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2020 – today
- 2023
[j11]Tingting Zhao, Guangyu Zhu, Harsh Vardhan Dubey, Patrick Flaherty
:
Identification of significant gene expression changes in multiple perturbation experiments using knockoffs. Briefings Bioinform. 24(2) (2023)- 2022
- [j10]Vishal Kumar Sarsani, Berent Aldikacti, Shai He, Rilee Zeinert, Peter Chien, Patrick Flaherty:
Model-based identification of conditionally-essential genes from transposon-insertion sequencing data. PLoS Comput. Biol. 18(3) (2022) - [i5]Thomas Cook, Harsh Vardhan Dubey, Ji Ah Lee, Guangyu Zhu, Tingting Zhao, Patrick Flaherty:
Cost-aware Generalized α-investing for Multiple Hypothesis Testing. CoRR abs/2210.17514 (2022) - 2021
- [c5]Sebastian Macaluso, Craig S. Greenberg, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum:
Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering. AISTATS 2021: 2467-2475 - [c4]Aaron Schein, Anjali Nagulpally, Hanna M. Wallach, Patrick Flaherty:
Doubly non-central beta matrix factorization for DNA methylation data. UAI 2021: 1895-1904 - [c3]Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Avinava Dubey, Patrick Flaherty, Manzil Zaheer, Amr Ahmed, Kyle Cranmer, Andrew McCallum:
Exact and approximate hierarchical clustering using A. UAI 2021: 2061-2071 - [i4]Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Avinava Dubey, Patrick Flaherty, Manzil Zaheer, Amr Ahmed, Kyle Cranmer, Andrew McCallum:
Exact and Approximate Hierarchical Clustering Using A. CoRR abs/2104.07061 (2021) - [i3]Aaron Schein, Anjali Nagulpally, Hanna M. Wallach, Patrick Flaherty:
Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data. CoRR abs/2106.06691 (2021) - 2020
- [j9]Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He, Patrick Flaherty:
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data. BMC Bioinform. 21(1): 215 (2020) - [i2]Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum:
Compact Representation of Uncertainty in Hierarchical Clustering. CoRR abs/2002.11661 (2020)
2010 – 2019
- 2019
- [i1]Patrick Flaherty, Pitchaya Wiratchotisatian, Ji Ah Lee, Andrew C. Trapp:
Maximum a-Posteriori Estimation for the Gaussian Mixture Model via Mixed Integer Nonlinear Programming. CoRR abs/1911.04285 (2019) - 2018
- [j8]Andrew C. Trapp, Chao Li, Patrick Flaherty:
Recovering all generalized order-preserving submatrices: new exact formulations and algorithms. Ann. Oper. Res. 263(1-2): 385-404 (2018) - [c2]Craig S. Greenberg, Nicholas Monath, Ari Kobren, Patrick Flaherty, Andrew McGregor, Andrew McCallum:
Compact Representation of Uncertainty in Clustering. NeurIPS 2018: 8639-8649 - 2017
- [j7]Fan Zhang, Patrick Flaherty:
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. BMC Bioinform. 18(1): 45:1-45:10 (2017) - 2016
- [j6]Timothy DeFreitas, Hachem Saddiki, Patrick Flaherty:
GEMINI: a computationally-efficient search engine for large gene expression datasets. BMC Bioinform. 17: 102 (2016) - 2015
- [j5]Hachem Saddiki, Jon McAuliffe, Patrick Flaherty:
GLAD: a mixed-membership model for heterogeneous tumor subtype classification. Bioinform. 31(2): 225-232 (2015) - [j4]Yuting He, Fan Zhang, Patrick Flaherty:
RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data. Bioinform. 31(17): 2785-2793 (2015) - [j3]Patrick Flaherty, Ronald W. Davis:
Robust Optimization of Biological Protocols. Technometrics 57(2): 234-244 (2015)
2000 – 2009
- 2008
- [j2]Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin:
A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction. PLoS Comput. Biol. 4(9) (2008) - 2005
- [j1]Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin:
A latent variable model for chemogenomic profiling. Bioinform. 21(15): 3286-3293 (2005) - [c1]Patrick Flaherty, Michael I. Jordan, Adam P. Arkin:
Robust design of biological experiments. NIPS 2005: 363-370
Coauthor Index
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