-
1
-
-
84865712382
-
Annotation of functional variation in personal genomes using RegulomeDB
-
Boyle, A.P. et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22, 1790-1797 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 1790-1797
-
-
Boyle, A.P.1
-
2
-
-
77954407332
-
Genomewide association studies and assessment of the risk of disease
-
Manolio, T.A. Genomewide association studies and assessment of the risk of disease. N. Engl. J. Med. 363, 166-176 (2010).
-
(2010)
N. Engl. J. Med
, vol.363
, pp. 166-176
-
-
Manolio, T.A.1
-
3
-
-
84865822182
-
Systematic localization of common disease-associated variation in regulatory DNA
-
Maurano, M.T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
-
(2012)
Science
, vol.337
, pp. 1190-1195
-
-
Maurano, M.T.1
-
4
-
-
77955499945
-
From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus
-
Musunuru, K. et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466, 714-719 (2010).
-
(2010)
Nature
, vol.466
, pp. 714-719
-
-
Musunuru, K.1
-
5
-
-
84885620722
-
An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level
-
Bauer, D.E. et al. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science 342, 253-257 (2013).
-
(2013)
Science
, vol.342
, pp. 253-257
-
-
Bauer, D.E.1
-
6
-
-
84863541919
-
Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer
-
van den Boogaard, M. et al. Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. J. Clin. Invest. 122, 2519-2530 (2012).
-
(2012)
J. Clin. Invest
, vol.122
, pp. 2519-2530
-
-
Van Den Boogaard, M.1
-
7
-
-
84897855294
-
Obesity-associated variants within FTO form long-range functional connections with IRX3
-
Smemo, S. et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 507, 371-375 (2014).
-
(2014)
Nature
, vol.507
, pp. 371-375
-
-
Smemo, S.1
-
8
-
-
84898747287
-
Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon
-
Spieler, D. et al. Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon. Genome Res. 24, 592-603 (2014).
-
(2014)
Genome Res
, vol.24
, pp. 592-603
-
-
Spieler, D.1
-
9
-
-
55449120805
-
Genetic mapping in human disease
-
Altshuler, D., Daly, M.J. & Lander, E.S. Genetic mapping in human disease. Science 322, 881-888 (2008).
-
(2008)
Science
, vol.322
, pp. 881-888
-
-
Altshuler, D.1
Daly, M.J.2
Lander, E.S.3
-
10
-
-
84884623924
-
Re-ranking sequencing variants in the post-GWAS era for accurate causal variant identification
-
Faye, L.L., Machiela, M.J., Kraft, P., Bull, S.B. & Sun, L. Re-ranking sequencing variants in the post-GWAS era for accurate causal variant identification. PLoS Genet. 9, e1003609 (2013).
-
(2013)
PLoS Genet
, vol.9
, pp. e1003609
-
-
Faye, L.L.1
MacHiela, M.J.2
Kraft, P.3
Bull, S.B.4
Sun, L.5
-
11
-
-
84878682420
-
The Genotype-Tissue Expression (GTEx) project
-
The GTEx Consortium
-
The GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580-585 (2013).
-
(2013)
Nat. Genet
, vol.45
, pp. 580-585
-
-
-
12
-
-
84885645853
-
Transcriptome and genome sequencing uncovers functional variation in humans
-
Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013).
-
(2013)
Nature
, vol.501
, pp. 506-511
-
-
Lappalainen, T.1
-
13
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population
-
Montgomery, S.B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-777 (2010).
-
(2010)
Nature
, vol.464
, pp. 773-777
-
-
Montgomery, S.B.1
-
14
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
Pickrell, J.K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768-772 (2010).
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
-
15
-
-
55449112450
-
High-resolution mapping of expression-QTLs yields insight into human gene regulation
-
Veyrieras, J.B. et al. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4, e1000214 (2008).
-
(2008)
PLoS Genet
, vol.4
, pp. e1000214
-
-
Veyrieras, J.B.1
-
16
-
-
84900338300
-
Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes
-
Raj, T. et al. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science 344, 519-523 (2014).
-
(2014)
Science
, vol.344
, pp. 519-523
-
-
Raj, T.1
-
17
-
-
84891685308
-
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
-
Battle, A. et al. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res. 24, 14-24 (2014).
-
(2014)
Genome Res
, vol.24
, pp. 14-24
-
-
Battle, A.1
-
18
-
-
84857111200
-
DNase i sensitivity QTLs are a major determinant of human expression variation
-
Degner, J.F. et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482, 390-394 (2012).
