Faculty Directory

Krishna Shrinivas

Assistant Professor of Chemical and Biological Engineering and (by courtesy) Engineering Sciences and Applied Mathematics and Cell and Developmental Biology

Contact

Website

Shrinivas Lab Website

Centers

Center for Synthetic Biology

National Institute of Theory and Math in Biology (NITMB)

Departments

Chemical and Biological Engineering

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Research Interests

Living cells are dynamic, constantly changing, complex, squishy, and utterly remarkable in what they can achieve. The vision of the Shrinivas lab is to develop computational frameworks to predict and engineer the processes that power life at the molecular and cellular scales. To do this, we have to adopt an interdisciplinary approach - bridging ideas across biology, physics, machine learning, and engineering to decipher fundamental scientific mechanisms while also pursuing translational and engineering applications. 

This approach is further bolstered by our lab's extensive Chicago ties (Cell and Dev Bio at NU Medical School, Eng. Sciences and Applied Math, Center for Synthetic Biology, National Institute for Theory and Math in Biology) and broader collaborations with scientists across the country. 

A sampling of the lab's current directions include:

• Probing mechanisms of genome organization and gene regulation.
• Developing physics-centered ML/AI approaches for design of biomolecules and organelles in health and disease.
• Fundamental statistical physics of soft, multiphase, and active matter.
• Exploring computation and learning in biological and physical systems.

Selected Publications

1. Aidan Zentner, Ethan Halingstad, Cameron Chalk, Michael P Brenner, Arvind Murugan, Erik Winfree, Krishna Shrinivas Combinatorial decision making by surface condensation in multicomponent fluids, arXiv (2025): 2025-09 | Link to Preprint: https://arxiv.org/abs/2509.08100
2. Ryan Krueger, Michael P Brenner , Krishna Shrinivas Generalized design of sequence-ensemble-function relationships for intrinsically disordered proteins, Nature Computational Science (2025) | Link to Paper: https://www.nature.com/articles/s43588-025-00881-y | Media coverage by Northwestern: https://www.mccormick.northwestern.edu/news/articles/2025/10/order-from-disordered-proteins/
3. Wilton T Sneadc, Mary K Skillicorn, Krishna Shrinivas, Amy Gladfelter Immiscible proteins compete for RNA binding to order condensate layers, PNAS 122 (32):e2504778122 (2025) | Link to Paper: https://www.pnas.org/doi/10.1073/pnas.2504778122 | Media coverage by Northwestern: https://www.mccormick.northwestern.edu/news/articles/2025/08/cell-feature-implicated-in-cancer-forms-differently-than-previously-thought/ and highlighted in Science Magazine: https://www.science.org/doi/10.1126/science.aec1443
4. Schede, H.H., Natarajan, P., Chakraborty, A.K., and Shrinivas, K. (2023). A model for organization and regulation of nuclear condensates by gene activity. Nat. Commun. 14, 4152. https://doi.org/10.1038/s41467-023-39878-4.
5. Shrinivas, K., and Brenner, M.P. (2021). Phase separation in fluids with many interacting components. Proc. Natl. Acad. Sci. 118. https://doi.org/10.1073/pnas.2108551118.
6. Henninger, J.E., Oksuz, O., Shrinivas, K., Sagi, I., LeRoy, G., Zheng, M.M., Andrews, J.O., Zamudio, A.V., Lazaris, C., Hannett, N.M., et al. (2021). RNA-Mediated Feedback Control of Transcriptional Condensates. Cell 184, 207-225.e24. https://doi.org/10.1016/j.cell.2020.11.030.
7. Shrinivas, K., Sabari, B.R., Coffey, E.L., Klein, I.A., Boija, A., Zamudio, A.V., Schuijers, J., Hannett, N.M., Sharp, P.A., Young, R.A., et al. (2019). Enhancer Features that Drive Formation of Transcriptional Condensates. Mol. Cell 75, 549-561.e7. https://doi.org/10.1016/j.molcel.2019.07.009.
8. Hnisz, D., Shrinivas, K., Young, R.A., Chakraborty, A.K., and Sharp, P.A. (2017). A Phase Separation Model for Transcriptional Control. Cell 169, 13–23. https://doi.org/10.1016/j.cell.2017.02.007.

Scholar Profile for extensive bibliography.