-
1
-
-
84884311355
-
Genetic interaction networks: Toward an understanding of heritability
-
Baryshnikova, A., M. Costanzo, C. L. Myers, B. Andrews, and C. Boone, 2013 Genetic interaction networks: toward an understanding of heritability. Annu. Rev. Genom. Hum. G 14: 111- 133.
-
(2013)
Annu. Rev. Genom. Hum. G
, vol.14
, pp. 111-133
-
-
Baryshnikova, A.1
Costanzo, M.2
Myers, C.L.3
Andrews, B.4
Boone, C.5
-
2
-
-
22144454660
-
Genetical genomics analysis of a yeast segregant population for transcription network inference
-
Bing, N., and I. Hoeschele, 2005 Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics 170: 533-542.
-
(2005)
Genetics
, vol.170
, pp. 533-542
-
-
Bing, N.1
Hoeschele, I.2
-
3
-
-
84873722165
-
Finding the sources of missing heritability in a yeast cross
-
Bloom, J. S., I. M. Ehrenreich, W. T. Loo, T.-L. V. Lite, and L. Kruglyak, 2013 Finding the sources of missing heritability in a yeast cross. Nature 494: 234-237.
-
(2013)
Nature
, vol.494
, pp. 234-237
-
-
Bloom, J.S.1
Ehrenreich, I.M.2
Loo, W.T.3
Lite, T.-L.V.4
Kruglyak, L.5
-
4
-
-
55449096399
-
Genetical genomics: Spotlight on QTL hotspots
-
Breitling, R., Y. Li, B. M. Tesson, J. Fu, C. Wu 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
-
5
-
-
13444306165
-
The landscape of genetic complexity across 5,700 gene expression traits in yeast
-
Brem, R. B., and L. Kruglyak, 2005 The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA 102: 1572-1577.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 1572-1577
-
-
Brem, R.B.1
Kruglyak, L.2
-
6
-
-
0037177625
-
Genetic dissection of transcriptional regulation in budding yeast
-
Brem, R. B., G. Yvert, R. Clinton, and L. Kruglyak, 2002 Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
-
(2002)
Science
, vol.296
, pp. 752-755
-
-
Brem, R.B.1
Yvert, G.2
Clinton, R.3
Kruglyak, L.4
-
8
-
-
0037958742
-
R/qtl: QTL mapping in experimental crosses
-
Broman, K. W., H. Wu, S. Sen, and G. A. Churchill, 2003 R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889-890.
-
(2003)
Bioinformatics
, vol.19
, pp. 889-890
-
-
Broman, K.W.1
Wu, H.2
Sen, S.3
Churchill, G.A.4
-
9
-
-
33845523872
-
A robust procedure for Gaussian graphical model search from microarray data with p larger than n
-
Castelo, R., and A. Roverato, 2006 A robust procedure for Gaussian graphical model search from microarray data with p larger than n. J. Mach. Learn. Res. 7: 2621-2650.
-
(2006)
J. Mach. Learn. Res
, vol.7
, pp. 2621-2650
-
-
Castelo, R.1
Roverato, A.2
-
10
-
-
59649121280
-
Reverse engineering molecular regulatory networks from microarray data with qp-graphs
-
Castelo, R., and A. Roverato, 2009 Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comput. Biol. 16: 213-227.
-
(2009)
J. Comput. Biol
, vol.16
, pp. 213-227
-
-
Castelo, R.1
Roverato, A.2
-
11
-
-
49849090353
-
Inferring causal phenotype networks from segregating populations
-
Chaibub Neto, E., C. T. Ferrara, A. D. Attie, and B. S. Yandell, 2008 Inferring causal phenotype networks from segregating populations. Genetics 179: 1089-1100.
-
(2008)
Genetics
, vol.179
, pp. 1089-1100
-
-
Chaibub Neto, E.1
Ferrara, C.T.2
Attie, A.D.3
Yandell, B.S.4
-
12
-
-
84870284276
-
Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes
-
Chaibub Neto, E., M. P. Keller, A. D. Attie, and B. S. Yandell, 2010 Causal graphical models in systems genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Ann. Appl. Stat. 4: 320-339.