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.F.1
-
19
-
-
77649086970
-
A map of open chromatin in human pancreatic islets
-
Gaulton, K.J. et al. A map of open chromatin in human pancreatic islets. Nat. Genet. 42, 255-259 (2010).
-
(2010)
Nat. Genet
, vol.42
, pp. 255-259
-
-
Gaulton, K.J.1
-
20
-
-
77950833803
-
Variation in transcription factor binding among humans
-
Kasowski, M. et al. Variation in transcription factor binding among humans. Science 328, 232-235 (2010).
-
(2010)
Science
, vol.328
, pp. 232-235
-
-
Kasowski, M.1
-
21
-
-
77950854479
-
Heritable individual-specific and allele-specific chromatin signatures in humans
-
McDaniell, R. et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328, 235-239 (2010).
-
(2010)
Science
, vol.328
, pp. 235-239
-
-
McDaniell, R.1
-
22
-
-
85027956980
-
Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data
-
Ni, Y., Hall, A.W., Battenhouse, A. & Iyer, V.R. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genet. 13, 46 (2012).
-
(2012)
BMC Genet
, vol.13
, pp. 46
-
-
Ni, Y.1
Hall, A.W.2
Battenhouse, A.3
Iyer, V.R.4
-
23
-
-
84866179291
-
Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays
-
Smith, A.J. et al. Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays. PLoS Genet. 8, e1002908 (2012).
-
(2012)
PLoS Genet
, vol.8
, pp. e1002908
-
-
Smith, A.J.1
-
24
-
-
84887320760
-
Extensive variation in chromatin states across humans
-
Kasowski, M. et al. Extensive variation in chromatin states across humans. Science 342, 750-752 (2013).
-
(2013)
Science
, vol.342
, pp. 750-752
-
-
Kasowski, M.1
-
25
-
-
84887320563
-
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription
-
Kilpinen, H. et al. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342, 744-747 (2013).
-
(2013)
Science
, vol.342
, pp. 744-747
-
-
Kilpinen, H.1
-
26
-
-
84887322043
-
Identification of genetic variants that affect histone modifications in human cells
-
McVicker, G. et al. Identification of genetic variants that affect histone modifications in human cells. Science 342, 747-749 (2013).
-
(2013)
Science
, vol.342
, pp. 747-749
-
-
McVicker, G.1
-
27
-
-
77956331627
-
Integrating common and rare genetic variation in diverse human populations
-
Altshuler, D.M. et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58 (2010).
-
(2010)
Nature
, vol.467
, pp. 52-58
-
-
Altshuler, D.M.1
-
28
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
The 1000 Genomes Project Consortium.
-
The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1, 092 human genomes. Nature 491, 56-65 (2012).
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
29
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40, 897-903 (2008).
-
(2008)
Nat. Genet
, vol.40
, pp. 897-903
-
-
Wang, Z.1
-
30
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112 (2009).
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
-
31
-
-
84880310432
-
Uniform, optimal signal processing of mapped deep-sequencing data
-
Kumar, V. et al. Uniform, optimal signal processing of mapped deep-sequencing data. Nat. Biotechnol. 31, 615-622 (2013).
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 615-622
-
-
Kumar, V.1
-
32
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein, M.B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
-
33
-
-
84865708757
-
An expansive human regulatory lexicon encoded in transcription factor footprints
-
Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90 (2012).
-
(2012)
Nature
, vol.489
, pp. 83-90
-
-
Neph, S.1
-
34
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
-
(2011)
Nat. Genet
, vol.43
, pp. 491-498
-
-
Depristo, M.A.1
-
35
-
-
80054746492
-
Exome sequencing as a tool for Mendelian disease gene discovery
-
Bamshad, M.J. et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745-755 (2011).
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 745-755
-
-
Bamshad, M.J.1
-
36
-
-
84962646530
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57, 289-300 (1995).
-
(1995)
J. R. Stat. Soc. Series B Stat. Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
37
-
-
78651356371
-
Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution
-
Potapova, A. et al. Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution. BMC Biotechnol. 11, 6 (2011).
-
(2011)
BMC Biotechnol
, vol.11
, pp. 6
-
-
Potapova, A.1
-
38
-
-
84870326659
-
Identification of a susceptibility locus in STAT4 for Behcet's disease in Han Chinese in a genome-wide association study
-
Hou, S. et al. Identification of a susceptibility locus in STAT4 for Behcet's disease in Han Chinese in a genome-wide association study. Arthritis Rheum. 64, 4104-4113 (2012).
