Faculty Directory

Contact Information

Life Sciences & Bioengineering Center, 3003
Phone: +1-508-831-6583
Fax: +1-508-831-4121

Patrick Flaherty

I’m interested in using large-scale genomic data to provide the best clinical diagnosis and treatment of cancer and other genetic diseases. To do that, my research involves designing computationally efficient statistical tools to interpret and integrate large-scale data sets generated by sequencing, microarray and other high-throughput experimental platforms. New biological detection and measurement technologies are drastically changing the amount of data we can obtain from a clinical or experimental sample. However, the statistical tools that are currently available to address genomics data are overwhelmed by the amount of data new technologies are capable of delivering. The goal of my research is to develop statistical methods for very large data sets to understand and quantify the contribution of genetic factors to improve the diagnosis and treatment of cancer and other genetic diseases.

At WPI and within the Biomedical Engineering department, we create a learning environment to support students who want to address major societal needs. The project- oriented curriculum at WPI allows students to bring their ideas, talents and energy to bear on the solution of important, interdisciplinary challenges. As a teacher, I aim to catalyze the transformation of that raw talent and energy into new knowledge and applications in the classroom, in major projects and in the laboratory. WPI and my lab provide a space for students to work together, combining their efforts to innovate new ways of addressing the challenge of understanding and treating disease. It is very rewarding to work with students as they create solutions that will contribute to improving patients’ lives.

Research Interests

  • Bioinformatics
  • Machine Learning
  • Cancer Genomics


  • BS, Rochester Institute of Technology, 2000
  • MS, University of California at Berkeley, 2003
  • PhD, University of California at Berkeley, 2006
  • Postdoc, Stanford University, 2007-2012

Featured Publications

  • 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 Res. 2012; 40 (1): e2. 
  • Schiffman JD, Hodgson JG, VandenBerg SR, Flaherty P, Polley MY, Yu M, Fisher PG, Rowitch DH, Ford JM, Berger MS, Ji H, Gutmann DH, James CD. “Oncogenic BRAF mutation with CDKN2A inactivation is characteristic of a subset of pediatric malignant astrocytomas” Cancer Res. 2010 Jan 15;70(2):512-9. 
  • 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 2008 September; 4(9):1-11. 
  • Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M. “Functional Profiling of the Saccharomyces cerevisiae Genome” Nature. 2002 Jul 25; 418(6896):387-91. 
  • Flaherty P, Jordan MI, Arkin AP. “Robust Design of Biological Experiments” Proceedings of the Neural Information Processing Systems Meeting 2005.

Professional Highlights

  • Outstanding Student Paper Award – Neural Information processing Symposium 2005
  • NIH T32 Ruth L. Kirschstein National Research Service Award (NRSA) - 2008
  • Email a Friend
  • Bookmark this Page
  • Share this Page