-
1
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
1000 Genomes Project Consortium. doi: 10.1038/nature09534
-
1000 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073. doi: 10.1038/nature09534
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
2
-
-
79951970227
-
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
-
doi: 10.1101/gr.114876.110
-
Abyzov, A., Urban, A. E., Snyder, M., and Gerstein, M. (2011). CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974-984. doi: 10.1101/gr.114876.110
-
(2011)
Genome Res.
, vol.21
, pp. 974-984
-
-
Abyzov, A.1
Urban, A.E.2
Snyder, M.3
Gerstein, M.4
-
3
-
-
79954672317
-
Genome structural variation discovery and genotyping
-
doi: 10.1038/nrg2958
-
Alkan, C., Coe, B. P., and Eichler, E. E. (2011). Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363-376. doi: 10.1038/nrg2958
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 363-376
-
-
Alkan, C.1
Coe, B.P.2
Eichler, E.E.3
-
4
-
-
58149178561
-
Autdb: a gene reference resource for autism research
-
doi: 10.1093/nar/gkn835
-
Basu, S. N., Kollu, R., and Banerjee-Basu, S. (2009). Autdb: a gene reference resource for autism research. Nucleic Acids Res. 37, D832-D836. doi: 10.1093/nar/gkn835
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Basu, S.N.1
Kollu, R.2
Banerjee-Basu, S.3
-
5
-
-
78651318769
-
Casnp: a database for interrogating copy number alterations of cancer genome from snp array data
-
doi: 10.1093/nar/gkq997
-
Cao, Q., Zhou, M., Wang, X., Meyer, C. A., Zhang, Y., Chen, Z., et al. (2011). Casnp: a database for interrogating copy number alterations of cancer genome from snp array data. Nucleic Acids Res. 39, D968-D974. doi: 10.1093/nar/gkq997
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Cao, Q.1
Zhou, M.2
Wang, X.3
Meyer, C.A.4
Zhang, Y.5
Chen, Z.6
-
6
-
-
34347339520
-
Methods and strategies for analyzing copy number variation using DNA microarrays
-
doi: 10.1038/ng2028
-
Carter, N. P. (2007). Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet. 39(Suppl. 7), S16-S21. doi: 10.1038/ng2028
-
(2007)
Nat. Genet.
, vol.39
, Issue.SUPPL. 7
-
-
Carter, N.P.1
-
7
-
-
69549116107
-
Breakdancer: an algorithm for high-resolution mapping of genomic structural variation
-
doi: 10.1038/nmeth.1363
-
Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., et al. (2009). Breakdancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677-681. doi: 10.1038/nmeth.1363
-
(2009)
Nat. Methods
, vol.6
, pp. 677-681
-
-
Chen, K.1
Wallis, J.W.2
McLellan, M.D.3
Larson, D.E.4
Kalicki, J.M.5
Pohl, C.S.6
-
8
-
-
84867524318
-
Svmš: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data
-
doi: 10.1093/nar/gks606
-
Chiara, M., Pesole, G., and Horner, D. S. (2012). Svmš: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data. Nucleic Acids Res. 40:e145. doi: 10.1093/nar/gks606
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Chiara, M.1
Pesole, G.2
Horner, D.S.3
-
9
-
-
77950461601
-
Origins and functional impact of copy number variation in the human genome
-
doi: 10.1038/nature08516
-
Conrad, D. F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., et al. (2010). Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712. doi: 10.1038/nature08516
-
(2010)
Nature
, vol.464
, pp. 704-712
-
-
Conrad, D.F.1
Pinto, D.2
Redon, R.3
Feuk, L.4
Gokcumen, O.5
Zhang, Y.6
-
10
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation dna sequencing data
-
doi: 10.1038/ng.806
-
DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., et al. (2011). A framework for variation discovery and genotyping using next-generation dna sequencing data. Nat. Genet. 43, 491-498. doi: 10.1038/ng.806
-
(2011)
Nat. Genet.
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
Hartl, C.6
-
11
-
-
33746741125
-
Copy number variation: New insights in genome diversity
-
doi: 10.1101/gr.3677206
-
Freeman, J. L., Perry, G. H., Feuk, L., Redon, R., McCarroll, S. A., Altshuler, D. M., et al. (2006). Copy number variation: New insights in genome diversity. Genome Res. 16, 949-961. doi: 10.1101/gr.3677206
-
(2006)
Genome Res.
, vol.16
, pp. 949-961
-
-
Freeman, J.L.1
Perry, G.H.2
Feuk, L.3
Redon, R.4
McCarroll, S.A.5
Altshuler, D.M.6
-
12
-
-
79952194317
-
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
-
doi: 10.1038/ng.768
-
Handsaker, R. E., Korn, J. M., Nemesh, J., and McCarroll, S. A. (2011). Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat. Genet. 43, 269-276. doi: 10.1038/ng.768
-
(2011)
Nat. Genet.