-
(2012)
Arthritis Rheum
, vol.64
, pp. 4104-4113
-
-
Hou, S.1
-
39
-
-
84873091770
-
Genome-wide association analysis identifies new susceptibility loci for Behcet's disease and epistasis between HLA-B∗51 and ERAP1
-
Kirino, Y. et al. Genome-wide association analysis identifies new susceptibility loci for Behcet's disease and epistasis between HLA-B∗51 and ERAP1. Nat. Genet. 45, 202-207 (2013).
-
(2013)
Nat. Genet
, vol.45
, pp. 202-207
-
-
Kirino, Y.1
-
40
-
-
84868154284
-
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
-
Pai, A.A. et al. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 8, e1003000 (2012).
-
(2012)
PLoS Genet
, vol.8
, pp. e1003000
-
-
Pai, A.A.1
-
41
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002).
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
-
42
-
-
0036043393
-
The use of MassARRAY technology for high throughput genotyping
-
Jurinke, C., van den Boom, D., Cantor, C.R. & Koster, H. The use of MassARRAY technology for high throughput genotyping. Adv. Biochem. Eng. Biotechnol. 77, 57-74 (2002).
-
(2002)
Adv. Biochem. Eng. Biotechnol
, vol.77
, pp. 57-74
-
-
Jurinke, C.1
Van Den Boom, D.2
Cantor, C.R.3
Koster, H.4
-
43
-
-
84862249935
-
Association testing for next-generation sequencing data using score statistics
-
Skotte, L., Korneliussen, T.S. & Albrechtsen, A. Association testing for next-generation sequencing data using score statistics. Genet. Epidemiol. 36, 430-437 (2012).
-
(2012)
Genet. Epidemiol
, vol.36
, pp. 430-437
-
-
Skotte, L.1
Korneliussen, T.S.2
Albrechtsen, A.3
-
44
-
-
0000846686
-
Algorithm AS 47: Function minimization using a simplex procedure
-
ONeill, R. Algorithm AS 47: function minimization using a simplex procedure. J. R. Stat. Soc. Ser. C Appl. Stat. 20, 338-345 (1971).
-
(1971)
J. R. Stat. Soc. Ser. C Appl. Stat
, vol.20
, pp. 338-345
-
-
Oneill, R.1
-
45
-
-
0000238336
-
A simplex method for function minimization
-
Nelder, J.A. & Mead, R. A simplex method for function minimization. Comput. J. 7, 308-313 (1965).
-
(1965)
Comput. J
, vol.7
, pp. 308-313
-
-
Nelder, J.A.1
Mead, R.2
-
46
-
-
0035733108
-
The control of the false discovery rate in multiple testing under dependency
-
Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165-1188 (2001).
-
(2001)
Ann. Stat
, vol.29
, pp. 1165-1188
-
-
Benjamini, Y.1
Yekutieli, D.2
-
47
-
-
70349910898
-
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
-
Degner, J.F. et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25, 3207-3212 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 3207-3212
-
-
Degner, J.F.1
-
48
-
-
84898985349
-
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
-
Kheradpour, P. & Kellis, M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res. 42, 2976-2987 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 2976-2987
-
-
Kheradpour, P.1
Kellis, M.2
-
49
-
-
84891790401
-
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
-
Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001-D1006 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D1001-D1006
-
-
Welter, D.1
-
50
-
-
84887058596
-
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
-
Beecham, A.H. et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat. Genet. 45, 1353-1360 (2013).
-
(2013)
Nat. Genet
, vol.45
, pp. 1353-1360
-
-
Beecham, A.H.1
-
51
-
-
84870512735
-
Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity
-
Tsoi, L.C. et al. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat. Genet. 44, 1341-1348 (2012).
-
(2012)
Nat. Genet
, vol.44
, pp. 1341-1348
-
-
Tsoi, L.C.1
-
52
-
-
84870531924
-
High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis
-
Eyre, S. et al. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat. Genet. 44, 1336-1340 (2012).
-
(2012)
Nat. Genet
, vol.44
, pp. 1336-1340
-
-
Eyre, S.1
-
53
-
-
84879691837
-
Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci
-
Cortes, A. et al. Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci. Nat. Genet. 45, 730-738 (2013).
-
(2013)
Nat. Genet
, vol.45
, pp. 730-738
-
-
Cortes, A.1
|