-
(2010)
Ann. Appl. Stat
, vol.4
, pp. 320-339
-
-
Chaibub Neto, E.1
Keller, M.P.2
Attie, A.D.3
Yandell, B.S.4
-
13
-
-
84876452797
-
Modeling causality for pairs of phenotypes in systems genetics
-
Chaibub Neto, E., A. T. Broman, M. P. Keller, A. D. Attie, B. Zhang et al., 2013 Modeling causality for pairs of phenotypes in systems genetics. Genetics 193: 1003-1013.
-
(2013)
Genetics
, vol.193
, pp. 1003-1013
-
-
Chaibub Neto, E.1
Broman, A.T.2
Keller, M.P.3
Attie, A.D.4
Zhang, B.5
-
14
-
-
42949144555
-
Harnessing naturally randomized transcription to infer regulatory relationships among genes
-
Chen, L. S., F. Emmert-Streib, and J. D. Storey, 2007 Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biol. 8: R219.
-
(2007)
Genome Biol
, vol.8
, pp. R219
-
-
Chen, L.S.1
Emmert-Streib, F.2
Storey, J.D.3
-
15
-
-
68949211709
-
Genetics of human gene expression: Mapping DNA variants that influence gene expression
-
Cheung, V. G., and R. S. Spielman, 2009 Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat. Rev. Genet. 10: 595-604.
-
(2009)
Nat. Rev. Genet
, vol.10
, pp. 595-604
-
-
Cheung, V.G.1
Spielman, R.S.2
-
16
-
-
45849120994
-
Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways
-
Chin, C.-S., V. Chubukov, E. R. Jolly, J. DeRisi, and H. Li, 2008 Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol. 6: e146.
-
(2008)
PLoS Biol
, vol.6
-
-
Chin, C.-S.1
Chubukov, V.2
Jolly, E.R.3
De Risi, J.4
Li, H.5
-
17
-
-
67849118749
-
Expression quantitative trait loci mapping with multivariate sparse partial least squares regression
-
Chun, H., and S. Keleş, 2009 Expression quantitative trait loci mapping with multivariate sparse partial least squares regression. Genetics 182: 79-90.
-
(2009)
Genetics
, vol.182
, pp. 79-90
-
-
Chun, H.1
Keleş, S.2
-
18
-
-
75649111192
-
The genetic landscape of a cell
-
Costanzo, M., A. Baryshnikova, J. Bellay, Y. Kim, E. D. Spear et al., 2010 The genetic landscape of a cell. Science 327: 425-431.
-
(2010)
Science
, vol.327
, pp. 425-431
-
-
Costanzo, M.1
Baryshnikova, A.2
Bellay, J.3
Kim, Y.4
Spear, E.D.5
-
19
-
-
84875203794
-
Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules
-
Curtis, R. E., S. Kim, J. L. Woolford, Jr., W. Xu, and E. P. Xing, 2013 Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules. BMC Genomics 14: 1-17.
-
(2013)
BMC Genomics
, vol.14
, pp. 1-17
-
-
Curtis, R.E.1
Kim, S.2
Woolford, J.L.3
Xu, W.4
Xing, E.P.5
-
20
-
-
10444281626
-
Collapsibility of graphical cgregression models
-
Didelez, V., and D. Edwards, 2004 Collapsibility of graphical cgregression models. Scand. J. Stat. 31: 535-551.
-
(2004)
Scand. J. Stat
, vol.31
, pp. 535-551
-
-
Didelez, V.1
Edwards, D.2
-
22
-
-
76949106424
-
Selecting high-dimensional mixed graphical models using minimal aic or bic forests
-
Edwards, D., G. C. G. de Abreu, and R. Labouriau, 2010 Selecting high-dimensional mixed graphical models using minimal aic or bic forests. BMC Bioinformatics 11: 18.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 18
-
-
Edwards, D.1
de Abreu, G.C.G.2
Labouriau, R.3
-
23
-
-
47849109874
-
Positive definite completions of partial Hermitian matrices
-
Grone, R., C. Johnson, E. Sá, and H. Wolkowicz, 1984 Positive definite completions of partial Hermitian matrices. Linear Algebra Appl. 58: 109-124.
