-
1
-
-
79951970227
-
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
-
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
-
2
-
-
84871380200
-
cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data
-
Bellos, E., Johnson, M. R., and Coin, L. J. (2012). cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data. Genome Biol. 13:R120. doi: 10.1186/gb-2012-13-12-r120
-
(2012)
Genome Biol
, vol.13
-
-
Bellos, E.1
Johnson, M.R.2
Coin, L.J.3
-
3
-
-
84899618905
-
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing
-
Bodian, D. L., McCutcheon, J. N., Kothiyal, P., Huddleston, K. C., Iyer, R. K., Vockley, J. G., et al. (2014). Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. PLoS ONE 9:e94554. doi: 10.1371/journal.pone.0094554
-
(2014)
PLoS ONE
, vol.9
-
-
Bodian, D.L.1
McCutcheon, J.N.2
Kothiyal, P.3
Huddleston, K.C.4
Iyer, R.K.5
Vockley, J.G.6
-
4
-
-
84893695366
-
TIGRA: a targeted iterative graph routing assembler for breakpoint assembly
-
Chen, K., Chen, L., Fan, X., Wallis, J., Ding, L., and Weinstock, G. (2014). TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 24, 310-317. doi: 10.1101/gr.162883.113
-
(2014)
Genome Res.
, vol.24
, pp. 310-317
-
-
Chen, K.1
Chen, L.2
Fan, X.3
Wallis, J.4
Ding, L.5
Weinstock, G.6
-
5
-
-
69549116107
-
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
-
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
-
6
-
-
58149218240
-
High-resolution mapping of copy-number alterations with massively parallel sequencing
-
Chiang, D. Y., Getz, G., Jaffe, D. B., O'Kelly, M. J. T., Zhao, X., Carter, S. L., et al. (2009). High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103. doi: 10.1038/nmeth.1276
-
(2009)
Nat. Methods
, vol.6
, pp. 99-103
-
-
Chiang, D.Y.1
Getz, G.2
Jaffe, D.B.3
O'Kelly, M.J.T.4
Zhao, X.5
Carter, S.L.6
-
7
-
-
84867524318
-
SVM2: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data
-
Chiara, M., Pesole, G., and Horner, D. S. (2012). SVM2: 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
-
8
-
-
34447333117
-
Unsupervised segmentation of continuous genomic data
-
Day, N., Hemmaplardh, A., Thurman, R. E., Stamatoyannopoulos, J. A., and Noble, W. S. (2007). Unsupervised segmentation of continuous genomic data. Bioinformatics 23, 1424-1426. doi: 10.1093/bioinformatics/btm096
-
(2007)
Bioinformatics
, vol.23
, pp. 1424-1426
-
-
Day, N.1
Hemmaplardh, A.2
Thurman, R.E.3
Stamatoyannopoulos, J.A.4
Noble, W.S.5
-
9
-
-
84857810661
-
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
-
Emde, A.-K., Schulz, M. H., Weese, D., Sun, R., Vingron, M., Kalscheuer, V. M., et al. (2012). Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics 28, 619-627. doi: 10.1093/bioinformatics/bts019
-
(2012)
Bioinformatics
, vol.28
, pp. 619-627
-
-
Emde, A.-K.1
Schulz, M.H.2
Weese, D.3
Sun, R.4
Vingron, M.5
Kalscheuer, V.M.6
-
10
-
-
84877983704
-
PeSV-Fisher: identification of somatic and non-somatic structural variants using next generation sequencing data
-
Escaramís, G., Tornador, C., Bassaganyas, L., Rabionet, R., Tubio, J. M. C., Martínez-Fundichely, A., et al. (2013). PeSV-Fisher: identification of somatic and non-somatic structural variants using next generation sequencing data. PLoS ONE 8:e63377. doi: 10.1371/journal.pone.0063377
-
(2013)
PLoS ONE
, vol.8
-
-
Escaramís, G.1
Tornador, C.2
Bassaganyas, L.3
