Patrick Flaherty

Postdoc, Stanford University
Ph.D. University of California, Berkeley
B.S. Rochester Institute of Technology

Recent advances in DNA sequencing technology are beginning to provide data sets that have the potential to measure the genomic changes that drive development of many diseases. However, statistically rigorous, computationally efficient methods are needed to analyze these massive, complex data sets in order to drive improvements in patient care.

The long-term goal of my research is to develop statistical models and scalable algorithms to enable the interpretation of massive biomedical data sets. To achieve this goal, we work in diverse fields including: machine learning, bioinformatics, statistics, and genetics.

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

Giaever G, et. al "Functional Profiling of the Saccharomyces cerevisiae Genome" Nature 418(6896) July 25, 2002

Links: Lab website