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Inverse covariance estimation for high-dimensional data in linear time and space: Spectral methods for riccati and sparse models. arXiv preprint arXiv:13096838. 2013."},{"key":"ref20","first-page":"1059","article-title":"The huge package for high-dimensional undirected graph estimation in R","volume":"13","author":"T Zhao","year":"2012","journal-title":"The Journal of Machine Learning Research"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1101\/gr.142521.112","article-title":"A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines","volume":"23","author":"L Liang","year":"2013","journal-title":"Genome research"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/nar\/gkg091","article-title":"ArrayExpress\u2014a public repository for microarray gene expression data at the EBI","volume":"31","author":"A Brazma","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.jaci.2007.10.028","article-title":"Targeting TNF-alpha: a novel therapeutic approach for asthma","volume":"121","author":"C Brightling","year":"2008","journal-title":"J Allergy Clin Immunol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"14410","DOI":"10.1073\/pnas.0507189102","article-title":"Role for macrophage migration inhibitory factor in asthma","volume":"102","author":"Y Mizue","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/j.tiv.2003.10.007","article-title":"Microarray analysis of the effect of diesel exhaust particles on in vitro cultured macrophages","volume":"18","author":"GR Verheyen","year":"2004","journal-title":"Toxicol In Vitro"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"106","DOI":"10.4168\/aair.2015.7.2.106","article-title":"Endoplasmic reticulum stress and the related signaling networks in severe asthma","volume":"7","author":"SR Kim","year":"2015","journal-title":"Allergy Asthma Immunol Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.biopsych.2014.09.006","article-title":"Altered glutamate protein co-expression network topology linked to spine loss in the auditory cortex of schizophrenia","volume":"77","author":"ML MacDonald","year":"2015","journal-title":"Biol Psychiatry"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/bti062","article-title":"An empirical Bayes approach to inferring large-scale gene association networks","volume":"21","author":"J Schafer","year":"2005","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3565","DOI":"10.1093\/bioinformatics\/bth445","article-title":"Discovery of meaningful associations in genomic data using partial correlation coefficients","volume":"20","author":"A De La Fuente","year":"2004","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/bts038","article-title":"Using biologically interrelated experiments to identify pathway genes in Arabidopsis","volume":"28","author":"K Kim","year":"2012","journal-title":"Bioinformatics"},{"key":"ref31","first-page":"ass058","article-title":"Covariate-adjusted precision matrix estimation with an application in genetical genomics","author":"TT Cai","year":"2012","journal-title":"Biometrika"},{"key":"ref32","first-page":"2630","article-title":"A Sparse Conditional Gaussian Graphical Model for Analysis of Genetical Genomics Data. 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