Mindy Perkins

Mindy Perkins

My name is Mindy Perkins and I am a fourth-year Ph.D. student in electrical engineering at the University of California, Berkeley, advised by Prof. Murat Arcak. My work focuses on developing mathematical theory to analyze pattern formation in biological systems, both real and synthetic.

Research Interest

All living organisms grow and function by way of gene expression, or the process by which genes coded in DNA are translated into proteins. One of the central tools of synthetic biology is the ability to modify gene expression within individual cells, causing them to exhibit certain characteristics (e.g., fluorescence when illuminated, resistance to antibiotics) or to carry out certain behaviors (e.g., producing pharmaceutical chemicals, performing computations). Researchers recognized early on that the ability to modify not just individual cells, but also the way cells interact with each other, would greatly expand the possible applications for synthetic biology. This is a challenging problem for both theorists and practitioners, and an important one for medical applications such as growing tissues and organs to replace or repair damaged ones in patients.

In natural organisms, tissues form in developing embryos through complex processes that dictate what genes are expressed in which cells and when. The history of gene expression in a cell ultimately determines the cell's fate, such as whether it becomes a neuron or a skin cell. During development, cells interact with each other and the environment, such that the spatial location of a cell in an embryo affects its gene expression and hence the fate it will adopt. Therefore, understanding spatial patterns in gene expression is essential to understanding tissue growth. How do these patterns arise? How do they change over time? How do cell-cell and cell-environment interactions influence patterning? I am interested in developing mathematical theory to help answer these questions, leveraging techniques from signals and networked systems analysis. I am also working to translate theory into practice, so that synthetic biologists can make intelligent design choices guided by mathematical predictions and insights.


2015 - present Ph.D. in Electrical Engineering (anticipated)
University of California, Berkeley (Berkeley, CA)
2011 - 2015 B.S. in Electrical Engineering, Minor in Biology
Stanford University (Stanford, CA)


mindylp (at) eecs (dot) berkeley (dot) edu