-
1
-
-
84929001104
-
The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans
-
ARDLIE, K.G., DELUCA, D.S., SEGRÈ, A.V., SULLIVAN, T.J., YOUNG, T.R., GELFAND, E.T., TROWBRIDGE, C.A., MALLER, J.B., TUKIAINEN, T., LEK, M. et al. (2015). The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348 648-660.
-
(2015)
Science
, vol.348
, pp. 648-660
-
-
Ardlie, K.G.1
Deluca, D.S.2
Segrè, A.V.3
Sullivan, T.J.4
Young, T.R.5
Gelfand, E.T.6
Trowbridge, C.A.7
Maller, J.B.8
Tukiainen, T.9
Lek, M.10
-
2
-
-
0035671699
-
Bayesian methods for quantitative trait loci mapping based on model selection: Approximate analysis using the Bayesian information criterion
-
BALL, R. D. (2001). Bayesian methods for quantitative trait loci mapping based on model selection: Approximate analysis using the Bayesian information criterion. Genetics 159 1351-1364.
-
(2001)
Genetics
, vol.159
, pp. 1351-1364
-
-
Ball, R.D.1
-
3
-
-
84907584646
-
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
-
BANOVICH, N. E., LAN, X., MCVICKER, G., VAN DE GEIJN, B., DEGNER, J. F., BLIS-CHAK, J.D., ROUX, J., PRITCHARD, J.K. and GILAD, Y. (2014). Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet. 10 e1004663.
-
(2014)
Plos Genet
, vol.10
-
-
Banovich, N.E.1
Lan, X.2
McVicker, G.3
Van De Geijn, B.4
Degner, J.F.5
Blis-Chak, J.D.6
Roux, J.7
Pritchard, J.K.8
Gilad, Y.9
-
4
-
-
84856387609
-
Deciphering the genetic architecture of variation in the immune response to mycobacterium tuberculosis infection
-
BARREIRO, L.B., TAILLEUX, L., PAI, A.A., GICQUEL, B., MARIONI, J.C. and GILAD, Y. (2012). Deciphering the genetic architecture of variation in the immune response to mycobacterium tuberculosis infection. Proc. Natl. Acad. Sci. USA 109 1204-1209.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 1204-1209
-
-
Barreiro, L.B.1
Tailleux, L.2
Pai, A.A.3
Gicquel, B.4
Marioni, J.C.5
Gilad, Y.6
-
5
-
-
84990876234
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
BENJAMINI, Y. and HOCHBERG, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B. Stat. Methodol. 57 289-300.
-
(1995)
J. R. Stat. Soc. Ser. B. Stat. Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
6
-
-
84959919704
-
Approximately independent linkage disequilibrium blocks in human populations
-
BERISA, T. and PICKRELL, J. K. (2016). Approximately independent linkage disequilibrium blocks in human populations. Bioinformatics 32 283-285.
-
(2016)
Bioinformatics
, vol.32
, pp. 283-285
-
-
Berisa, T.1
Pickrell, J.K.2
-
7
-
-
55449096399
-
Genetical genomics: Spotlight on QTL hotspots
-
BREITLING, R., LI, Y., TESSON, B. M., FU, J., WU, C., WILTSHIRE, T., GERRITS, A., BYSTRYKH, L.V., DE HAAN, G., SU, A. I. et al. (2008). Genetical genomics: Spotlight on QTL hotspots. PLoS Genet. 4 e1000232.
-
(2008)
Plos Genet
, vol.4
-
-
Breitling, R.1
Li, Y.2
Tesson, B.M.3
Fu, J.4
Wu, C.5
Wiltshire, T.6
Gerrits, A.7
Bystrykh, L.V.8
De Haan, G.9
Su, A.I.10
-
8
-
-
62549125109
-
High-dimensional sparse factor modeling: Applications in gene expression genomics
-
CARVALHO, C.M., CHANG, J., LUCAS, J.E., NEVINS, J.R., WANG, Q. and WEST, M. (2008). High-dimensional sparse factor modeling: Applications in gene expression genomics. J. Amer. Statist. Assoc. 103 1438-1456.