Rabionet, R.4
Tubio, J.M.C.5
Martínez-Fundichely, A.6
-
11
-
-
84892380814
-
Optimal scaling of digital transcriptomes
-
Glusman, G., Caballero, J., Robinson, M., Kutlu, B., and Hood, L. (2013). Optimal scaling of digital transcriptomes. PLoS ONE 8:e77885. doi: 10.1371/journal.pone.0077885
-
(2013)
PLoS ONE
, vol.8
-
-
Glusman, G.1
Caballero, J.2
Robinson, M.3
Kutlu, B.4
Hood, L.5
-
12
-
-
79952194317
-
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
-
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
-
-
84892656321
-
SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations
-
Hart, S. N., Sarangi, V., Moore, R., Baheti, S., Bhavsar, J. D., Couch, F. J., et al. (2013). SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations. PLoS ONE 8:e83356. doi: 10.1371/journal.pone.0083356
-
(2013)
PLoS ONE
, vol.8
-
-
Hart, S.N.1
Sarangi, V.2
Moore, R.3
Baheti, S.4
Bhavsar, J.D.5
Couch, F.J.6
-
14
-
-
84871668815
-
A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data
-
Hayes, M., Pyon, Y. S., and Li, J. (2012). A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data. PLoS ONE 7:e52881. doi: 10.1371/journal.pone.0052881
-
(2012)
PLoS ONE
, vol.7
-
-
Hayes, M.1
Pyon, Y.S.2
Li, J.3
-
15
-
-
33644874573
-
The UCSC Genome Browser Database: update 2006
-
Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., et al. (2006). The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590-D598. doi: 10.1093/nar/gkj144
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D590-D598
-
-
Hinrichs, A.S.1
Karolchik, D.2
Baertsch, R.3
Barber, G.P.4
Bejerano, G.5
Clawson, H.6
-
16
-
-
77954205450
-
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
-
Hormozdiari, F., Hajirasouliha, I., Dao, P., Hach, F., Yorukoglu, D., Alkan, C., et al. (2010). Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26, i350-i357. doi: 10.1093/bioinformatics/btq216
-
(2010)
Bioinformatics
, vol.26
, pp. i350-i357
-
-
Hormozdiari, F.1
Hajirasouliha, I.2
Dao, P.3
Hach, F.4
Yorukoglu, D.5
Alkan, C.6
-
17
-
-
79951748341
-
CNAseg-a novel framework for identification of copy number changes in cancer from second-generation sequencing data
-
Ivakhno, S., Royce, T., Cox, A. J., Evers, D. J., Cheetham, R. K., and Tavaré, S. (2010). CNAseg-a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics 26, 3051-3058. doi: 10.1093/bioinformatics/btq587
-
(2010)
Bioinformatics
, vol.26
, pp. 3051-3058
-
-
Ivakhno, S.1
Royce, T.2
Cox, A.J.3
Evers, D.J.4
Cheetham, R.K.5
Tavaré, S.6
-
18
-
-
84870460670
-
PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants
-
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
-
19
-
-
84856409929
-
Detection of structural variants and indels within exome data
-
Karakoc, E., Alkan, C., O'Roak, B. J., Dennis, M. Y., Vives, L., Mark, K., et al. (2012). Detection of structural variants and indels within exome data. Nat. Methods 9, 176-178. doi: 10.1038/nmeth.1810
-
(2012)
Nat. Methods
, vol.9
, pp. 176-178
-
-
Karakoc, E.1
Alkan, C.2
O'Roak, B.J.3
Dennis, M.Y.4
Vives, L.5
Mark, K.6
-
20
-
-
84861400043
-
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
-
Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U., et al. (2012). cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res. 40:e69. doi: 10.1093/nar/gks003
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Klambauer, G.1
