-
1
-
-
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: 1061-1073.
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
2
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
Abecasis GR, Auton A, Brooks L.D., DePristo MA, Durbin RM, Handsaker RE, Kang H.M., Marth GT, McVean GA 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Abecasis, G.R.1
Auton, A.2
Brooks, L.D.3
DePristo, M.A.4
Durbin, R.M.5
Handsaker, R.E.6
Kang, H.M.7
Marth, G.T.8
McVean, G.A.9
-
3
-
-
79957932376
-
Dindel: Accurate indel calls from short-read data
-
Albers CA, Lunter G, Macarthur D.G., McVean G., Ouwehand WH, Durbin R. 2011. Dindel: Accurate indel calls from short-read data. Genome Res 21: 961-973.
-
(2011)
Genome Res
, vol.21
, pp. 961-973
-
-
Albers, C.A.1
Lunter, G.2
Macarthur, D.G.3
McVean, G.4
Ouwehand, W.H.5
Durbin, R.6
-
5
-
-
35348817330
-
Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
-
Browning SR, Browning BL 2007. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81: 1084-1097.
-
(2007)
Am J Hum Genet
, vol.81
, pp. 1084-1097
-
-
Browning, S.R.1
Browning, B.L.2
-
6
-
-
0346373654
-
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium
-
Carlson CS, Eberle MA, Rieder M.J., Yi Q., Kruglyak L, Nickerson DA 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74: 106-120.
-
(2004)
Am J Hum Genet
, vol.74
, pp. 106-120
-
-
Carlson, C.S.1
Eberle, M.A.2
Rieder, M.J.3
Yi, Q.4
Kruglyak, L.5
Nickerson, D.A.6
-
7
-
-
61449086542
-
Shape-IT: New rapid and accurate algorithm for haplotype inference
-
Delaneau O, Coulonges C, Zagury J-F. 2008. Shape-IT: New rapid and accurate algorithm for haplotype inference. BMC Bioinformatics 9: 540.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 540
-
-
Delaneau, O.1
Coulonges, C.2
Zagury, J.-F.3
-
8
-
-
84856478855
-
A linear complexity phasing method for thousands of genomes
-
Delaneau O, Marchini J, Zagury J-F. 2012. A linear complexity phasing method for thousands of genomes. Nat Methods 9: 179-181.
-
(2012)
Nat Methods
, vol.9
, pp. 179-181
-
-
Delaneau, O.1
Marchini, J.2
Zagury, J.-F.3
-
10
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo MA, Banks E, Poplin R., Garimella KV, Maguire JR, Hartl C, Philippakis A.A., del Angel G, Rivas MA, Hanna M, et al 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
-
(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
Philippakis, A.A.7
Del Angel, G.8
Rivas, M.A.9
Hanna, M.10
-
11
-
-
79951527739
-
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
-
Duitama J, Kennedy J, Dinakar S., Hernández Y, Wu Y., Mandoiu II 2011. Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. BMC Bioinformatics 12: S53.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Duitama, J.1
Kennedy, J.2
Dinakar, S.3
Hernández, Y.4
Wu, Y.5
Mandoiu, I.I.6
-
12
-
-
4143145578
-
Model-based inference of haplotype block variation
-
Greenspan G, Geiger D. 2004. Model-based inference of haplotype block variation. J Comput Biol 11: 493-504.
-
(2004)
J Comput Biol
, vol.11
, pp. 493-504
-
-
Greenspan, G.1
Geiger, D.2
-
13
-
-
79952194317
-
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
-
Handsaker RE, Korn JM, Nemesh J, McCarroll SA 2011. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet 43: 269-276.
-
(2011)
Nat Genet
, vol.43
, pp. 269-276
-
-
Handsaker, R.E.1
Korn, J.M.2
Nemesh, J.3
McCarroll, S.A.4
-
14
-
-
65449144325
-
Evaluation of next generation sequencing platforms for population targeted sequencing studies
-
Harismendy O, Ng PC, Strausberg R.L., Wang X., Stockwell TB, Beeson KY, Schork NJ, Murray S.S., Topol EJ, Levy S, et al 2009. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10: R32.
