Emmett Smith, Ph.D.

Assistant professor of biology

Email:[email protected]

Department: Biology

Program: Honors Program

Location: Stanley Hall Room 137
801 National Road
Richmond, Indiana 47374

About me

I am a 2007 graduate of Purdue University with a B.S. in Biology. I earned my Ph.D. in Biomedical Sciences at the University of Massachusetts Medical School in 2014. I taught for biology one semester at Worcester Polytechnic Institute. From there I came to Earlham as a Visiting Assistant Professor in 2015, and became an Assistant Professor at Earlham in 2016.

If I’m not in the classroom or in my office, look for me at the Equestrian Barn where you’ll find me riding my American Quarter Horse, Maker Sweet Dreams (we call her Sista). I also enjoy relaxing on my front porch, love to read and am learning to play the ukulele. I like to throw a disk around, specifically at stationary baskets.

Earlham is a unique community that I am happy to be part of. Not only do I grow intellectually, by pursing research and scholarship, I also grow emotionally and spiritually each semester. I am stimulated by conversation with colleagues across the college, not just in my department or division. I am inspired by the students who bring passion and conviction to this campus and my classroom.


  • Ph.D., University of Massachusetts Medical School
  • B.S. Purdue University

Professional memberships

Research projects

I am currently setting up my human cell culture lab at Earlham. I will be working on the CFTR gene and its regulatory elements. I will be using the cutting-edge genome editing technique known as CRISPR to edit human cells and compare their 3d genome structure with non-edited cells. I will analyze the effects of mutation on CFTR expression. I will be collaborating with Dr. Kat Bartlow to examine the 3D genomic differences between two types of neuronal cells expressing different genes. Students who are interested in a particular disease gene are welcome to bring their own project to the lab, and we will examine its 3D structure.

Scholarly interest

Did you know that if you stretched out the genome from one of your cells, it would be as tall as Conan O’Brien? And yet that long strand of DNA must squeeze itself into a microscopic cell nucleus. I know how to measure the 3D structure of that packaging, and I am using that technology in my lab. I want to understand how genes are regulated. Specifically, I am interested in how a cell turns a gene on or off; how it regulates the amount of gene product; and why. I am particularly interested in the gene which, when mutated, causes the human disorder Cystic Fibrosis. This gene, called CFTR, is turned on in a very specific set of tissues in the human body. Comparing tissues where the gene is on and off led me to discover regulatory elements that make three-dimensional looping contacts with the CFTR promoter. I am interested in expanding this research to other genes, as well as manipulating CFTR regulatory elements to see what happens to gene expression if they are deleted, swapped, or mutated.

Published works

E.M. Smith, B. Lajoie, G. Jain and J. Dekker. Invariant TAD boundaries constrain cell type-specific looping interactions between promoters and distal elements around the CFTR locus. 2016. AJHG Vol. 98 pg. 185–201

E.M. Smith. The three-dimensional structure of the Cystic Fibrosis locus. Dissertation, University of Massachusetts Medical School. 2014.

N. Naumova*, E.M. Smith*, Y. Zhan* and J. Dekker. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. 2012. Methods Vol. 58 pg. 192-203

N. Gheldof*, E.M. Smith*, T.M. Tabuchi, C.M. Koch, I. Dunham, J.A. Stamatoyannopoulos and J. Dekker. Cell-type- specific long-range looping interactions identify distant regulatory elements of the CFTR gene. 2010. NAR Vol. 38 pg. 4325–4336

*Authors contributed equally to this work