-
(2008)
J. Amer. Statist. Assoc
, vol.103
, pp. 1438-1456
-
-
Carvalho, C.M.1
Chang, J.2
Lucas, J.E.3
Nevins, J.R.4
Wang, Q.5
West, M.6
-
10
-
-
84857111200
-
DNase [thinsp] I sensitivity QTLs are a major determinant of human expression variation
-
DEGNER, J. F., PAI, A. A., PIQUE-REGI, R., VEYRIERAS, J.-B., GAFFNEY, D. J., PICK-RELL, J.K., DE LEON, S., MICHELINI, K., LEWELLEN, N., CRAWFORD, G. E. et al. (2012). DNase [thinsp] I sensitivity QTLs are a major determinant of human expression variation. Nature 482 390-394.
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.F.1
Pai, A.A.2
Pique-Regi, R.3
Veyrieras, J.-B.4
Gaffney, D.J.5
Pick-Rell, J.K.6
De Leon, S.7
Michelini, K.8
Lewellen, N.9
Crawford, G.E.10
-
11
-
-
77949853541
-
Gene, region and pathway level analyses in whole-genome studies
-
DE LACRUZ, O., WEN, X., KE, B., SONG, M. and NICOLAE, D. L. (2010). Gene, region and pathway level analyses in whole-genome studies. Genet. Epidemiol. 34 222-231.
-
(2010)
Genet. Epidemiol
, vol.34
, pp. 222-231
-
-
De Lacruz, O.1
Wen, X.2
Ke, B.3
Song, M.4
Nicolae, D.L.5
-
12
-
-
84912078506
-
Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association
-
DING, Z., NI, Y., TIMMER, S.W., LEE, B.-K., BATTENHOUSE, A., LOUZADA, S., YANG, F., DUNHAM, I., CRAWFORD, G.E., LIEB, J. D. et al. (2014). Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLOS Genet. 10 e1004798.
-
(2014)
PLOS Genet
, vol.10
-
-
Ding, Z.1
Ni, Y.2
Timmer, S.W.3
Lee, B.-K.4
Battenhouse, A.5
Louzada, S.6
Yang, F.7
Dunham, I.8
Crawford, G.E.9
Lieb, J.D.10
-
13
-
-
0030052609
-
Permutation tests for multiple loci affecting a quantitative character
-
DOERGE, R.W. and CHURCHILL, G. A. (1996). Permutation tests for multiple loci affecting a quantitative character. Genetics 142 285-294.
-
(1996)
Genetics
, vol.142
, pp. 285-294
-
-
Doerge, R.W.1
Churchill, G.A.2
-
14
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
et al
-
ENCODE PROJECT CONSORTIUM et al. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
15
-
-
84878476783
-
A statistical framework for joint eQTL analysis in multiple tissues
-
FLUTRE, T., WEN, X., PRITCHARD, J. and STEPHENS, M. (2013). A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet. 9 e1003486.
-
(2013)
Plos Genet
, vol.9
-
-
Flutre, T.1
Wen, X.2
Pritchard, J.3
Stephens, M.4
-
16
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
KUNDAJE, A., MEULEMAN, W., ERNST, J., BILENKY, M., YEN, A., HERAVI-MOUSSAVI, A., KHERADPOUR, P., ZHANG, Z., WANG, J., ZILLER, M. J. et al. (2015). Integrative analysis of 111 reference human epigenomes. Nature 518 317-330.
