LGRT 1527

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.


Postdoc, Stanford University

Ph.D. University of California, Berkeley

B.S. Rochester Institute of Technology

Research Interests

large-scale genomic data, hierarchical Bayesian models, variational inference, robust experiment design

Selected Publications

  • Sarsani V, Aldikacti B, He S, Zeinert R, Chien P, Flaherty P "Model-based identification of conditionally-essential genes from transposon-insertion sequencing data" PLOS Computational Biology 18(3) Mar 2022 doi: 10.1371/journal.pcbi.1009273.
  • He S, Schein A, Sarsani V, and Flaherty P "A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structured DNA Sequencing Data" Annals of Applied Statistics 15(2) Jun 2021 doi: 10.1214/20-aoas1434.
  • Flaherty P and Davis RW. "Robust Optimization of Biological Protocols" Technometrics 57(2) July 13, 2015 doi: 10.1080/00401706.2014.915890
  • 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, 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