-
(1984)
Linear Algebra Appl
, vol.58
, pp. 109-124
-
-
Grone, R.1
Johnson, C.2
Sá, E.3
Wolkowicz, H.4
-
26
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T. R., M. J. Marton, A. R. Jones, C. J. Roberts, R. Stoughton et al., 2000 Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
-
27
-
-
0035400051
-
Genetical genomics: The added value from segregation
-
Jansen, R. C., and J.-P. Nap, 2001 Genetical genomics: the added value from segregation. Trends Genet. 17: 388-390.
-
(2001)
Trends Genet
, vol.17
, pp. 388-390
-
-
Jansen, R.C.1
Nap, J.-P.2
-
28
-
-
33947524259
-
Estimating high-dimensional directed acyclic graphs with the pc-algorithm
-
Kalisch, M., and P. Bühlmann, 2007 Estimating high-dimensional directed acyclic graphs with the pc-algorithm. J. Mach. Learn. Res. 8: 613-636.
-
(2007)
J. Mach. Learn. Res
, vol.8
, pp. 613-636
-
-
Kalisch, M.1
Bühlmann, P.2
-
29
-
-
77950825718
-
Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples
-
Kang, E. Y., C. Ye, I. Shpitser, and E. Eskin, 2010 Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples. J. Comput. Biol. 17: 533-546.
-
(2010)
J. Comput. Biol
, vol.17
, pp. 533-546
-
-
Kang, E.Y.1
Ye, C.2
Shpitser, I.3
Eskin, E.4
-
30
-
-
61849171085
-
Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots
-
Kang, H. M., C. Ye, and E. Eskin, 2008 Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics 180: 1909-1925.
-
(2008)
Genetics
, vol.180
, pp. 1909-1925
-
-
Kang, H.M.1
Ye, C.2
Eskin, E.3
-
31
-
-
33645068841
-
Statistical methods for expression quantitative trait loci (eQTL) mapping
-
Kendziorski, C., M. Chen, M. Yuan, H. Lan, and A. Attie, 2006 Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics 62: 19-27.
-
(2006)
Biometrics
, vol.62
, pp. 19-27
-
-
Kendziorski, C.1
Chen, M.2
Yuan, M.3
Lan, H.4
Attie, A.5
-
32
-
-
70149098541
-
Statistical estimation of correlated genome associations to a quantitative trait network
-
Kim, S., and E. P. Xing, 2009 Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet. 5: e1000587.
-
(2009)
PLoS Genet
, vol.5
-
-
Kim, S.1
Xing, E.P.2
-
33
-
-
84860916660
-
Hive plots: Rational approach to visualizing networks
-
Krzywinski, M., I. Birol, S. J. Jones, and M. A. Marra, 2012 Hive plots: rational approach to visualizing networks. Brief. Bioinform. 13: 627-644.
-
(2012)
Brief. Bioinform
, vol.13
, pp. 627-644
-
-
Krzywinski, M.1
Birol, I.2
Jones, S.J.3
Marra, M.A.4
-
34
-
-
0004047518
-
-
Oxford University Press, Oxford
-
Lauritzen, S., 1996 Graphical Models. Oxford University Press, Oxford.
-
(1996)
Graphical Models
-
-
Lauritzen, S.1
-
35
-
-
0002480085
-
Graphical models for associations between variables, some of which are qualitative and some quantitative
-
Lauritzen, S., and N. Wermuth, 1989 Graphical models for associations between variables, some of which are qualitative and some quantitative. Ann. Stat. 17: 31-57.
-
(1989)
Ann. Stat
, vol.17
, pp. 31-57
-
-
Lauritzen, S.1
Wermuth, N.2
-
36
-
-
79952489475
-
Estimating missing heritability for disease from genomewide association studies
-
Lee, S. H., N. R. Wray, M. E. Goddard, and P. M. Visscher, 2011 Estimating missing heritability for disease from genomewide association studies. Am. J. Hum. Genet. 88: 294-305.
-
(2011)
Am. J. Hum. Genet
, vol.88
, pp. 294-305
-
-
Lee, S.H.1
Wray, N.R.2
Goddard, M.E.3
Visscher, P.M.4
-
37
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
Leek, J. T., and J. D. Storey, 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
-
38
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
Leek, J. T., R. B. Scharpf, H. C. Bravo, D. Simcha, B. Langmead et al., 2010 Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. 11: 733-739.
