Robust design of biological experiments. - Patrick Flaherty; Michael I. Jordan; Adam P. Arkin (NIPS, 2005)

A latent variable model for chemogenomic profiling. - Patrick Flaherty; Guri Giaever; Jochen Kumm; Michael I. Jordan; Adam P. Arkin (Bioinform., 2005)

A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction. - Patrick Flaherty; Mala L. Radhakrishnan; Tuan Dinh; Robert A. Rebres; Tamara I. Roach; Michael I. Jordan; Adam P. Arkin (PLoS Comput. Biol., 2008)

RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data. - Yuting He; Fan Zhang; Patrick Flaherty (Bioinform., 2015)

GLAD: a mixed-membership model for heterogeneous tumor subtype classification. - Hachem Saddiki; Jon McAuliffe; Patrick Flaherty (Bioinform., 2015)

Robust Optimization of Biological Protocols. - Patrick Flaherty; Ronald W. Davis (Technometrics, 2015)

GEMINI: a computationally-efficient search engine for large gene expression datasets. - Timothy DeFreitas; Hachem Saddiki; Patrick Flaherty (BMC Bioinform., 2016)

Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. - Fan Zhang; Patrick Flaherty (BMC Bioinform., 2017)

Compact Representation of Uncertainty in Clustering. - Craig S. Greenberg; Nicholas Monath; Ari Kobren; Patrick Flaherty; Andrew McGregor 001; Andrew McCallum (NeurIPS, 2018)

Recovering all generalized order-preserving submatrices: new exact formulations and algorithms. - Andrew C. Trapp; Chao Li; Patrick Flaherty (Ann. Oper. Res., 2018)

Maximum a-Posteriori Estimation for the Gaussian Mixture Model via Mixed Integer Nonlinear Programming. - Patrick Flaherty; Pitchaya Wiratchotisatian; Ji Ah Lee; Andrew C. Trapp (CoRR, 2019)

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)

Compact Representation of Uncertainty in Hierarchical Clustering. - Craig S. Greenberg; Sebastian Macaluso; Nicholas Monath; Ji Ah Lee; Patrick Flaherty; Kyle Cranmer; Andrew McGregor 001; Andrew McCallum (CoRR, 2020)

Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering. - Sebastian Macaluso; Craig S. Greenberg; Nicholas Monath; Ji Ah Lee; Patrick Flaherty; Kyle Cranmer; Andrew McGregor 001; Andrew McCallum (AISTATS, 2021)

Exact and approximate hierarchical clustering using A. - Craig S. Greenberg; Sebastian Macaluso; Nicholas Monath; Avinava Dubey; Patrick Flaherty; Manzil Zaheer; Amr Ahmed 001; Kyle Cranmer; Andrew McCallum (UAI, 2021)

Doubly non-central beta matrix factorization for DNA methylation data. - Aaron Schein; Anjali Nagulpally; Hanna M. Wallach; Patrick Flaherty (UAI, 2021)

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)

Model-based identification of conditionally-essential genes from transposon-insertion sequencing data. - Vishal Kumar Sarsani; Berent Aldikacti; Shai He; Rilee Zeinert; Peter Chien; Patrick Flaherty (PLoS Comput. Biol., 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)

Doubly Non-Central Beta Matrix Factorization for Stable Dimensionality Reduction of Bounded Support Matrix Data. - Anjali Nagulpally; Patrick Flaherty; Aaron Schein (CoRR, 2024)

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