-
(2009)
Genome Biol
, vol.10
-
-
Harismendy, O.1
Ng, P.C.2
Strausberg, R.L.3
Wang, X.4
Stockwell, T.B.5
Beeson, K.Y.6
Schork, N.J.7
Murray, S.S.8
Topol, E.J.9
Levy, S.10
-
15
-
-
74249110768
-
Human triallelic sites: Evidence for a new mutational mechanism?
-
Hodgkinson A, Eyre-Walker A. 2010. Human triallelic sites: Evidence for a new mutational mechanism? Genetics 184: 233-241.
-
(2010)
Genetics
, vol.184
, pp. 233-241
-
-
Hodgkinson, A.1
Eyre-Walker, A.2
-
16
-
-
70450177746
-
BFAST: An alignment tool for large scale genome resequencing
-
Homer N, Merriman B, Nelson SF 2009. BFAST: An alignment tool for large scale genome resequencing. PLoS ONE 4: e7767.
-
(2009)
PLoS ONE
, vol.4
-
-
Homer, N.1
Merriman, B.2
Nelson, S.F.3
-
17
-
-
0000424609
-
Testing the constant-rate neutral allele model with protein sequence
-
Hudson R. 1983. Testing the constant-rate neutral allele model with protein sequence. Evolution 37: 203-217.
-
(1983)
Evolution
, vol.37
, pp. 203-217
-
-
Hudson, R.1
-
18
-
-
79959524146
-
A haplotype map of the human genome
-
International HapMap Consortium
-
International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
-
(2005)
Nature
, vol.437
, pp. 1299-1320
-
-
-
19
-
-
0002556819
-
Genealogy populations
-
Kingman J. 1982. Genealogy populations. J Appl Probab 19: 27-43.
-
(1982)
J Appl Probab
, vol.19
, pp. 27-43
-
-
Kingman, J.1
-
20
-
-
69949122158
-
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples
-
Koboldt DC, Chen K, Wylie T., Larson DE, McLellan MD, Mardis ER, Weinstock G.M., Wilson RK, Ding L. 2009. VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25: 2283-2285.
-
(2009)
Bioinformatics
, vol.25
, pp. 2283-2285
-
-
Koboldt, D.C.1
Chen, K.2
Wylie, T.3
Larson, D.E.4
McLellan, M.D.5
Mardis, E.R.6
Weinstock, G.M.7
Wilson, R.K.8
Ding, L.9
-
21
-
-
79957950801
-
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
-
Le SQ, Durbin R. 2011. SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res 21: 952-960.
-
(2011)
Genome Res
, vol.21
, pp. 952-960
-
-
Le, S.Q.1
Durbin, R.2
-
22
-
-
80054915847
-
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
-
Li H. 2011a. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27: 2987-2993.
-
(2011)
Bioinformatics
, vol.27
, pp. 2987-2993
-
-
Li, H.1
-
23
-
-
79954553212
-
Improving SNP discovery by base alignment quality
-
Li H. 2011b. Improving SNP discovery by base alignment quality. Bioinformatics 27: 1157-1158.
-
(2011)
Bioinformatics
, vol.27
, pp. 1157-1158
-
-
Li, H.1
-
24
-
-
67649884743
-
Fast and accurate short read alignment with burrows-wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
25
-
-
0347361674
-
Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
-
Li N, Stephens M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 2233: 2213-2233.
-
(2003)
Genetics
, vol.2233
, pp. 2213-2233
-
-
Li, N.1
Stephens, M.2
-
26
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
-
(2008)
Genome Res
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
27
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A., Fennell T, Ruan J, Homer N., Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(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
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
28
-
-
78649508578
-
MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes
-
Li Y, Willer CJ, Ding J, Scheet P., Abecasis GR 2010. MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34: 816-834.