-
(2010)
Nat. Rev. Genet
, vol.11
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
-
39
-
-
0036839549
-
Locus control regions
-
Li, Q., K. R. Peterson, X. Fang, and G. Stamatoyannopoulos, 2002 Locus control regions. Blood 100: 3077-3086.
-
(2002)
Blood
, vol.100
, pp. 3077-3086
-
-
Li, Q.1
Peterson, K.R.2
Fang, X.3
Stamatoyannopoulos, G.4
-
40
-
-
78049312702
-
Correction for hidden confounders in the genetic analysis of gene expression
-
Listgarten, J., C. Kadie, and D. Heckerman, 2010 Correction for hidden confounders in the genetic analysis of gene expression. Proc. Natl. Acad. Sci. USA 107: 16465-16470.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 16465-16470
-
-
Listgarten, J.1
Kadie, C.2
Heckerman, D.3
-
41
-
-
45149096374
-
Gene network inference via structural equation modeling in genetical genomics experiments
-
Liu, B., A. de la Fuente, and I. Hoeschele, 2008 Gene network inference via structural equation modeling in genetical genomics experiments. Genetics 178: 1763-1776.
-
(2008)
Genetics
, vol.178
, pp. 1763-1776
-
-
Liu, B.1
de la Fuente, A.2
Hoeschele, I.3
-
42
-
-
77957342854
-
Data-driven assessment of eQTL mapping methods
-
Michaelson, J. J., R. Alberts, K. Schughart, and A. Beyer, 2010 Data-driven assessment of eQTL mapping methods. BMC Genomics 11: 502.
-
(2010)
BMC Genomics
, vol.11
, pp. 502
-
-
Michaelson, J.J.1
Alberts, R.2
Schughart, K.3
Beyer, A.4
-
43
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population
-
Montgomery, S. B., M. Sammeth, M. Gutierrez-Arcelus, R. P. Lach, C. Ingle et al., 2010 Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773- 777.
-
(2010)
Nature
, vol.464
, pp. 773-777
-
-
Montgomery, S.B.1
Sammeth, M.2
Gutierrez-Arcelus, M.3
Lach, R.P.4
Ingle, C.5
-
44
-
-
79851507206
-
Joint genetic analysis of gene expression data with inferred cellular phenotypes
-
Parts, L., O. Stegle, J. Winn, and R. Durbin, 2011 Joint genetic analysis of gene expression data with inferred cellular phenotypes. PLoS Genet. 7: e1001276.
-
(2011)
PLoS Genet
, vol.7
-
-
Parts, L.1
Stegle, O.2
Winn, J.3
Durbin, R.4
-
45
-
-
33750481513
-
Heritability and tissue specificity of expression quantitative trait loci
-
Petretto, E., J. Mangion, N. J. Dickens, S. A. Cook, M. K. Kumaran et al., 2006 Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet. 2: e172.
-
(2006)
PLoS Genet
, vol.2
-
-
Petretto, E.1
Mangion, J.2
Dickens, N.J.3
Cook, S.A.4
Kumaran, M.K.5
-
47
-
-
35748949257
-
A comparison of background correction methods for two-colour microarrays
-
Ritchie, M. E., J. Silver, A. Oshlack, M. Holmes, D. Diyagama et al., 2007 A comparison of background correction methods for two-colour microarrays. Bioinformatics 23: 2700-2707.
-
(2007)
Bioinformatics
, vol.23
, pp. 2700-2707
-
-
Ritchie, M.E.1
Silver, J.2
Oshlack, A.3
Holmes, M.4
Diyagama, D.5
-
48
-
-
57649124192
-
Reverse engineering the genotype- phenotype map with natural genetic variation
-
Rockman, M. V., 2008 Reverse engineering the genotype- phenotype map with natural genetic variation. Nature 456: 738-744.
-
(2008)
Nature
, vol.456
, pp. 738-744
-
-
Rockman, M.V.1
-
49
-
-
33750204290
-
Genetics of global gene expression
-
Rockman, M. V., and L. Kruglyak, 2006 Genetics of global gene expression. Nat. Rev. Genet. 7: 862-872.
