Patrick Flaherty

发表

Robust design of biological experiments

Michael I. Jordan, Adam P. Arkin, Patrick Flaherty, 2005, NIPS.

Functional profiling of the Saccharomyces cerevisiae genome

Ronald W. Davis, J. Hegemann, P. Philippsen, 2002, Nature.

MAP Clustering under the Gaussian Mixture Model via Mixed Integer Nonlinear Optimization.

Patrick Flaherty, Andrew C. Trapp, Pitchaya Wiratchotisatian, 2019, 1911.04285.

GEMINI: a computationally-efficient search engine for large gene expression datasets

Patrick Flaherty, Hachem Saddiki, Timothy DeFreitas, 2016, BMC Bioinformatics.

Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents

Robert P. St.Onge, Patrick Flaherty, Corey Nislow, 2005, PLoS genetics.

Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.

Michael I. Jordan, Patrick Flaherty, Corey Nislow, 2004, Proceedings of the National Academy of Sciences of the United States of America.

A Global Optimization Algorithm for Sparse Mixed Membership Matrix Factorization

Andrew C. Trapp, Patrick Flaherty, Fan Zhang, 2016, Contemporary Biostatistics with Biopharmaceutical Applications.

A Deterministic Global Optimization Method for Variational Inference

Andrew C. Trapp, Patrick Flaherty, Hachem Saddiki, 2017, 1703.07169.

Exact Inference on Hierarchical Clustering in Particle Physics and Cancer Genomics

Craig S. Greenberg, Patrick Flaherty, A. McCallum, 2020 .

Erratum for Mor et al., “Identification of a New Class of Antifungals Targeting the Synthesis of Fungal Sphingolipids”

Patrick Flaherty, G. Giaever, Xuewen Pan, 2018, mBio.

Identification of a New Class of Antifungals Targeting the Synthesis of Fungal Sphingolipids

Patrick Flaherty, G. Giaever, Xuewen Pan, 2015, mBio.

RESEARCH GEMINI : A Search Engine for Genomic Data

Patrick Flaherty, T. DeFreitas, 2015 .

Cost-aware Generalized $\alpha$-investing for Multiple Hypothesis Testing

Patrick Flaherty, John A. Lee, Harshit Dubey, 2022, 2210.17514.

Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions

Patrick Flaherty, G. Giaever, C. Nislow, 2016, PLoS genetics.

Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data

Patrick Flaherty, Fan Zhang, 2016, BMC Bioinformatics.

A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction

Michael I. Jordan, Adam P. Arkin, Tuan Dinh, 2008, PLoS Comput. Biol..

A Dual Receptor Cross-talk Model of G protein-coupled Signal Transduction Running Head : Dual Receptor GPCR Crosstalk Model

Michael I. Jordan, Mala L. Radhakrishnan, A. Arkin, 2008 .

RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data

Fan Zhang, Patrick Flaherty, Yuting He, 2015, Bioinform..

Identification of Significant Gene Expression Changes in Multiple Perturbation Experiments using Knockoffs

Patrick Flaherty, Ting Zhao, Guangyu Zhu, 2021, bioRxiv.

A latent variable model for chemogenomic profiling

Michael I. Jordan, Adam P. Arkin, Patrick Flaherty, 2005, Bioinform..

Robust Optimization of Biological Protocols

Patrick Flaherty, Ronald W. Davis, Patrick Flaherty, 2015, Technometrics.

Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress

Patrick Flaherty, G. Giaever, C. Nislow, 2017, Open Biology.

A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structured DNA Sequencing Data

Aaron Schein, Patrick Flaherty, Shai He, 2020, bioRxiv.

Exact and Approximate Hierarchical Clustering Using A

Andrew McCallum, Amr Ahmed, Manzil Zaheer, 2021, UAI.

Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering

Craig S. Greenberg, Patrick Flaherty, A. McCallum, 2020, AISTATS.

Compact Representation of Uncertainty in Clustering

Andrew McCallum, Ari Kobren, Andrew McGregor, 2018, NeurIPS.

Model-based identification of conditionally-essential genes from transposon-insertion sequencing data

Patrick Flaherty, Shai He, V. Sarsani, 2021, bioRxiv.

SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data

Patrick Flaherty, Vishal Kumar Sarsani, Collin Giguere, 2020, bioRxiv.

Compact Representation of Uncertainty in Hierarchical Clustering pdf

Andrew McCallum, Kyle Cranmer, Craig S. Greenberg, 2020, ArXiv.

Recovering all generalized order-preserving submatrices: new exact formulations and algorithms

Chao Li, Patrick Flaherty, Andrew C. Trapp, 2018, Ann. Oper. Res..

Recovering all generalized order-preserving submatrices: new exact formulations and algorithms

Andrew C. Trapp, Patrick Flaherty, Chao Li, 2016, Annals of Operations Research.

Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data

Hanna M. Wallach, Aaron Schein, Patrick Flaherty, 2021, UAI.