He Y, Zhang F, Flaherty P. "RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data." Bioinformatics 31(17) Sept. 1, 2015 doi: 10.1093/bioinformatics/btv275
Flaherty P and Davis RW. "Robust Optimization of Biological Protocols" Technometrics 57(2) July 13, 2015 doi: 10.1080/00401706.2014.915890
Saddiki H, McAuliffe J, Flaherty P. "GLAD: A mixed-membership model for heterogeneous tumor subtype classification" Bioinformatics 31(2) Jan. 15, 2015 doi: 10.1093/bioinformatics/btu618
Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. "Ultrasensitive detection of rare mutations using next-generation targeted resequencing" Nucleic Acids Research 40(1) Jan. 1, 2012 doi: 10.1093/nar/gkr861
Flaherty P, Radhakrishnan M, Dinh, T, Jordan MI, Arkin AP. "A Dual Receptor Cross-talk Model of G protein-coupled Signal Transduction in RAW Macrophage Cells" PLOS Computational Biology 4(9) Sept. 26, 2008 doi: 10.1371/journal.pcbi.1000185
Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP. "A Latent Variable Model for Chemogenomic Profiling" Bioinformatics 21(15) Aug. 1, 2005
Flaherty P, Jordan MI, Arkin AP. "Robust Design of Biological Experiments" Proceedings of Neural Information Processing Systems (NIPS) 1(0) Jan. 1, 2005
Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW. "Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast" Proc. Natl. Acad. Sci. USA 101(3) Jan. 20, 2004
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