Faculty Directory

Krishna Shrinivas

Assistant Professor of Chemical and Biological Engineering

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

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

The Shrinivas lab's vision is to understand and engineer life at the molecular and cellular scales through theory and computation. The functions of life emerge from dynamic interactions amongst billions of biomolecules that self-organize and chemically react in a crowded and squishy cellular environment. To probe this, we thus necessarily 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 machine learning 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. Krueger, R., Brenner, M.P., and Shrinivas, K. (2024). Generalized design of sequence-ensemble-function relationships for intrinsically disordered proteins. Preprint at bioRxiv, https://doi.org/10.1101/2024.10.10.617695.

2. 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.

3. 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.

4. 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.

5. 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.

6. Gao, A., Shrinivas, K., Lepeudry, P., Suzuki, H.I., Sharp, P.A., and Chakraborty, A.K. (2018). Evolution of weak cooperative interactions for biological specificity. Proc. Natl. Acad. Sci. 115, E11053–E11060. https://doi.org/10.1073/pnas.1815912115.

7. 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.

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