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@article{schafer05,
	Author = {Sch{\"a}fer, Juliane and Strimmer, Korbinian},
	Date-Added = {2020-05-19 14:25:29 -0400},
	Date-Modified = {2020-05-19 14:25:56 -0400},
	Journal = {Statistical Applications in Genetics and Molecular Biology},
	Number = {1},
	Pages = {Article 32},
	Publisher = {De Gruyter},
	Title = {A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics},
	Volume = {4},
	Year = {2005}}

@article{biomart,
	Author = {Steffen Durinck and Paul T. Spellman and Ewan Birney and Wolfgang Huber},
	Date-Added = {2020-05-19 14:19:44 -0400},
	Date-Modified = {2020-05-19 14:20:03 -0400},
	Journal = {Nature Protocols},
	Pages = {1184--1191},
	Title = {Mapping Identifiers for the Integration of Genomic Datasets with the {R/B}ioconductor Package {biomaRt}},
	Volume = {4},
	Year = {2009}}

@manual{reactome,
	Author = {Willem Ligtenberg},
	Date-Added = {2020-05-19 14:17:24 -0400},
	Date-Modified = {2020-05-19 14:20:29 -0400},
	Note = {R package version 1.68.0},
	Title = {{reactome.db}: A Set of Annotation Maps for Reactome},
	Year = {2019}}

@manual{seqnet,
	Author = {Tyler Grimes and Somnath Datta},
	Date-Added = {2020-05-19 13:39:52 -0400},
	Date-Modified = {2020-05-19 13:39:52 -0400},
	Note = {R package version 1.1.0},
	Title = {SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks},
	Url = {https://CRAN.R-project.org/package=SeqNet},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=SeqNet}}

@manual{corpcor,
	Author = {Juliane Schafer and Rainer Opgen-Rhein and Verena Zuber and Miika Ahdesmaki and A. Pedro Duarte Silva and Korbinian Strimmer.},
	Date-Added = {2020-05-19 13:24:27 -0400},
	Date-Modified = {2020-05-19 13:24:27 -0400},
	Note = {R package version 1.6.9},
	Title = {corpcor: Efficient Estimation of Covariance and (Partial) Correlation},
	Url = {https://CRAN.R-project.org/package=corpcor},
	Year = {2017},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=corpcor}}

@manual{huge,
	Author = {Haoming Jiang and Xinyu Fei and Han Liu and Kathryn Roeder and John Lafferty and Larry Wasserman and Xingguo Li and Tuo Zhao},
	Date-Added = {2020-05-19 13:17:41 -0400},
	Date-Modified = {2020-05-19 13:17:41 -0400},
	Note = {R package version 1.3.3},
	Title = {huge: High-Dimensional Undirected Graph Estimation},
	Url = {https://CRAN.R-project.org/package=huge},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=huge}}

@manual{dwlasso,
	Author = {Nurgazy Sulaimanov and Sunil Kumar and Heinz Koeppl},
	Date-Added = {2020-05-19 13:10:32 -0400},
	Date-Modified = {2020-05-19 13:10:32 -0400},
	Note = {R package version 1.1},
	Title = {DWLasso: Degree Weighted Lasso},
	Url = {https://CRAN.R-project.org/package=DWLasso},
	Year = {2017},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=DWLasso}}

@manual{bc3net,
	Author = {Ricardo {de Matos Simoes} and Frank Emmert-Streib},
	Date-Added = {2020-05-19 13:05:22 -0400},
	Date-Modified = {2020-05-19 13:05:22 -0400},
	Note = {R package version 1.0.4},
	Title = {bc3net: Gene Regulatory Network Inference with Bc3net},
	Url = {https://CRAN.R-project.org/package=bc3net},
	Year = {2016},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=bc3net}}

@article{grimes19,
	Author = {Grimes, Tyler and Potter, S Steven and Datta, Somnath},
	Date-Added = {2020-05-19 12:33:26 -0400},
	Date-Modified = {2020-05-19 12:33:26 -0400},
	Journal = {Scientific reports},
	Number = {1},
	Pages = {5479},
	Publisher = {Nature Publishing Group},
	Title = {Integrating Gene Regulatory Pathways into Differential Network Analysis of Gene Expression Data},
	Volume = {9},
	Year = {2019}}

@article{barzel13,
	Author = {Barzel, Baruch and Barab{\'a}si, Albert-L{\'a}szl{\'o}},
	Date-Added = {2020-05-19 12:31:52 -0400},
	Date-Modified = {2020-05-19 12:31:52 -0400},
	Journal = {Nature Biotechnology},
	Number = {8},
	Pages = {720},
	Publisher = {Nature Publishing Group},
	Title = {Network Link Prediction by Global Silencing of Indirect Correlations},
	Volume = {31},
	Year = {2013}}

