An empirical assessment of validation practices for molecular classifiers. - Peter J. Castaldi; Issa J. Dahabreh; John P. A. Ioannidis (Briefings Bioinform., 2011)

Dual beta process priors for latent cluster discovery in chronic obstructive pulmonary disease. - James C. Ross; Peter J. Castaldi; Michael H. Cho; Jennifer G. Dy (KDD, 2014)

Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. - Jen-hwa Chu; Craig P. Hersh; Peter J. Castaldi; Michael H. Cho; Benjamin A. Raby; Nan M. Laird; Russell Bowler; Stephen I. Rennard; Joseph Loscalzo; John Quackenbush; Edwin K. Silverman (BMC Syst. Biol., 2014)

Interpretable Clustering via Discriminative Rectangle Mixture Model. - Junxiang Chen; Yale Chang; Brian D. Hobbs; Peter J. Castaldi; Michael H. Cho; Edwin K. Silverman; Jennifer G. Dy (ICDM, 2016)

Bipartite Community Structure of eQTLs. - John Platig; Peter J. Castaldi; Dawn L. DeMeo; John Quackenbush (PLoS Comput. Biol., 2016)

Clustering from Multiple Uncertain Experts. - Yale Chang; Junxiang Chen; Michael H. Cho; Peter J. Castaldi; Edwin K. Silverman; Jennifer G. Dy (AISTATS, 2017)

Multiple Clustering Views from Multiple Uncertain Experts. - Yale Chang; Junxiang Chen; Michael H. Cho; Peter J. Castaldi; Edwin K. Silverman; Jennifer G. Dy (ICML, 2017)

Clustering with Domain-Specific Usefulness Scores. - Yale Chang; Junxiang Chen; Michael H. Cho; Peter J. Castaldi; Edwin K. Silverman; Jennifer G. Dy (SDM, 2017)

A Bayesian Nonparametric Model for Disease Subtyping: Application to Emphysema Phenotypes. - James C. Ross; Peter J. Castaldi; Michael H. Cho; Junxiang Chen; Yale Chang; Jennifer G. Dy; Edwin K. Silverman; George R. Washko; Raúl San José Estépar (IEEE Trans. Medical Imaging, 2017)

Crowdclustering with Partition Labels. - Junxiang Chen; Yale Chang; Peter J. Castaldi; Michael H. Cho; Brian D. Hobbs; Jennifer G. Dy (AISTATS, 2018)

Unsupervised discovery of phenotype-specific multi-omics networks. - W. Jenny Shi; Yonghua Zhuang; Pamela H. Russell; Brian D. Hobbs; Margaret M. Parker; Peter J. Castaldi; Pratyaydipta Rudra; Brian Vestal; Craig P. Hersh; Laura M. Saba; Katerina J. Kechris (Bioinform., 2019)

Instance-wise Feature Grouping. - Aria Masoomi; Chieh Wu; Tingting Zhao; Zifeng Wang 002; Peter J. Castaldi; Jennifer G. Dy (NeurIPS, 2020)

Improved prediction of smoking status via isoform-aware RNA-seq deep learning models. - Zifeng Wang 002; Aria Masoomi; Zhonghui Xu; Adel Boueiz; Sool Lee; Tingting Zhao; Russell Bowler; Michael H. Cho; Edwin K. Silverman; Craig P. Hersh; Jennifer G. Dy; Peter J. Castaldi (PLoS Comput. Biol., 2021)

Explanations of Black-Box Models based on Directional Feature Interactions. - Aria Masoomi; Davin Hill; Zhonghui Xu; Craig P. Hersh; Edwin K. Silverman; Peter J. Castaldi; Stratis Ioannidis; Jennifer G. Dy (ICLR, 2022)

Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals. - Michele Gentili; Kimberly Glass; Enrico Maiorino; Brian D. Hobbs; Zhonghui Xu; Peter J. Castaldi; Michael H. Cho; Craig P. Hersh; Dandi Qiao; Jarrett D. Morrow; Vincent J. Carey; John Platig; et al. (PLoS Comput. Biol., 2024)

A generalized higher-order correlation analysis framework for multi-omics network inference. - Weixuan Liu; Katherine A. Pratte; Peter J. Castaldi; Craig P. Hersh; Russell P. Bowler; Farnoush Banaei Kashani; Katerina J. Kechris (PLoS Comput. Biol., 2025)

A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies. - Xihao Li; Han Chen; Margaret Sunitha Selvaraj; Eric Van Buren; Hufeng Zhou; Yuxuan Wang 008; Ryan Sun; Zachary R. McCaw; Zhi Yu; Min-Zhi Jiang; Daniel DiCorpo; Sheila M. Gaynor; et al. (Nat. Comput. Sci., 2025)