, vol.43
, pp. 269-276
-
-
Handsaker, R.E.1
Korn, J.M.2
Nemesh, J.3
McCarroll, S.A.4
-
13
-
-
67651098662
-
Mechanisms of change in gene copy number
-
doi: 10.1038/nrg2593
-
Hastings, P. J., Lupski, J. R., Rosenberg, S. M., and Ira, G. (2009). Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551-564. doi: 10.1038/nrg2593
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 551-564
-
-
Hastings, P.J.1
Lupski, J.R.2
Rosenberg, S.M.3
Ira, G.4
-
14
-
-
0032849859
-
Cap3: a dna sequence assembly program
-
doi: 10.1101/gr.9.9.868
-
Huang, X., and Madan, A. (1999). Cap3: a dna sequence assembly program. Genome Res. 9, 868-877. doi: 10.1101/gr.9.9.868
-
(1999)
Genome Res.
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
15
-
-
84870460670
-
Prism: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants
-
doi: 10.1093/bioinformatics/bts484
-
Jiang, Y., Wang, Y., and Brudno, M. (2012). Prism: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics 28, 2576-2583. doi: 10.1093/bioinformatics/bts484
-
(2012)
Bioinformatics
, vol.28
, pp. 2576-2583
-
-
Jiang, Y.1
Wang, Y.2
Brudno, M.3
-
16
-
-
0036226603
-
Blat-the blast-like alignment tool
-
Kent, W. J. (2002). Blat-the blast-like alignment tool. Genome Res. 12, 656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
17
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
doi: 10.1038/nmeth.1923
-
Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with bowtie 2. Nat. Methods 9, 357-359. doi: 10.1038/nmeth.1923
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
18
-
-
84864119729
-
Exploring single-sample snp and indel calling with whole-genome de novo assembly
-
doi: 10.1093/bioinformatics/bts280
-
Li, H. (2012). Exploring single-sample snp and indel calling with whole-genome de novo assembly. Bioinformatics 28, 1838-1844. doi: 10.1093/bioinformatics/bts280
-
(2012)
Bioinformatics
, vol.28
, pp. 1838-1844
-
-
Li, H.1
-
19
-
-
67649884743
-
Fast and accurate short read alignment with burrows-wheeler transform
-
doi: 10.1093/bioinformatics/btp324
-
Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25, 1754-1760. doi: 10.1093/bioinformatics/btp324
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
20
-
-
77949587649
-
Fast and accurate long-read alignment with burrows-wheeler transform
-
doi: 10.1093/bioinformatics/btp698
-
Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics 26, 589-595. doi: 10.1093/bioinformatics/btp698
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
21
-
-
68549104404
-
The sequence Alignment/Map format and SAMtools
-
doi: 10.1093/bioinformatics/btp352
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079. doi: 10.1093/bioinformatics/btp352
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
22
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
doi: 10.1093/bib/bbq015
-
Li, H., and Homer, N. (2010). A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 11, 473-483. doi: 10.1093/bib/bbq015
-
(2010)
Brief Bioinform.
, vol.11
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
23
-
-
79951475133
-
A decade's perspective on DNA sequencing technology
-
doi: 10.1038/nature09796
-
Mardis, E. R. (2011). A decade's perspective on DNA sequencing technology. Nature 470, 198-203. doi: 10.1038/nature09796
-
(2011)
Nature
, vol.470
, pp. 198-203
-
-
Mardis, E.R.1
-
24
-
-
77956295988
-
The genome analysis toolkit: a mapreduce framework for analyzing next-generation dna sequencing data
-
doi: 10.1101/gr.107524.110
-
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., et al. (2010). The genome analysis toolkit: a mapreduce framework for analyzing next-generation dna sequencing data. Genome Res. 20, 1297-1303. doi: 10.1101/gr.107524.110
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
-
25
-
-
78649309503
-
Detecting copy number variation with mated short reads
-
doi: 10.1101/gr.106344.110
-
Medvedev, P., Fiume, M., Dzamba, M., Smith, T., and Brudno, M. (2010). Detecting copy number variation with mated short reads. Genome Res. 20, 1613-1622. doi: 10.1101/gr.106344.110
-
(2010)
Genome Res.
