References

Akbani, Rehan, Patrick Kwok Shing Ng, Henrica MJ Werner, Maria Shahmoradgoli, Fan Zhang, Zhenlin Ju, Wenbin Liu, et al. 2014. “A Pan-Cancer Proteomic Perspective on the Cancer Genome Atlas.” Nature Communications 5 (1): 1–15.
Attias, Hagai, John Platt, Alex Acero, and Li Deng. 2000. “Speech Denoising and Dereverberation Using Probabilistic Models.” Advances in Neural Information Processing Systems 13.
Baladandayuthapani, Veerabhadran, Yuan Ji, Rajesh Talluri, Luis E Nieto-Barajas, and Jeffrey S Morris. 2010. “Bayesian Random Segmentation Models to Identify Shared Copy Number Aberrations for Array CGH Data.” Journal of the American Statistical Association 105 (492): 1358–75.
Danaher, Patrick, Pei Wang, and Daniela M Witten. 2014. “The Joint Graphical Lasso for Inverse Covariance Estimation Across Multiple Classes.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 76 (2): 373–97.
Friedman, Jerome, Trevor Hastie, and Robert Tibshirani. 2008. “Sparse Inverse Covariance Estimation with the Graphical Lasso.” Biostatistics 9 (3): 432–41.
Ji, Yuan, Guosheng Yin, Kam-Wah Tsui, Mikhail G Kolonin, Jessica Sun, Wadih Arap, Renata Pasqualini, and Kim-Anh Do. 2007. “Bayesian Mixture Models for Complex High Dimensional Count Data in Phage Display Experiments.” Journal of the Royal Statistical Society: Series C (Applied Statistics) 56 (2): 139–52.
Lauritzen, Steffen L. 1996. Graphical Models. Vol. 17. Clarendon Press.
Li, Jun, Yiling Lu, Rehan Akbani, Zhenlin Ju, Paul L Roebuck, Wenbin Liu, Ji-Yeon Yang, et al. 2013. “TCPA: A Resource for Cancer Functional Proteomics Data.” Nature Methods 10 (11): 1046–47.
Liu, Han, Xi Chen, Larry Wasserman, and John Lafferty. 2010. “Graph-Valued Regression.” Advances in Neural Information Processing Systems 23.
Liu, Han, Kathryn Roeder, and Larry Wasserman. 2010. “Stability Approach to Regularization Selection (Stars) for High Dimensional Graphical Models.” Advances in Neural Information Processing Systems 23.
Malta, Tathiane M, Artem Sokolov, Andrew J Gentles, Tomasz Burzykowski, Laila Poisson, John N Weinstein, Bożena Kamińska, et al. 2018. “Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.” Cell 173 (2): 338–54.
Matthews, Brian W. 1975. “Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme.” Biochimica Et Biophysica Acta (BBA)-Protein Structure 405 (2): 442–51.
Meinshausen, Nicolai, and Peter Bühlmann. 2010. “Stability Selection.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 72 (4): 417–73.
Mohammadi, Abdolreza, and Ernst C Wit. 2015. “Bayesian Structure Learning in Sparse Gaussian Graphical Models.” Bayesian Analysis 10 (1): 109–38.
Morris, Jeffrey S, Philip J Brown, Richard C Herrick, Keith A Baggerly, and Kevin R Coombes. 2008. “Bayesian Analysis of Mass Spectrometry Proteomic Data Using Wavelet-Based Functional Mixed Models.” Biometrics 64 (2): 479–89.
Ni, Yang, Francesco C Stingo, and Veerabhadran Baladandayuthapani. 2019. “Bayesian Graphical Regression.” Journal of the American Statistical Association 114 (525): 184–97.
Parker, Joel S, Michael Mullins, Maggie CU Cheang, Samuel Leung, David Voduc, Tammi Vickery, Sherri Davies, et al. 2009. “Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes.” Journal of Clinical Oncology 27 (8): 1160.
Peterson, Christine, Francesco C Stingo, and Marina Vannucci. 2015. “Bayesian Inference of Multiple Gaussian Graphical Models.” Journal of the American Statistical Association 110 (509): 159–74.
Saegusa, Takumi, and Ali Shojaie. 2016. “Joint Estimation of Precision Matrices in Heterogeneous Populations.” Electronic Journal of Statistics 10 (1): 1341.
Ståhl, Patrik L, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, et al. 2016. “Visualization and Analysis of Gene Expression in Tissue Sections by Spatial Transcriptomics.” Science 353 (6294): 78–82.
Storey, John D. 2003. “The Positive False Discovery Rate: A Bayesian Interpretation and the q-Value.” The Annals of Statistics 31 (6): 2013–35.
Sun, Shiquan, Jiaqiang Zhu, Sahar Mozaffari, Carole Ober, Mengjie Chen, and Xiang Zhou. 2019. “Heritability Estimation and Differential Analysis of Count Data with Generalized Linear Mixed Models in Genomic Sequencing Studies.” Bioinformatics 35 (3): 487–96.
Sun, Shiquan, Jiaqiang Zhu, and Xiang Zhou. 2020. “Statistical Analysis of Spatial Expression Patterns for Spatially Resolved Transcriptomic Studies.” Nature Methods 17 (2): 193–200.
Titsias, Michalis, and Miguel Lázaro-Gredilla. 2011. “Spike and Slab Variational Inference for Multi-Task and Multiple Kernel Learning.” Advances in Neural Information Processing Systems 24.
Wang, Zeya, Veerabhadran Baladandayuthapani, Ahmed O Kaseb, Hesham M Amin, Manal M Hassan, Wenyi Wang, and Jeffrey S Morris. 2021. “Bayesian Edge Regression in Undirected Graphical Models to Characterize Interpatient Heterogeneity in Cancer.” Journal of the American Statistical Association, no. just-accepted: 1–31.
Weinstein, John N, Eric A Collisson, Gordon B Mills, Kenna R Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, and Joshua M Stuart. 2013. “The Cancer Genome Atlas Pan-Cancer Analysis Project.” Nature Genetics 45 (10): 1113–20.
Zhang, Jingfei, and Yi Li. 2022. “High-Dimensional Gaussian Graphical Regression Models with Covariates.” Journal of the American Statistical Association, 1–13.