Prof. Sushmita Roy

Position title: Pathway Analysis Core Principal Investigator


Phone: (608) 316-4453

330 North Orchard Street
Madison WI 53715
Room 3168


Professor Sushmita Roy is an expert in computational approaches in bioinformatics. Specifically, Professor Roy focuses on using complex gene expression data and machine learning approaches to correlate inputs (e.g. exposure to a toxic substance) with specific gene regulatory networks. The Pathway Analysis Core will provide the ability to identify which specific cell phenotypes are influenced by a toxin, and identify gene regulatory networks associated with toxin exposure.

Lab Website: Please click here

Select Publications

  • D. Chasman, A. Fotuhi Siahpirani, and S. Roy, “Network-based approaches for analysis of complex biological systems,” Current Opinion in Biotechnology, vol. 39, pp. 157-166, Jun. 2016. [Online]. Available
  • Z. Niu, D. Chasman, A. J. Eisfeld, Y. Kawaoka, and S. Roy (2015), “Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions.” Bioinformatics (Oxford, England), Jan. 2016. [Online]. Available
  • S. Roy, A. F. Siahpirani, D. Chasman, S. Knaack, F. Ay, R. Stewart, M. Wilson, and R. Sridharan (2015), “A predictive modeling approach for cell line-specific long-range regulatory interactions,” Nucleic Acids Research, vol. 43, no. 18, pp. 8694-8712, Oct. 2015. [Online].Available
  • D. Thompson, A. Regev, and S. Roy (2015), “Comparative analysis of gene regulatory networks: From network reconstruction to evolution,” Annual Review of Cell and Developmental Biology, vol. 31, no. 1, pp. null+, 2015. [Online]. Available
  • S. Roy and D. Thompson, “Evolution of regulatory networks in candida glabrata: learning to live with the human host,” FEMS Yeast Research, pp. fov087+, Oct. 2015. [Online]. Available