, vol.20
, pp. 1613-1622
-
-
Medvedev, P.1
Fiume, M.2
Dzamba, M.3
Smith, T.4
Brudno, M.5
-
26
-
-
79551621409
-
Readdepth: a parallel r package for detecting copy number alterations from short sequencing reads
-
doi: 10.1371/journal.pone.0016327
-
Miller, C. A., Hampton, O., Coarfa, C., and Milosavljevic, A. (2011). Readdepth: a parallel r package for detecting copy number alterations from short sequencing reads. PLoS ONE 6:e16327. doi: 10.1371/journal.pone.0016327
-
(2011)
PLoS ONE
, vol.6
-
-
Miller, C.A.1
Hampton, O.2
Coarfa, C.3
Milosavljevic, A.4
-
27
-
-
84975804424
-
Mapping copy number variation by population-scale genome sequencing
-
doi: 10.1038/nature09708
-
Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., et al. (2011). Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65. doi: 10.1038/nature09708
-
(2011)
Nature
, vol.470
, pp. 59-65
-
-
Mills, R.E.1
Walter, K.2
Stewart, C.3
Handsaker, R.E.4
Chen, K.5
Alkan, C.6
-
28
-
-
84866440781
-
Delly: structural variant discovery by integrated paired-end and split-read analysis
-
doi: 10.1093/bioinformatics/bts378
-
Rausch, T., Zichner, T., Schlattl, A., StÃijtz, A. M., Benes, V., and Korbel, J. O. (2012). Delly: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339. doi: 10.1093/bioinformatics/bts378
-
(2012)
Bioinformatics
, vol.28
-
-
Rausch, T.1
Zichner, T.2
Schlattl, A.3
Stãijtz, A.M.4
Benes, V.5
Korbel, J.O.6
-
29
-
-
66349083341
-
A geometric approach for classification and comparison of structural variants
-
doi: 10.1093/bioinformatics/btp208
-
Sindi, S., Helman, E., Bashir, A., and Raphael, B. J. (2009). A geometric approach for classification and comparison of structural variants. Bioinformatics 25, i222-i230. doi: 10.1093/bioinformatics/btp208
-
(2009)
Bioinformatics
, vol.25
-
-
Sindi, S.1
Helman, E.2
Bashir, A.3
Raphael, B.J.4
-
30
-
-
84868016827
-
Statistical challenges associated with detecting copy number variations with next-generation sequencing
-
doi: 10.1093/bioinformatics/bts535
-
Teo, S. M., Pawitan, Y., Ku, C. S., Chia, K. S., and Salim, A. (2012). Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics 28, 2711-2718. doi: 10.1093/bioinformatics/bts535
-
(2012)
Bioinformatics
, vol.28
, pp. 2711-2718
-
-
Teo, S.M.1
Pawitan, Y.2
Ku, C.S.3
Chia, K.S.4
Salim, A.5
-
31
-
-
79961007031
-
Crest maps somatic structural variation in cancer genomes with base-pair resolution
-
doi: 10.1038/nmeth.1628
-
Wang, J., Mullighan, C. G., Easton, J., Roberts, S., Heatley, S. L., Ma, J., et al. (2011). Crest maps somatic structural variation in cancer genomes with base-pair resolution. Nat. Methods 8, 652-654. doi: 10.1038/nmeth.1628
-
(2011)
Nat. Methods
, vol.8
, pp. 652-654
-
-
Wang, J.1
Mullighan, C.G.2
Easton, J.3
Roberts, S.4
Heatley, S.L.5
Ma, J.6
-
32
-
-
84874776644
-
A survey of copy-number variation detection tools based on high-throughput sequencing data
-
doi: 10.1002/0471142905.hg0719s75
-
Xi, R., Lee, S., and Park, P. J. (2012). A survey of copy-number variation detection tools based on high-throughput sequencing data. Curr. Protoc. Hum. Genet. 75, 7.19.1-7.19.15. doi: 10.1002/0471142905.hg0719s75
-
(2012)
Curr. Protoc. Hum. Genet.
, vol.75
, pp. 7191-71915
-
-
Xi, R.1
Lee, S.2
Park, P.J.3
-
33
-
-
70350694443
-
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
-
doi: 10.1093/bioinformatics/btp394
-
Ye, K., Schulz, M. H., Long, Q., Apweiler, R., and Ning, Z. (2009). Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871. doi: 10.1093/bioinformatics/btp394
-
(2009)
Bioinformatics
, vol.25
, pp. 2865-2871
-
-
Ye, K.1
Schulz, M.H.2
Long, Q.3
Apweiler, R.4
Ning, Z.5
-
34
-
-
69749122557
-
Sensitive and accurate detection of copy number variants using read depth of coverage
-
doi: 10.1101/gr.092981.109
-
Yoon, S., Xuan, Z., Makarov, V., Ye, K., and Sebat, J. (2009). Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19, 1586-1592. doi: 10.1101/gr.092981.109
-
(2009)
Genome Res.
, vol.19
, pp. 1586-1592
-
-
Yoon, S.1
Xuan, Z.2
Makarov, V.3
Ye, K.4
Sebat, J.5
|