for GC-content bias in high throughput sequencing
-
doi:10.1093/nar/gks001
-
Benjamini, Y. and Speed, T.P. (2012) Summarizing and correction for GC-content bias in high throughput sequencing. Nucleic Acids Res., 40, e72. doi:10.1093/nar/gks001.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Benjamini, Y.1
Speed, T.P.2
-
6
-
-
84856561659
-
Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data
-
Boeva, V. et al. (2012) Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics, 28, 423-33.
-
(2012)
Bioinformatics
, vol.28
, pp. 423-433
-
-
Boeva, V.1
-
7
-
-
69549116107
-
BreakDancer: An algorithm for high resolution mapping of genomic structural variation
-
Chen, K. et al. (2009) BreakDancer: an algorithm for high resolution mapping of genomic structural variation. Nat. Methods, 6, 677-33.
-
(2009)
Nat. Methods
, vol.6
, pp. 677-733
-
-
Chen, K.1
-
8
-
-
58149218240
-
High-resolution mapping of copy-number alterations with massively parallel sequencing
-
Chiang, D.Y. et al. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-33.
-
(2009)
Nat. Methods
, vol.6
, pp. 99-33
-
-
Chiang, D.Y.1
-
10
-
-
77950461601
-
Origins and functional impact of copy number variation in the human genome
-
Conrad, D.F. et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-33.
-
(2010)
Nature
, vol.464
, pp. 704-733
-
-
Conrad, D.F.1
-
11
-
-
77954402321
-
Inversion variants in the human genome: Role in disease and genome architecture
-
Feuk, L. (2010) Inversion variants in the human genome: role in disease and genome architecture. Genome Med., 2, 11.
-
(2010)
Genome Med.
, vol.2
, pp. 11
-
-
Feuk, L.1
-
12
-
-
79952194317
-
Discovery and genotyping of genome structural polymorphism by sequencing on population scale
-
Handsaker, R.E. et al. (2011) Discovery and genotyping of genome structural polymorphism by sequencing on population scale. Nat. Genet., 43, 269-33.
-
(2011)
Nat. Genet.
, vol.43
, pp. 269-333
-
-
Handsaker, R.E.1
-
13
-
-
65449144325
-
Evaluation of next generation sequencing platforms for population targeted sequencing studies
-
doi: 10.1186/gb-2009-10-3-r32
-
Harismendy, O. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, R32. doi: 10.1186/gb-2009-10-3-r32.
-
(2009)
Genome Biol.
, vol.10
-
-
Harismendy, O.1
-
14
-
-
79957842730
-
Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions
-
He, D. et al. (2011) Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions. Bioinformatics, 27, 1513-33.
-
(2011)
Bioinformatics
, vol.27
, pp. 1513-1533
-
-
He, D.1
-
15
-
-
67650064593
-
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
-
Hormozdiari, F. et al. (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19, 1270-33.
-
(2009)
Genome Res.
, vol.19
, pp. 1270-2243
-
-
Hormozdiari, F.1
-
16
-
-
84856246802
-
De novo assembly and genotyping of variants using colored de Bruijn graphs
-
Iqbal, Z. et al. (2011) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet., 44, 226-33.
-
(2011)
Nat. Genet.
, vol.44
, pp. 226-233
-
-
Iqbal, Z.1
-
17
-
-
62549131646
-
PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
-
Korbel, J. et al. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
-
(2009)
Genome Biol.
, vol.10
-
-
Korbel, J.1
-
18
-
-
79952088032
-
A computer simulator for assessing different challenges and strategies of de novo sequence assembly
-
Knudsen, B. et al. (2010) A computer simulator for assessing different challenges and strategies of de novo sequence assembly. Genes, 1, 263-33.
-
(2010)
Genes
, vol.1
, pp. 263-333
-
-
Knudsen, B.1
-
19
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li, H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-33.
-
(2008)
Genome Res.
, vol.18
, pp. 1851-2843
-
-
Li, H.1
-
20
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li, R. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-33.
-
(2010)
Genome Res.
, vol.20
, pp. 265-333
-
-
Li, R.1
-
21
-
-
52949141845
-
Integrated detection and population-genetic analysis of SNPs and copy number variation
-
McCarroll, S.A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-33.
-
(2008)
Nat. Genet.
, vol.40
, pp. 1166-2143
-
-
McCarroll, S.A.1
-
22
-
-
69749090013
-
Sequence and structural variation in a human genome uncovered by massively parallel ligation sequencing using two-base encoding
-
McKernan, K.J. et al. (2009) Sequence and structural variation in a human genome uncovered by massively parallel ligation sequencing using two-base encoding. Genome Res., 19, 1527-33.
-
(2009)
Genome Res.
, vol.19
, pp. 1527-1533
-
-
McKernan, K.J.1
-
23
-
-
70449704529
-
Computational methods for discovering structural variation with next-generation sequencing
-
Medvedev, P. et al. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6 (11 Suppl.), S13-S20.
-
(2009)
Nat. Methods
, vol.6
, Issue.11 SUPPL.
-
-
Medvedev, P.1
-
24
-
-
78649309503
-
Detecting copy number variation with mated short reads
-
Medvedev, P. et al. (2010) Detecting copy number variation with mated short reads. Genome Res., 20, 1613-33.
-
(2010)
Genome Res.
, vol.20
, pp. 1613-1633
-
-
Medvedev, P.1
-
25
-
-
72849144434
-
Sequencing technologies\the next generation
-
Metzker, M.L. (2010) Sequencing technologies\the next generation. Nat. Rev. Genet., 11, 31-33.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 31-33
-
-
Metzker, M.L.1
-
26
-
-
84975804424
-
Mapping copy number variation by population-scale genome sequencing
-
Mills, R.E. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-33.