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Kundaje, A.1
Meuleman, W.2
Ernst, J.3
Bilenky, M.4
Yen, A.5
Heravi-Moussavi, A.6
Kheradpour, P.7
Zhang, Z.8
Wang, J.9
Ziller, M.J.10
-
17
-
-
84885645853
-
Transcriptome and genome sequencing uncovers functional variation in humans
-
LAPPALAINEN, T., SAMMETH, M., FRIEDLÄNDER, M.R., HOEN, P.A.C.T., MONLONG, J., RIVAS, M.A., GONZÀLEZ-PORTA, M., KURBATOVA, N., GRIEBEL, T., FERREIRA, P.G. et al. (2013). Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501 506-511.
-
(2013)
Nature
, vol.501
, pp. 506-511
-
-
Lappalainen, T.1
Sammeth, M.2
Friedländer, M.R.3
Hoen, P.A.C.T.4
Monlong, J.5
Rivas, M.A.6
Gonzàlez-Porta, M.7
Kurbatova, N.8
Griebel, T.9
Ferreira, P.G.10
-
18
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
LEEK, J.T. and STOREY, J. D. (2007). Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3 e161.
-
(2007)
Plos Genet
, vol.3
-
-
Leek, J.T.1
Storey, J.D.2
-
19
-
-
0035628553
-
Implementations of the Monte Carlo EM algorithm
-
LEVINE, R.A. and CASELLA, G. (2001). Implementations of the Monte Carlo EM algorithm. J. Comput. Graph. Statist. 10 422-439.
-
(2001)
J. Comput. Graph. Statist
, vol.10
, pp. 422-439
-
-
Levine, R.A.1
Casella, G.2
-
20
-
-
79960967243
-
Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes
-
MARANVILLE, J.C., LUCA, F., RICHARDS, A.L., WEN, X., WITONSKY, D.B., BAXTER, S., STEPHENS, M., DI RIENZO, A. and GIBSON, G. (2011). Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLOS Genet. 7 e1002162.
-
(2011)
PLOS Genet
, vol.7
-
-
Maranville, J.C.1
Luca, F.2
Richards, A.L.3
Wen, X.4
Witonsky, D.B.5
Baxter, S.6
Stephens, M.7
Di Rienzo, A.8
Gibson, G.9
-
22
-
-
84887322043
-
Identification of genetic variants that affect histone modifications in human cells
-
MCVICKER, G., VAN DE GEIJN, B., DEGNER, J.F., CAIN, C.E., BANOVICH, N.E., RAJ, A., LEWELLEN, N., MYRTHIL, M., GILAD, Y. and PRITCHARD, J. K. (2013). Identification of genetic variants that affect histone modifications in human cells. Science 342 747-749.
-
(2013)
Science
, vol.342
, pp. 747-749
-
-
McVicker, G.1
Van De Geijn, B.2
Degner, J.F.3
Cain, C.E.4
Banovich, N.E.5
Raj, A.6
Lewellen, N.7
Myrthil, M.8
Gilad, Y.9
Pritchard, J.K.10
-
23
-
-
10844254626
-
Optimal sample size for multiple testing: The case of gene expression microarrays
-
MÜLLER, P., PARMIGIANI, G., ROBERT, C. and ROUSSEAU, J. (2004). Optimal sample size for multiple testing: The case of gene expression microarrays. J. Amer. Statist. Assoc. 99 990-1001.
-
(2004)
J. Amer. Statist. Assoc.
, vol.99
, pp. 990-1001
-
-
Müller, P.1
Parmigiani, G.2
Robert, C.3
Rousseau, J.4
-
24
-
-
84865079468
-
Quantile-based permutation thresholds for quantitative trait loci hotspots
-
NETO, E.C., KELLER, M.P., BROMAN, A.F., ATTIE, A.D., JANSEN, R.C., BROMAN, K.W. and YANDELL, B. S. (2012). Quantile-based permutation thresholds for quantitative trait loci hotspots. Genetics 191 1355-1365.
