@article{williams_null,
 title={On Accepting the Null Hypothesis of Conditional Independence in Partial Correlation Networks: A Bayesian Analysis},
 journal={PsyArXiv},
 author={Williams, Donald R and Briganti, Giovanni and Linkowski, Paul and Mulder, Joris},
 year={2021},
}

@article{sustik2012glassofast,
  title={GLASSOFAST: An efficient GLASSO implementation},
  author={Sustik, M{\'a}ty{\'a}s A and Calderhead, Ben},
  journal={UTCS Technical Report TR-12-29 2012},
  year={2012},
  publisher={University of Texas at Austin Austin}
}


@article{williams_2021,
 title={The Confidence Interval that Wasn't:
 Bootstrapped "Confidence Intervals" in L1-Regularized Partial Correlation Networks},
 DOI={10.31234/osf.io/kjh2f},
 Journal={PsyArXiv},
 author={Williams, Donald R},
 year={2021}
}

@article{van2017comparing,
  title={Comparing network structures on three aspects: A permutation test},
  author={Van Borkulo, Claudia D and Boschloo, Lynn and Kossakowski, J and Tio,
  Pia and Schoevers, Robert A and Borsboom, Denny and Waldorp, Lourens J},
  journal={Manuscript submitted for publication},
  volume={10},
  year={2017}
}

@article{javanmard2014confidence,
  title={Confidence intervals and hypothesis testing for high-dimensional regression},
  author={Javanmard, Adel and Montanari, Andrea},
  journal={The Journal of Machine Learning Research},
  volume={15},
  number={1},
  pages={2869--2909},
  year={2014},
  publisher={JMLR. org}
}

@article{van2014asymptotically,
  title={On asymptotically optimal confidence regions and tests for high-dimensional models},
  author={Van de Geer, Sara and B{\"u}hlmann, Peter and Ritov, Ya’acov and Dezeure, Ruben},
  journal={The Annals of Statistics},
  volume={42},
  number={3},
  pages={1166--1202},
  year={2014},
  publisher={Institute of Mathematical Statistics}
}

@article{zhang2014confidence,
  title={Confidence intervals for low dimensional parameters in high dimensional linear models},
  author={Zhang, Cun-Hui and Zhang, Stephanie S},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={76},
  number={1},
  pages={217--242},
  year={2014},
  publisher={Wiley Online Library}
}

@article{rodriguez_williams_rast_mulder_2020,
 title={On Formalizing Theoretical Expectations: Bayesian Testing of Central
        Structures in Psychological Networks},
 DOI={10.31234/osf.io/zw7pf},
 publisher={PsyArXiv},
 author={Rodriguez, Josue E and Williams, Donald R and Rast, Philippe and Mulder, Joris},
 year={2020},
 journal={PsyArXiv}
}

@article{emmert2019constrained,
  title={Constrained covariance matrices with a biologically realistic structure:
  Comparison of methods for generating high-dimensional Gaussian graphical models},
  author={Emmert-Streib, Frank and Tripathi, Shailesh and Dehmer, Matthias},
  journal={Frontiers in Applied Mathematics and Statistics},
  volume={5},
  pages={17},
  year={2019},
  publisher={Frontiers}
}

@book{hastie2009elements,
  title={The elements of statistical learning: data mining, inference, and prediction},
  author={Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome},
  year={2009},
  publisher={Springer Science \& Business Media}
}

@article{stephens1998,
  title={On the Inverse of the Covariance Matrix in Portfolio Analysis},
  author={Stephens, Guy},
  journal={The Journal of Finance},
  number={5},
  pages={1821--1827},
  volume={53},
  year={1998}
}

@article{dicker2013variable,
  title={Variable selection and estimation with the seamless-L 0 penalty},
  author={Dicker, Lee and Huang, Baosheng and Lin, Xihong},
  journal={Statistica Sinica},
  pages={929--962},
  year={2013},
  publisher={JSTOR}
}

@article{wang2016variable,
  title={Variable selection and parameter estimation with the Atan regularization method},
  author={Wang, Yanxin and Zhu, Li},
  journal={Journal of Probability and Statistics},
  year={2016},
  publisher={Hindawi}
}

@article{wang2018variable,
  title={Variable selection and estimation using a continuous approximation to the L0 penalty},
  author={Wang, Yanxin and Fan, Qibin and Zhu, Li},
  journal={Annals of the Institute of Statistical Mathematics},
  volume={70},
  number={1},
  pages={191--214},
  year={2018},
  publisher={Springer}
}

@article{fan2001variable,
  title={Variable selection via nonconcave penalized likelihood and its oracle properties},
  author={Fan, Jianqing and Li, Runze},
  journal={Journal of the American statistical Association},
  volume={96},
  number={456},
  pages={1348--1360},
  year={2001},
  publisher={Taylor \& Francis}
}

@article{zhang2010nearly,
  title={Nearly unbiased variable selection under minimax concave penalty},
  author={Zhang, Cun-Hui},
  journal={The Annals of statistics},
  volume={38},
  number={2},
  pages={894--942},
  year={2010},
  publisher={Institute of Mathematical Statistics}
}