Schwarzbauer, K.2
Mayr, A.3
Clevert, D.-A.4
Mitterecker, A.5
Bodenhofer, U.6
-
21
-
-
62549131646
-
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
-
Korbel, J. O., Abyzov, A., Mu, X. J., Carriero, N., Cayting, P., Zhang, Z., 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. doi: 10.1186/gb-2009-10-2-r23
-
(2009)
Genome Biol
, vol.10
-
-
Korbel, J.O.1
Abyzov, A.2
Mu, X.J.3
Carriero, N.4
Cayting, P.5
Zhang, Z.6
-
22
-
-
84867722841
-
COPS: a sensitive and accurate tool for detecting somatic copy number alterations using short-read sequence data from paired samples
-
Krishnan, N. M., Gaur, P., Chaudhary, R., Rao, A. A., and Panda, B. (2012). COPS: a sensitive and accurate tool for detecting somatic copy number alterations using short-read sequence data from paired samples. PLoS ONE 7:e47812. doi: 10.1371/journal.pone.0047812
-
(2012)
PLoS ONE
, vol.7
-
-
Krishnan, N.M.1
Gaur, P.2
Chaudhary, R.3
Rao, A.A.4
Panda, B.5
-
23
-
-
84857956783
-
Detecting and annotating genetic variations using the HugeSeq pipeline
-
Lam, H. Y. K., Pan, C., Clark, M. J., Lacroute, P., Chen, R., Haraksingh, R., et al. (2012). Detecting and annotating genetic variations using the HugeSeq pipeline. Nat. Biotechnol. 30, 226-229. doi: 10.1038/nbt.2134
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 226-229
-
-
Lam, H.Y.K.1
Pan, C.2
Clark, M.J.3
Lacroute, P.4
Chen, R.5
Haraksingh, R.6
-
24
-
-
84912096454
-
LUMPY: a probabilistic framework for structural variant discovery
-
Layer, R. M., Chiang, C., Quinlan, A. R., and Hall, I. M. (2014). LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15:R84. doi: 10.1186/gb-2014-15-6-r84
-
(2014)
Genome Biol
, vol.15
-
-
Layer, R.M.1
Chiang, C.2
Quinlan, A.R.3
Hall, I.M.4
-
25
-
-
79951993896
-
Tabix: fast retrieval of sequence features from generic TAB-delimited files
-
Li, H. (2011). Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics 27, 718-719. doi: 10.1093/bioinformatics/btq671
-
(2011)
Bioinformatics
, vol.27
, pp. 718-719
-
-
Li, H.1
-
26
-
-
68549104404
-
The Sequence alignment/map format and SAMtools
-
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
-
27
-
-
79961202047
-
Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm
-
Magi, A., Benelli, M., Yoon, S., Roviello, F., and Torricelli, F. (2011). Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Res. 39:e65. doi: 10.1093/nar/gkr068
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Magi, A.1
Benelli, M.2
Yoon, S.3
Roviello, F.4
Torricelli, F.5
-
28
-
-
84869449997
-
CLEVER: clique-enumerating variant finder
-
Marschall, T., Costa, I. G., Canzar, S., Bauer, M., Klau, G. W., Schliep, A., et al. (2012). CLEVER: clique-enumerating variant finder. Bioinformatics 28, 2875-2882. doi: 10.1093/bioinformatics/bts566
-
(2012)
Bioinformatics
, vol.28
, pp. 2875-2882
-
-
Marschall, T.1
Costa, I.G.2
Canzar, S.3
Bauer, M.4
Klau, G.W.5
Schliep, A.6
-
29
-
-
78649309503
-
Detecting copy number variation with mated short reads
-
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
-
30
-
-
2942553957
-
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis
-
Meyers, B. C., Tej, S. S., Vu, T. H., Haudenschild, C. D., Agrawal, V., Edberg, S. B., et al. (2004). The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res. 14, 1641-1653. doi: 10.1101/gr.2275604.1
-
(2004)
Genome Res.
