SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data. - Collin Giguere; Harsh Vardhan Dubey; Vishal Kumar Sarsani; Hachem Saddiki; Shai He; Patrick Flaherty (BMC Bioinform., 2020)

Cost-aware Generalized α-investing for Multiple Hypothesis Testing. - Thomas Cook; Harsh Vardhan Dubey; Ji Ah Lee; Guangyu Zhu 008; Tingting Zhao; Patrick Flaherty (CoRR, 2022)

Identification of significant gene expression changes in multiple perturbation experiments using knockoffs. - Tingting Zhao; Guangyu Zhu 008; Harsh Vardhan Dubey; Patrick Flaherty (Briefings Bioinform., 2023)

Maximum a Posteriori Inference for Factor Graphs via Benders' Decomposition. - Harsh Vardhan Dubey; Ji Ah Lee; Patrick Flaherty (CoRR, 2024)