-
(2012)
Genetics
, vol.191
, pp. 1355-1365
-
-
Neto, E.C.1
Keller, M.P.2
Broman, A.F.3
Attie, A.D.4
Jansen, R.C.5
Broman, K.W.6
Yandell, B.S.7
-
25
-
-
84876452797
-
Modeling causality for pairs of phenotypes in system genetics
-
NETO, E.C., BROMAN, A.T., KELLER, M.P., ATTIE, A.D., ZHANG, B., ZHU, J. and YAN-DELL, B. S. (2013). Modeling causality for pairs of phenotypes in system genetics. Genetics 193 1003-1013.
-
(2013)
Genetics
, vol.193
, pp. 1003-1013
-
-
Neto, E.C.1
Broman, A.T.2
Keller, M.P.3
Attie, A.D.4
Zhang, B.5
Zhu, J.6
Yan-Dell, B.S.7
-
26
-
-
4444235995
-
Detecting differential gene expression with a semiparametric hierarchical mixture method
-
NEWTON, M.A., NOUEIRY, A., SARKAR, D. and AHLQUIST, P. (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5 155-176.
-
(2004)
Biostatistics
, vol.5
, pp. 155-176
-
-
Newton, M.A.1
Noueiry, A.2
Sarkar, D.3
Ahlquist, P.4
-
27
-
-
79952266465
-
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
-
PIQUE-REGI, R., DEGNER, J.F., PAI, A.A., GAFFNEY, D.J., GILAD, Y. and PRITCHARD, J.K. (2011). Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 21 447-455.
-
(2011)
Genome Res
, vol.21
, pp. 447-455
-
-
Pique-Regi, R.1
Degner, J.F.2
Pai, A.A.3
Gaffney, D.J.4
Gilad, Y.5
Pritchard, J.K.6
-
28
-
-
34547622688
-
Imputation-based analysis of association studies: Candidate regions and quantitative traits
-
SERVIN, B. and STEPHENS, M. (2007). Imputation-based analysis of association studies: Candidate regions and quantitative traits. PLoS Genet. 3 e114.
-
(2007)
Plos Genet
, vol.3
-
-
Servin, B.1
Stephens, M.2
-
29
-
-
84861153094
-
Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
-
SHABALIN, A. A. (2012). Matrix eQTL: Ultra fast eQTL analysis via large matrix operations. Bioinformatics 28 1353-1358.
-
(2012)
Bioinformatics
, vol.28
, pp. 1353-1358
-
-
Shabalin, A.A.1
-
30
-
-
0032893464
-
Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data
-
SILLANPÄÄ, M.J. and ARJAS, E. (1999). Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151 1605-1619.
-
(1999)
Genetics
, vol.151
, pp. 1605-1619
-
-
Sillanpää, M.J.1
Arjas, A.E.2
-
31
-
-
84861734626
-
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
-
STEGLE, O., PARTS, L., PIIPARI, M., WINN, J. and DURBIN, R. (2012). Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat. Protoc. 7 500-507.
-
(2012)
Nat. Protoc
, vol.7
, pp. 500-507
-
-
Stegle, O.1
Parts, L.2
Piipari, M.3
Winn, J.4
Durbin, R.5
-
32
-
-
0032434484
-
Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo
-
STEPHENS, D.A. and FISCH, R. D. (1998). Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo. Biometrics 54 1334-1347.
-
(1998)
Biometrics
, vol.54
, pp. 1334-1347
-
-
Stephens, D.A.1
Fisch, R.D.2
-
33
-
-
0345822598
-
The positive false discovery rate: A Bayesian interpretation and the q-value
-
STOREY, J. D. (2003). The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Statist. 31 2013-2035.
-
(2003)
Ann. Statist
, vol.31
, pp. 2013-2035
-
-
Storey, J.D.1
-
34
-
-
84930024854
-
Accurate and fast multiple-testing correction in eQTL studies
-
SUL, J.H., RAJ, T., DE JONG, S., DE BAKKER, P.I., RAYCHAUDHURI, S., OPHOFF, R.A., STRANGER, B.E., ESKIN, E. and HAN, B. (2015). Accurate and fast multiple-testing correction in eQTL studies. The American Journal of Human Genetics 96 857-868.