@manual{friedman18,
	Author = {Jerome Friedman and Trevor Hastie and Rob Tibshirani},
	Date-Added = {2020-05-19 12:31:52 -0400},
	Date-Modified = {2020-05-19 12:31:52 -0400},
	Note = {\proglang{R} package version 1.10},
	Title = {\pkg{glasso}: {G}raphical Lasso: Estimation of Gaussian Graphical Models},
	Year = {2018}}

@article{meyer07,
	Author = {Meyer, Patrick E and Kontos, Kevin and Lafitte, Frederic and Bontempi, Gianluca},
	Date-Added = {2020-05-19 12:31:52 -0400},
	Date-Modified = {2020-05-19 12:31:52 -0400},
	Journal = {EURASIP Journal on Bioinformatics and Systems Biology},
	Pages = {8--8},
	Publisher = {Hindawi Publishing Corp.},
	Title = {Information-Theoretic Inference of Large Transcriptional Regulatory Networks},
	Volume = {2007},
	Year = {2007}}

@article{meyer08,
	Author = {Meyer, Patrick E and Lafitte, Frederic and Bontempi, Gianluca},
	Date-Added = {2020-05-19 12:31:52 -0400},
	Date-Modified = {2020-05-19 12:31:52 -0400},
	Journal = {BMC Bioinformatics},
	Number = {1},
	Pages = {461},
	Publisher = {BioMed Central},
	Title = {\pkg{minet}: A \proglang{R}/{B}ioconductor Package for Inferring Large Transcriptional Networks using Mutual Information},
	Volume = {9},
	Year = {2008}}

@article{altay10,
	Author = {Altay, G{\"o}kmen and Emmert-Streib, Frank},
	Date-Added = {2020-05-19 12:29:56 -0400},
	Date-Modified = {2020-05-19 12:29:56 -0400},
	Journal = {BMC Systems Biology},
	Number = {1},
	Pages = {132},
	Publisher = {BioMed Central},
	Title = {Inferring the Conservative Causal Core of Gene Regulatory Networks},
	Volume = {4},
	Year = {2010}}

@article{faith07,
	Author = {Faith, Jeremiah J and Hayete, Boris and Thaden, Joshua T and Mogno, Ilaria and Wierzbowski, Jamey and Cottarel, Guillaume and Kasif, Simon and Collins, James J and Gardner, Timothy S},
	Date-Added = {2020-05-19 12:29:56 -0400},
	Date-Modified = {2020-05-19 12:29:56 -0400},
	Journal = {PLoS Biology},
	Number = {1},
	Pages = {e8},
	Publisher = {Public Library of Science},
	Title = {Large-Scale Mapping and Validation of {E}scherichia Coli Transcriptional Regulation from a Compendium of Expression Profiles},
	Volume = {5},
	Year = {2007}}

@article{huynhthu10,
	Author = {Huynh-Thu, V{\^a}n Anh and Irrthum, Alexandre and Wehenkel, Louis and Geurts, Pierre},
	Date-Added = {2020-05-19 12:29:56 -0400},
	Date-Modified = {2020-05-19 12:29:56 -0400},
	Journal = {PloS ONE},
	Number = {9},
	Pages = {e12776},
	Publisher = {Public Library of Science},
	Title = {Inferring Regulatory Networks from Expression Data using Tree-Based Methods},
	Volume = {5},
	Year = {2010}}

@inproceedings{margolin06,
	Author = {Margolin, Adam A and Nemenman, Ilya and Basso, Katia and Wiggins, Chris and Stolovitzky, Gustavo and Dalla Favera, Riccardo and Califano, Andrea},
	Booktitle = {BMC Bioinformatics},
	Date-Added = {2020-05-19 12:29:56 -0400},
	Date-Modified = {2020-05-19 12:29:56 -0400},
	Number = {1},
	Organization = {BioMed Central},
	Pages = {S7},
	Title = {{ARACNE}: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context},
	Volume = {7},
	Year = {2006}}

@article{matos12,
	Author = {Matos Simoes, Ricardo de and Emmert-Streib, Frank},
	Date-Added = {2020-05-19 12:29:56 -0400},
	Date-Modified = {2020-05-19 12:29:56 -0400},
	Journal = {PloS ONE},
	Number = {3},
	Pages = {e33624},
	Publisher = {Public Library of Science},
	Title = {Bagging Statistical Network Inference from Large-Scale Gene Expression Data},
	Volume = {7},
	Year = {2012}}

@article{sulaimanov18,
	Author = {Sulaimanov, Nurgazy and Kumar, Sunil and Burdet, Fr{\'e}d{\'e}ric and Ibberson, Mark and Pagni, Marco and Koeppl, Heinz},
	Date-Added = {2020-05-19 12:29:56 -0400},
	Date-Modified = {2020-05-19 12:29:56 -0400},
	Journal = {Bioinformatics},
	Number = {6},
	Pages = {987--994},
	Publisher = {Oxford University Press},
	Title = {Inferring Gene Expression Networks with Hubs using a Degree Weighted {L}asso Approach},
	Volume = {35},
	Year = {2018}}
