Sushmita Roy, PhD

Credentials: Biostatistics and Medical Informatics

Position title: Associate Professor


Phone: 608-316-4453

Aligned Research Focus
Basic stem cell science, Computational biology, Cell fate specification

Research Description

A major research direction in my group is to define gene regulatory network dynamics underlying different cell fates. We are interested in developing and applying computational methods based on statistical machine learning for the inference, analysis and interpretation of molecular regulatory networks that control context-specific expression patterns. Our approaches harness the increasingly available repertoires of high-throughput molecular measurements at the bulk and single cell level to identify gene regulatory networks that drive cell type identity. Our methods can be used to different dynamic processes such as differentiation and cellular reprogramming.

Selected References
  1. Siahpirani AF, Knaack S, Chasman D, Seirup M, Sridharan R, Stewart R, Thomson J, Roy S. Dynamic regulatory module networks for inference of cell type-specific transcriptional networks. Genome Res. 2022 Jul;32(7):1367-1384. doi: 10.1101/gr.276542.121. Epub 2022 Jun 15. PMID: 35705328; PMCID: PMC9341506.
  2. Roy, Sushmita, and Rupa Sridharan. “Chromatin Module Inference on Cellular Trajectories Identifies Key Transition Points and Poised Epigenetic States in Diverse Developmental Processes.” Genome Research 27, no. 7 (2017): 1250–62.
  3. Chasman, Deborah, Nisha Iyer, Alireza Fotuhi Siahpirani, Maria Estevez Silva, Ethan Lippmann, Brian McIntosh, Mitchell D. Probasco, et al. “Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development.” Cell Systems 9, no. 2 (August 2019): 167-186.e12.
  4. Tran, Khoa A., Stefan J. Pietrzak, Nur Zafirah Zaidan, Alireza Fotuhi Siahpirani, Sunnie Grace McCalla, Amber S. Zhou, Gopal Iyer, Sushmita Roy, and Rupa Sridharan. “Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency.” Cell Reports 27, no. 6 (May 7, 2019): 1726-1741.e5.