-
(2015)
The American Journal of Human Genetics
, vol.96
, pp. 857-868
-
-
Sul, J.H.1
Raj, T.2
De Jong, S.3
De Bakker, P.I.4
Raychaudhuri, S.5
Ophoff, R.A.6
Stranger, B.E.7
Eskin, E.8
Han, B.9
-
35
-
-
55449112450
-
High-resolution mapping of expression-QTLs yields insight into human gene regulation
-
VEYRIERAS, J.-B., KUDARAVALLI, S., KIM, S. Y., DERMITZAKIS, E. T., GILAD, Y., STEPHENS, M. and PRITCHARD, J. K. (2008). High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLOS Genet. 4 e1000214.
-
(2008)
PLOS Genet
, vol.4
-
-
Veyrieras, J.-B.1
Kudaravalli, S.2
Kim, S.Y.3
Dermitzakis, E.T.4
Gilad, Y.5
Stephens, M.A.6
Pritchard, J.K.7
-
36
-
-
66049114148
-
Bayes factors for genome-wide association studies: Comparison with P-values
-
WAKEFIELD, J. (2009). Bayes factors for genome-wide association studies: Comparison with P-values. Genet. Epidemiol. 33 79-86.
-
(2009)
Genet. Epidemiol
, vol.33
, pp. 79-86
-
-
Wakefield, J.1
-
38
-
-
84895881336
-
Bayesian model selection in complex linear systems, as illustrated in genetic association studies
-
WEN, X. (2014). Bayesian model selection in complex linear systems, as illustrated in genetic association studies. Biometrics 70 73-83.
-
(2014)
Biometrics
, vol.70
, pp. 73-83
-
-
Wen, X.1
-
39
-
-
84943573016
-
Bayesian model comparison in genetic association analysis: Linear mixed modeling and SNP set testing
-
WEN, X. (2015). Bayesian model comparison in genetic association analysis: Linear mixed modeling and SNP set testing. Biostatistics 16 701-712.
-
(2015)
Biostatistics
, vol.16
, pp. 701-712
-
-
Wen, X.1
-
41
-
-
84930368286
-
Cross-population joint analysis of eQTLs: Fine mapping and functional annotation
-
WEN, X., LUCA, F. and PIQUE-REGI, R. (2015). Cross-population joint analysis of eQTLs: Fine mapping and functional annotation. PLoS Genet. 11 e1005176.
-
(2015)
Plos Genet
, vol.11
-
-
Wen, X.1
Luca, F.2
Pique-Regi, R.3
-
42
-
-
84898024088
-
Bayesian methods for genetic association analysis with heterogeneous subgroups: From meta-analyses to gene-environment interactions
-
WEN, X. and STEPHENS, M. (2014). Bayesian methods for genetic association analysis with heterogeneous subgroups: From meta-analyses to gene-environment interactions. Ann. Appl. Stat. 8 176-203.
-
(2014)
Ann. Appl. Stat
, vol.8
, pp. 176-203
-
-
Wen, X.1
Stephens, M.2
-
43
-
-
23344451313
-
Bayesian model selection for genome-wide epistatic quantitative trait loci analysis
-
YI, N., YANDELL, B.S., CHURCHILL, G.A., ALLISON, D.B., EISEN, E.J. and POMP, D. (2005). Bayesian model selection for genome-wide epistatic quantitative trait loci analysis. Genetics 170 1333-1344.
-
(2005)
Genetics
, vol.170
, pp. 1333-1344
-
-
Yi, N.1
Yandell, B.S.2
Churchill, G.A.3
Allison, D.B.4
Eisen, E.J.5
Pomp, D.6
|