, vol.14
, pp. 1641-1653
-
-
Meyers, B.C.1
Tej, S.S.2
Vu, T.H.3
Haudenschild, C.D.4
Agrawal, V.5
Edberg, S.B.6
-
31
-
-
84864457002
-
forestSV: structural variant discovery through statistical learning
-
Michaelson, J. J., and Sebat, J. (2012). forestSV: structural variant discovery through statistical learning. Nat. Methods 9, 819-821. doi: 10.1038/nmeth.2085
-
(2012)
Nat. Methods
, vol.9
, pp. 819-821
-
-
Michaelson, J.J.1
Sebat, J.2
-
32
-
-
79551621409
-
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads
-
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
-
33
-
-
84975804424
-
Mapping copy number variation by population-scale genome sequencing
-
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
-
34
-
-
84903947208
-
ISVP: an integrated structural variant calling pipeline from high-throughput sequencing data
-
Mimori, T., Nariai, N., Kojima, K., Takahashi, M., Ono, A., Sato, Y., et al. (2013). iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Syst. Biol. 7 (Suppl. 6):S8. doi: 10.1186/1752-0509-7-S6-S8
-
(2013)
BMC Syst. Biol
, vol.7
, Issue.SUPPL.6
-
-
Mimori, T.1
Nariai, N.2
Kojima, K.3
Takahashi, M.4
Ono, A.5
Sato, Y.6
-
35
-
-
84906253020
-
The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data
-
Nguyen, H. T., Merriman, T. R., and Black, M. A. (2014). The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data. Front. Genet. 5:248. doi: 10.3389/fgene.2014.00248
-
(2014)
Front. Genet
, vol.5
, pp. 248
-
-
Nguyen, H.T.1
Merriman, T.R.2
Black, M.A.3
-
36
-
-
84870777273
-
De novo detection of copy number variation by co-assembly
-
Nijkamp, J. F., van den Broek, M. A., Geertman, J.-M. A., Reinders, M. J. T., Daran, J.-M. G., and de Ridder, D. (2012). De novo detection of copy number variation by co-assembly. Bioinformatics 28, 3195-3202. doi: 10.1093/bioinformatics/bts601
-
(2012)
Bioinformatics
, vol.28
, pp. 3195-3202
-
-
Nijkamp, J.F.1
Van Den Broek, M.A.2
Geertman, J.-M.A.3
Reinders, M.J.T.4
Daran, J.-M.G.5
De Ridder, D.6
-
37
-
-
79959965448
-
inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data
-
Qi, J., and Zhao, F. (2011). inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res. 39, W567-W575. doi: 10.1093/nar/gkr506
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W567-W575
-
-
Qi, J.1
Zhao, F.2
-
38
-
-
77951860138
-
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
-
Quinlan, A. R., Clark, R. A., Sokolova, S., Leibowitz, M. L., Zhang, Y., Hurles, M. E., et al. (2010). Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res. 20, 623-635. doi: 10.1101/gr.102970.109
-
(2010)
Genome Res.
, vol.20
, pp. 623-635
-
-
Quinlan, A.R.1
Clark, R.A.2
Sokolova, S.3
Leibowitz, M.L.4
Zhang, Y.5
Hurles, M.E.6
-
39
-
-
84866440781
-
DELLY: structural variant discovery by integrated paired-end and split-read analysis
-
Rausch, T., Zichner, T., Schlattl, A., Stütz, 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
, pp. i333-i339
-
-
Rausch, T.1
Zichner, T.2
Schlattl, A.3
Stütz, A.M.4
Benes, V.5
Korbel, J.O.6
-
40
-
-
84878825544
-
Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies
-
Rieber, N., Zapatka, M., Lasitschka, B., Jones, D., Northcott, P., Hutter, B., et al. (2013). Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies. PLoS ONE 8:e66621. doi: 10.1371/journal.pone.0066621
-
(2013)
PLoS ONE
, vol.8
-
-
Rieber, N.1
Zapatka, M.2
Lasitschka, B.3
Jones, D.4
Northcott, P.5
Hutter, B.6
-
41
-
-
84922723995
-