-
(2006)
Nat. Rev. Genet
, vol.7
, pp. 862-872
-
-
Rockman, M.V.1
Kruglyak, L.2
-
50
-
-
0035995077
-
Hyper inverse Wishart distribution for nondecomposable graphs and its application to Bayesian inference for Gaussian graphical models
-
Roverato, A., 2002 Hyper inverse Wishart distribution for nondecomposable graphs and its application to Bayesian inference for Gaussian graphical models. Scand. J. Stat. 29: 391-411.
-
(2002)
Scand. J. Stat
, vol.29
, pp. 391-411
-
-
Roverato, A.1
-
51
-
-
0037456823
-
Genetics of gene expression surveyed in maize, mouse and man
-
Schadt, E. E., S. A. Monks, T. A. Drake, A. J. Lusis, N. Che et al., 2003 Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
-
(2003)
Nature
, vol.422
, pp. 297-302
-
-
Schadt, E.E.1
Monks, S.A.2
Drake, T.A.3
Lusis, A.J.4
Che, N.5
-
53
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth, G. K., and T. Speed, 2003 Normalization of cDNA microarray data. Methods 31: 265-273.
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.2
-
54
-
-
77955505742
-
A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies
-
Stegle, O., L. Parts, R. Durbin, and J. Winn, 2010 A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLOS Comput. Biol. 6: e1000770.
-
(2010)
PLOS Comput. Biol
, vol.6
-
-
Stegle, O.1
Parts, L.2
Durbin, R.3
Winn, J.4
-
55
-
-
84891806965
-
The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
-
Teixeira, M. C., P. T. Monteiro, J. F. Guerreiro, J. P. Gonçalves, N. P. Mira et al., 2014 The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res. 42: D161-D166.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D161-D166
-
-
Teixeira, M.C.1
Monteiro, P.T.2
Guerreiro, J.F.3
Gonçalves, J.P.4
Mira, N.P.5
-
56
-
-
73949149600
-
eQTL analysis in mice and rats
-
Springer, New York
-
Tesson, B. M., and R. C. Jansen, 2009 eQTL analysis in mice and rats, pp. 285-309 in Cardiovascular Genomics: Methods in Molecular Biology, Vol. 573. Springer, New York.
-
(2009)
Cardiovascular Genomics: Methods in Molecular Biology
, vol.573
, pp. 285-309
-
-
Tesson, B.M.1
Jansen, R.C.2
-
57
-
-
84885018609
-
Systematic identification of trans eQTLs as putative drivers of known disease associations
-
Westra, H.-J., M. J. Peters, T. Esko, H. Yaghootkar, C. Schurmann et al., 2013 Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 45: 1238-1243.
-
(2013)
Nat. Genet
, vol.45
, pp. 1238-1243
-
-
Westra, H.-J.1
Peters, M.J.2
Esko, T.3
Yaghootkar, H.4
Schurmann, C.5
-
58
-
-
0042856391
-
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
-
Yvert, G., R. B. Brem, J. Whittle, J. M. Akey, E. Foss et al., 2003 Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35: 57-64.
-
(2003)
Nat. Genet
, vol.35
, pp. 57-64
-
-
Yvert, G.1
Brem, R.B.2
Whittle, J.3
Akey, J.M.4
Foss, E.5
-
59
-
-
3242806720
-
An integrative genomics approach to the reconstruction of gene networks in segregating populations
-
Zhu, J., P. Y. Lum, J. Lamb, D. GuhaThakurta, S. W. Edwards et al., 2004 An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet. Genome Res. 105: 363-374.
-
(2004)
Cytogenet. Genome Res
, vol.105
, pp. 363-374
-
-
Zhu, J.1
Lum, P.Y.2
Lamb, J.3
Guha Thakurta, D.4
Edwards, S.W.5
-
60
-
-
45149106353
-
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
-
Zhu, J., B. Zhang, E. N. Smith, B. Drees, R. B. Brem et al., 2008 Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat. Genet. 40: 854-861.
-
(2008)
Nat. Genet
, vol.40
, pp. 854-861
-
-
Zhu, J.1
Zhang, B.2
Smith, E.N.3
Drees, B.4
Brem, R.B.5
|