-
(2010)
Genet Epidemiol
, vol.34
, pp. 816-834
-
-
Li, Y.1
Willer, C.J.2
Ding, J.3
Scheet, P.4
Abecasis, G.R.5
-
29
-
-
79957951017
-
Low-coverage sequencing: Implications for design of complex trait association studies
-
Li Y, Sidore C, Kang H.M., Boehnke M., Abecasis GR 2011. Low-coverage sequencing: Implications for design of complex trait association studies. Genome Res 21: 940-951.
-
(2011)
Genome Res
, vol.21
, pp. 940-951
-
-
Li, Y.1
Sidore, C.2
Kang, H.M.3
Boehnke, M.4
Abecasis, G.R.5
-
30
-
-
4444319904
-
Haplotype and missing data inference in nuclear families
-
Lin S, Chakravarti A, Cutler DJ 2004. Haplotype and missing data inference in nuclear families. Genome Res 14: 1624-1632.
-
(2004)
Genome Res
, vol.14
, pp. 1624-1632
-
-
Lin, S.1
Chakravarti, A.2
Cutler, D.J.3
-
31
-
-
62649089109
-
Population genomics of domestic and wild yeasts
-
Liti G, Carter DM, Moses A.M., Warringer J., Parts L, James SA, Davey R.P., Roberts IN, Burt A, Koufopanou V, et al 2009. Population genomics of domestic and wild yeasts. Nature 458: 337-341.
-
(2009)
Nature
, vol.458
, pp. 337-341
-
-
Liti, G.1
Carter, D.M.2
Moses, A.M.3
Warringer, J.4
Parts, L.5
James, S.A.6
Davey, R.P.7
Roberts, I.N.8
Burt, A.9
Koufopanou, V.10
-
32
-
-
84857460221
-
Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms
-
Lu JT, Wang Y, Gibbs R.A., Yu F. 2012. Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms. Genome Biol 13: R15.
-
(2012)
Genome Biol
, vol.13
-
-
Lu, J.T.1
Wang, Y.2
Gibbs, R.A.3
Yu, F.4
-
33
-
-
33344458848
-
A comparison of phasing algorithms for trios and unrelated individuals
-
Marchini J, Cutler D, Patterson N., Stephens M, Eskin E, Halperin E., Lin S, Qin ZS, Munro H.M., Abecasis GR, et al 2006. A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78: 437-450.
-
(2006)
Am J Hum Genet
, vol.78
, pp. 437-450
-
-
Marchini, J.1
Cutler, D.2
Patterson, N.3
Stephens, M.4
Eskin, E.5
Halperin, E.6
Lin, S.7
Qin, Z.S.8
Munro, H.M.9
Abecasis, G.R.10
-
34
-
-
77956295988
-
The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna A, Hanna M, Banks E., Sivachenko A, Cibulskis K, Kernytsky A., Garimella K, Altshuler D, Gabriel S., Daly M, et al 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
-
(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
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
-
35
-
-
84890547163
-
Genotype calling and phasing using next-generation sequencing reads andahaplotype scaffold
-
Menelaou A, Marchini J. 2012. Genotype calling and phasing using next-generation sequencing reads andahaplotype scaffold. Bioinformatics29: 1-8.
-
(2012)
Bioinformatics
, vol.29
, pp. 1-8
-
-
Menelaou, A.1
Marchini, J.2
-
37
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
Ning Z, Cox AJ, Mullikin JC 2001. SSAHA: A fast search method for large DNA databases. Genome Res 11: 1725-1729.
-
(2001)
Genome Res
, vol.11
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
38
-
-
33644974019
-
A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase
-
Scheet P, Stephens M. 2006. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629-644.
-
(2006)
Am J Hum Genet
, vol.78
, pp. 629-644
-
-
Scheet, P.1
Stephens, M.2
-
39
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
40
-
-
79956066785
-
Comparison of sequence reads obtained from three next-generation sequencing platforms
-
Suzuki S, Ono N, Furusawa C., Ying B-W, Yomo T. 2011. Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS ONE 6: e19534.
-
(2011)
PLoS ONE
, vol.6
-
-
Suzuki, S.1
Ono, N.2
Furusawa, C.3
Ying, B.-W.4
Yomo, T.5
|