-
(2011)
Nature
, vol.470
, pp. 59-33
-
-
Mills, R.E.1
-
27
-
-
77952296952
-
Towards a comprehensive structural variation map of an individual human genome
-
doi: 10.1186/gb-2010-11-5-r52
-
Pang, A.W. et al. (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol., 11, R52. doi: 10.1186/gb-2010-11- 5-r52.
-
(2010)
Genome Biol.
, vol.11
-
-
Pang, A.W.1
-
28
-
-
0035859921
-
An Eulerian path approach to DNA fragment assembly
-
Pevzner, P.A. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748-33.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 9748-10743
-
-
Pevzner, P.A.1
-
29
-
-
16644381328
-
Comparative genome assembly
-
Pop, M. et al. (2004) Comparative genome assembly. Brief. Bioinformatics, 5, 237-33.
-
(2004)
Brief. Bioinformatics
, vol.5
, pp. 237-333
-
-
Pop, M.1
-
30
-
-
77951860138
-
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
-
Quinlan, A.R. et al. (2010) Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res., 20, 623-33.
-
(2010)
Genome Res.
, vol.20
, pp. 623-633
-
-
Quinlan, A.R.1
-
31
-
-
80053446554
-
Exome sequencing-based copy number variation and loss of heterozygosity detection: ExomeCNV
-
Sathirapongsasuti, J.F. et al. (2011) Exome sequencing-based copy number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics, 27, 2648-33.
-
(2011)
Bioinformatics
, vol.27
, pp. 2648-3643
-
-
Sathirapongsasuti, J.F.1
-
32
-
-
78650868150
-
A window into third-generation sequencing
-
Schadt, E.E. et al. (2010) A window into third-generation sequencing. Hum. Mol. Genet., 19, R227-R240.
-
(2010)
Hum. Mol. Genet.
, vol.19
-
-
Schadt, E.E.1
-
33
-
-
77956279237
-
Assembly of large genomes using second generation sequencing
-
Schatz, M.C. et al. (2010) Assembly of large genomes using second generation sequencing. Genome Res., 20, 1165-33.
-
(2010)
Genome Res.
, vol.20
, pp. 1165-2143
-
-
Schatz, M.C.1
-
34
-
-
84866240316
-
Change-point model on nonhomogeneous poisson processes with application in copy number profiling by next-generation DNA sequencing
-
Shen, J.J. and Zhang, N. (2012) Change-point model on nonhomogeneous poisson processes with application in copy number profiling by next-generation DNA sequencing. Ann. Appl. Stat., 6, 476-33.
-
(2012)
Ann. Appl. Stat.
, vol.6
, pp. 476-533
-
-
Shen, J.J.1
Zhang, N.2
-
35
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-33.
-
(2009)
Genome Res.
, vol.19
, pp. 1117-1133
-
-
Simpson, J.T.1
-
36
-
-
78049412267
-
Diversity of human copy number variation and multicopy genes
-
Sudmant, P.H. et al. (2010) Diversity of human copy number variation and multicopy genes. Science, 330, 641-33.
-
(2010)
Science
, vol.330
, pp. 641-733
-
-
Sudmant, P.H.1
-
37
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
The 1000 Genomes Project Consortium.
-
The 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-33.
-
(2010)
Nature
, vol.467
, pp. 1061-2043
-
-
-
38
-
-
83855165105
-
Repetitive DNA and next-generation sequencing: Computational challenges and solutions
-
Treangen, T.J. and Salzberg, S.L. (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet., 13, 36-33.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 36-33
-
-
Treangen, T.J.1
Salzberg, S.L.2
-
39
-
-
35948984173
-
PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP geno-typing data
-
Wang, K. et al. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP geno-typing data. Genome Res., 17, 1665-33.
-
(2007)
Genome Res.
, vol.17
, pp. 1665-2643
-
-
Wang, K.1
-
40
-
-
55549097849
-
The diploid genome sequence of an Asian individual
-
Wang, J. et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-33.
-
(2008)
Nature
, vol.456
, pp. 60-33
-
-
Wang, J.1
-
41
-
-
79955004110
-
Detecting structural variations in the human genome using next generation sequencing
-
Xi, R. et al. (2011) Detecting structural variations in the human genome using next generation sequencing. Brief. Funct. Genomics, 9, 405-33.
-
(2011)
Brief. Funct. Genomics
, vol.9
, pp. 405-433
-
-
Xi, R.1
-
42
-
-
64849083125
-
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
-
Xie, C. and Tammi, M.T. (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics, 10, 80.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 80
-
-
Xie, C.1
Tammi, M.T.2
-
43
-
-
70350694443
-
Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
-
Ye, K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-33.
-
(2009)
Bioinformatics
, vol.25
, pp. 2865-3843
-
-
Ye, K.1
-
44
-
-
69749122557
-
Sensitive and accurate detection of copy number variants using read depth of coverage
-
Yoon, S. et al. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-33.
-
(2009)
Genome Res.
, vol.19
, pp. 1586-2543
-
-
Yoon, S.1
-
45
-
-
77955044283
-
SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
-
Zeitouni, B. et al. (2010) SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics, 26, 1895-33.
-
(2010)
Bioinformatics
, vol.26
, pp. 1895-2843
-
-
Zeitouni, B.1
-
46
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
-
(2008)
Genome Res.
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
|