@article{fan2009network,
  title={Network exploration via the adaptive LASSO and SCAD penalties},
  author={Fan, Jianqing and Feng, Yang and Wu, Yichao},
  journal={The annals of applied statistics},
  volume={3},
  number={2},
  pages={521},
  year={2009},
  publisher={NIH Public Access}
}

@article{zou2008one,
  title={One-step sparse estimates in nonconcave penalized likelihood models},
  author={Zou, Hui and Li, Runze},
  journal={Annals of statistics},
  volume={36},
  number={4},
  pages={1509},
  year={2008},
  publisher={NIH Public Access}
}

@article{zhang2018silggm,
  title={SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks},
  author={Zhang, Rong and Ren, Zhao and Chen, Wei},
  journal={PLoS computational biology},
  volume={14},
  number={8},
  pages={e1006369},
  year={2018},
  publisher={Public Library of Science}
}

@article{li2015flare,
  title={The flare package for high dimensional linear regression and precision matrix estimation in R},
  author={Li, Xingguo and Zhao, Tuo and Yuan, Xiaoming and Liu, Han},
  journal={Journal of machine learning research: JMLR},
  volume={16},
  pages={553},
  year={2015},
  publisher={NIH Public Access}
}

@article{jankova2015confidence,
  title={Confidence intervals for high-dimensional inverse covariance estimation},
  author={Jankova, Jana and Van De Geer, Sara},
  journal={Electronic Journal of Statistics},
  volume={9},
  number={1},
  pages={1205--1229},
  year={2015},
  publisher={The Institute of Mathematical Statistics and the Bernoulli Society}
}


@article{Buhlmann2014,
author = {B{\"{u}}hlmann, Peter and Kalisch, Markus and Meier, Lukas},
doi = {10.1146/annurev-statistics-022513-115545},
file = {:C$\backslash$:/Users/Donny/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/B{\"{u}}hlmann, Kalisch, Meier - 2014 - High-Dimensional Statistics with a View Toward Applications in Biology.pdf:pdf},
isbn = {2326-8298},
issn = {2326-8298},
journal = {Annual Review of Statistics and Its Application},
keywords = {and phrases,causal inference,graphical modeling,multiple testing,penalized estimation,regression},
mendeley-groups = {non{\_}reg},
number = {1},
pages = {255--278},
title = {{High-Dimensional Statistics with a View Toward Applications in Biology}},
volume = {1},
year = {2014}
}

@article{goeman2018l1,
  title={L1 and L2 penalized regression models},
  author={Goeman, Jelle and Meijer, Rosa and Chaturvedi, Nimisha},
  journal={Vignette R Package Penalized.},
  year={2018}
}

@article{bunea2011penalized,
  title={Penalized least squares regression methods and applications to neuroimaging},
  author={Bunea, Florentina and She, Yiyuan and Ombao, Hernando and Gongvatana, Assawin and Devlin, Kate and Cohen, Ronald},
  journal={NeuroImage},
  volume={55},
  number={4},
  pages={1519--1527},
  year={2011},
  publisher={Elsevier}
}

@book{hastie2015statistical,
  title={Statistical learning with sparsity: the lasso and generalizations},
  author={Hastie, Trevor and Tibshirani, Robert and Wainwright, Martin},
  year={2015},
  publisher={CRC press}
}


@article{armour2017network,
  title={A network analysis of DSM-5 posttraumatic stress disorder symptoms and correlates in US military veterans},
  author={Armour, Cherie and Fried, Eiko I and Deserno, Marie K and Tsai, Jack and Pietrzak, Robert H},
  journal={Journal of anxiety disorders},
  volume={45},
  pages={49--59},
  year={2017},
  publisher={Elsevier}
}

@article{mazumder2011sparsenet,
  title={Sparsenet: Coordinate descent with nonconvex penalties},
  author={Mazumder, Rahul and Friedman, Jerome H and Hastie, Trevor},
  journal={Journal of the American Statistical Association},
  volume={106},
  number={495},
  pages={1125--1138},
  year={2011},
  publisher={Taylor \& Francis}
}
@article{kass1995bayes,
  title={Bayes factors},
  author={Kass, Robert E and Raftery, Adrian E},
  journal={Journal of the american statistical association},
  volume={90},
  number={430},
  pages={773--795},
  year={1995},
  publisher={Taylor \& Francis}
}


@article{zhao2006model,
  title={On model selection consistency of Lasso},
  author={Zhao, Peng and Yu, Bin},
  journal={Journal of Machine learning research},
  volume={7},
  number={Nov},
  pages={2541--2563},
  year={2006}
}

@article{williams2020back,
  title={Back to the basics: Rethinking partial correlation network methodology},
  author={Williams, Donald R and Rast, Philippe},
  journal={British Journal of Mathematical and Statistical Psychology},
  volume={73},
  number={2},
  pages={187--212},
  year={2020},
  publisher={Wiley Online Library}
}

@article{williams2019nonregularized,
  title={On nonregularized estimation of psychological networks},
  author={Williams, Donald R and Rhemtulla, Mijke and Wysocki, Anna C and Rast, Philippe},
  journal={Multivariate behavioral research},
  volume={54},
  number={5},
  pages={719--750},
  year={2019},
  publisher={Taylor \& Francis}
}