MindTheGap: integrated detection and assembly of short and long insertions
-
Rizk, G., Gouin, A., Chikhi, R., and Lemaitre, C. (2014). MindTheGap: integrated detection and assembly of short and long insertions. Bioinformatics 30, 3451-3457. doi: 10.1093/bioinformatics/btu545
-
(2014)
Bioinformatics
, vol.30
, pp. 3451-3457
-
-
Rizk, G.1
Gouin, A.2
Chikhi, R.3
Lemaitre, C.4
-
42
-
-
77951799158
-
Analysis of genetic inheritance in a family quartet by whole-genome sequencing
-
Roach, J. C., Glusman, G., Smit, A. F. A., Huff, C. D., Hubley, R., Shannon, P. T., et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636-639. doi: 10.1126/science.1186802
-
(2010)
Science
, vol.328
, pp. 636-639
-
-
Roach, J.C.1
Glusman, G.2
Smit, A.F.A.3
Huff, C.D.4
Hubley, R.5
Shannon, P.T.6
-
43
-
-
84898847797
-
Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
-
Schröder, J., Hsu, A., Boyle, S. E., Macintyre, G., Cmero, M., Tothill, R. W., et al. (2014). Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. Bioinformatics 30, 1064-1072. doi: 10.1093/bioinformatics/btt767
-
(2014)
Bioinformatics
, vol.30
, pp. 1064-1072
-
-
Schröder, J.1
Hsu, A.2
Boyle, S.E.3
Macintyre, G.4
Cmero, M.5
Tothill, R.W.6
-
44
-
-
79960873055
-
A hidden Markov model for copy number variant prediction from whole genome resequencing data.
-
Shen, Y., Gu, Y., and Pe'er, I. (2011). A hidden Markov model for copy number variant prediction from whole genome resequencing data. BMC Bioinformatics 12 (Suppl. 6):S4. doi: 10.1186/1471-2105-12-S6-S4
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Shen, Y.1
Gu, Y.2
Pe'er, I.3
-
45
-
-
84858853457
-
An integrative probabilistic model for identification of structural variation in sequencing data
-
Sindi, S. S., Onal, S., Peng, L. C., Wu, H.-T., and Raphael, B. J. (2012). An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol. 13:R22. doi: 10.1186/gb-2012-13-3-r22
-
(2012)
Genome Biol
, vol.13
-
-
Sindi, S.S.1
Onal, S.2
Peng, L.C.3
Wu, H.-T.4
Raphael, B.J.5
-
46
-
-
84908251771
-
Mutations in NOTCH1 cause Adams-Oliver syndrome
-
Stittrich, A.-B., Lehman, A., Bodian, D. L., Ashworth, J., Zong, Z., Li, H., et al. (2014). Mutations in NOTCH1 cause Adams-Oliver syndrome. Am. J. Hum. Genet. 95, 275-284. doi: 10.1016/j.ajhg.2014.07.011
-
(2014)
Am. J. Hum. Genet.
, vol.95
, pp. 275-284
-
-
Stittrich, A.-B.1
Lehman, A.2
Bodian, D.L.3
Ashworth, J.4
Zong, Z.5
Li, H.6
-
47
-
-
84873664159
-
Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation
-
Szatkiewicz, J. P., Wang, W., Sullivan, P. F., Wang, W., and Sun, W. (2013). Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation. Nucleic Acids Res. 41, 1519-1532. doi: 10.1093/nar/gks1363
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 1519-1532
-
-
Szatkiewicz, J.P.1
Wang, W.2
Sullivan, P.F.3
Wang, W.4
Sun, W.5
-
48
-
-
84868016827
-
Statistical challenges associated with detecting copy number variations with next-generation sequencing
-
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
-
49
-
-
79961007031
-
CREST maps somatic structural variation in cancer genomes with base-pair resolution
-
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
-
50
-
-
84874746879
-
CNVeM: copy number variation detection using uncertainty of read mapping
-
Wang, Z., Hormozdiari, F., Yang, W.-Y., Halperin, E., and Eskin, E. (2013). CNVeM: copy number variation detection using uncertainty of read mapping. J. Comput. Biol. 20, 224-236. doi: 10.1089/cmb.2012.0258
-
(2013)
J. Comput. Biol.
, vol.20
, pp. 224-236
-
-
Wang, Z.1
Hormozdiari, F.2
Yang, W.-Y.3
Halperin, E.4
Eskin, E.5
-
51
-
-
78650663859
-
Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly
-
Wong, K., Keane, T. M., Stalker, J., and Adams, D. J. (2010). Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol. 11:R128. doi: 10.1186/gb-2010-11-12-r128
-
(2010)
Genome Biol
, vol.11
-
-
Wong, K.1
Keane, T.M.2
Stalker, J.3
Adams, D.J.4
-
52
-
-
84883492991
-
MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads
-
Wu, Y., Tian, L., Pirastu, M., Stambolian, D., and Li, H. (2013). MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads. Front. Genet. 4:157. doi: 10.3389/fgene.2013.00157
-
(2013)
Front. Genet
, vol.4
, pp. 157
-
-
Wu, Y.1
Tian, L.2
Pirastu, M.3
Stambolian, D.4
Li, H.5
-
53
-
-
81755172942
-
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
-
Xi, R., Hadjipanayis, A. G., Luquette, L. J., Kim, T.-M., Lee, E., Zhang, J., et al. (2011). Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc. Natl. Acad. Sci. U.S.A. 108, E1128-E1136. doi: 10.1073/pnas.1110574108
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. E1128-E1136
-
-
Xi, R.1
Hadjipanayis, A.G.2
Luquette, L.J.3
Kim, T.-M.4
Lee, E.5
Zhang, J.6
-
54
-
-
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. doi: 10.1186/1471-2105-10-80
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 80
-
-
Xie, C.1
Tammi, M.T.2
-
55
-
-
84867896249
-
ChopSticks: high-resolution analysis of homozygous deletions by exploiting concordant read pairs
-
Yasuda, T., Suzuki, S., Nagasaki, M., and Miyano, S. (2012). ChopSticks: high-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinformatics 13:279. doi: 10.1186/1471-2105-13-279
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 279
-
-
Yasuda, T.1
Suzuki, S.2
Nagasaki, M.3
Miyano, S.4
-
56
-
-
70350694443
-
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
-
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
-
57
-
-
69749122557
-
Sensitive and accurate detection of copy number variants using read depth of coverage
-
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
-
58
-
-
82255164279
-
SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data
-
Zhang, J., and Wu, Y. (2011). SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data. Bioinformatics 27, 3228-3234. doi: 10.1093/bioinformatics/btr563
-
(2011)
Bioinformatics
, vol.27
, pp. 3228-3234
-
-
Zhang, J.1
Wu, Y.2
-
59
-
-
77949501694
-
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
-
Zhang, Q., Ding, L., Larson, D. E., Koboldt, D. C., McLellan, M. D., Chen, K., et al. (2010). CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics 26, 464-469. doi: 10.1093/bioinformatics/btp708
-
(2010)
Bioinformatics
, vol.26
, pp. 464-469
-
-
Zhang, Q.1
Ding, L.2
Larson, D.E.3
Koboldt, D.C.4
McLellan, M.D.5
Chen, K.6
-
60
-
-
79960572201
-
Identification of genomic indels and structural variations using split reads
-
Zhang, Z. D., Du, J., Lam, H., Abyzov, A., Urban, A. E., Snyder, M., et al. (2011). Identification of genomic indels and structural variations using split reads. BMC Genomics 12:375. doi: 10.1186/1471-2164-12-375
-
(2011)
BMC Genomics
, vol.12
, pp. 375
-
-
Zhang, Z.D.1
Du, J.2
Lam, H.3
Abyzov, A.4
Urban, A.E.5
Snyder, M.6
-
61
-
-
84866092268
-
Using ERDS to infer copy-number variants in high-coverage genomes
-
Zhu, M., Need, A. C., Han, Y., Ge, D., Maia, J. M., Zhu, Q., et al. (2012). Using ERDS to infer copy-number variants in high-coverage genomes. Am. J. Hum. Genet. 91, 408-421. doi: 10.1016/j.ajhg.2012.07.004
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 408-421
-
-
Zhu, M.1
Need, A.C.2
Han, Y.3
Ge, D.4
Maia, J.M.5
Zhu, Q.6
|