@article{tibshirani2011regression,
  title={Regression shrinkage and selection via the lasso: a retrospective},
  author={Tibshirani, Robert},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={73},
  number={3},
  pages={273--282},
  year={2011},
  publisher={Wiley Online Library}
}

@inproceedings{loh2012structure,
  title={Structure estimation for discrete graphical models: Generalized covariance matrices and their inverses},
  author={Loh, Po-Ling and Wainwright, Martin J},
  booktitle={Advances in Neural Information Processing Systems},
  pages={2087--2095},
  year={2012}
}

@article{zou2006adaptive,
  title={The adaptive lasso and its oracle properties},
  author={Zou, Hui},
  journal={Journal of the American statistical association},
  volume={101},
  number={476},
  pages={1418--1429},
  year={2006},
  publisher={Taylor \& Francis}
}


@article{lv2009unified,
  title={A unified approach to model selection and sparse recovery using regularized least squares},
  author={Lv, Jinchi and Fan, Yingying},
  journal={The Annals of Statistics},
  volume={37},
  number={6A},
  pages={3498--3528},
  year={2009},
  publisher={Institute of Mathematical Statistics}
}

@article{knight2000asymptotics,
  title={Asymptotics for lasso-type estimators},
  author={Knight, Keith and Fu, Wenjiang},
  journal={Annals of statistics},
  pages={1356--1378},
  year={2000},
  publisher={JSTOR}
}

@article{tibshirani1996regression,
  title={Regression shrinkage and selection via the lasso},
  author={Tibshirani, Robert},
  journal={Journal of the Royal Statistical Society: Series B (Methodological)},
  volume={58},
  number={1},
  pages={267--288},
  year={1996},
  publisher={Wiley Online Library}
}
@article{kim2012consistent,
  title={Consistent model selection criteria on high dimensions},
  author={Kim, Yongdai and Kwon, Sunghoon and Choi, Hosik},
  journal={The Journal of Machine Learning Research},
  volume={13},
  pages={1037--1057},
  year={2012},
  publisher={JMLR. org}
}

@article{kwan2014regression,
  title={A regression-based interpretation of the inverse of the sample covariance matrix},
  author={Kwan, Clarence CY},
  journal={Spreadsheets in Education},
  volume={7},
  number={1},
  pages={4613},
  year={2014},
  publisher={Bond University}
}
@article{sachs2002bayesian,
  title={Bayesian network approach to cell signaling pathway modeling},
  author={Sachs, Karen and Gifford, David and Jaakkola, Tommi and Sorger, Peter and Lauffenburger, Douglas A},
  journal={Science's STKE},
  volume={2002},
  number={148},
  pages={pe38--pe38},
  year={2002},
  publisher={American Association for the Advancement of Science}
}


@article{berk2013valid,
  title={Valid post-selection inference},
  author={Berk, Richard and Brown, Lawrence and Buja, Andreas and Zhang, Kai and Zhao, Linda and others},
  journal={The Annals of Statistics},
  volume={41},
  number={2},
  pages={802--837},
  year={2013},
  publisher={Institute of Mathematical Statistics}
}


@article{lee2016exact,
  title={Exact post-selection inference, with application to the lasso},
  author={Lee, Jason D and Sun, Dennis L and Sun, Yuekai and Taylor, Jonathan E and others},
  journal={The Annals of Statistics},
  volume={44},
  number={3},
  pages={907--927},
  year={2016},
  publisher={Institute of Mathematical Statistics}
}


@article{ledoit2004well,
  title={A well-conditioned estimator for large-dimensional covariance matrices},
  author={Ledoit, Olivier and Wolf, Michael},
  journal={Journal of Multivariate Analysis},
  volume={88},
  number={2},
  pages={365--411},
  year={2004},
  publisher={Elsevier}
}


@article{Foygel2010,
archivePrefix = {arXiv},
arxivId = {1011.6640},
author = {Foygel, Rina and Drton, Mathias},
eprint = {1011.6640},
file = {:C$\backslash$:/Users/Donny/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Foygel, Drton - 2010 - Extended Bayesian Information Criteria for Gaussian Graphical Models.pdf:pdf},
isbn = {9781617823800},
journal = {Advances in Neural Information Processing Systems},
mendeley-groups = {non{\_}reg},
pages = {604--612},
title = {{Extended Bayesian Information Criteria for Gaussian Graphical Models}},
year = {2010}
}

@article{williams2020beyond,
  title={Beyond Lasso: A Survey of Nonconvex Regularization in Gaussian Graphical Models},
  author={Williams, Donald R},
  publisher={PsyArXiv},
  year={2020},
  journal={PsyArXiv}
}

@Manual{psych,
    title = {psych: Procedures for Psychological, Psychometric, and Personality Research},
    author = {William Revelle},
    organization = { Northwestern University},
    address = { Evanston, Illinois},
    year = {2019},
    note = {R package version 1.9.12},
    url = {https://CRAN.R-project.org/package=psych},
  }


