Amy K. Schmid

Associate Professor of Biology

125 Science Dr, French Family Science Center 4105, Durham, NC 27708
Campus Box: 
Box 90338, Durham, NC 27708-0338
(919) 613-4464
Research in my lab seeks to elucidate how cells make decisions in response to environmental cues. My particular focus is on how networks of molecules interact within free-living microbial cells. These networks govern the decision to grow when conditions are optimal or deploy damage repair systems when faced with stress. I study microbial stress responses in extremophiles of the domainArchaea, which represent extreme examples of microbes surviving damage by multiple stressors. These organisms remain viable on the extreme end of the gradient of environmental stress (e.g. high temperature, saturated salt, nutrient starvation). However, extremophiles also adapt during wide variations in conditions and nutrients and therefore provide a study system for both constant and dynamic stress resistance mechanisms. Because archaea resemble life’s earliest ancestors, they can teach us about the origins of stress response features shared amongst all life. In my recent and future work, I compare across species how networks function to regulate important aspects of cell physiology such as growth and division during stress. Ultimately, I seek to uncover how environmental conditions shape the regulatory network over evolutionary time. I use a combination of quantitative and experimental biology approaches, including computational modeling, functional genomics and molecular microbiology. I work across the disciplines of systems biology, microbial stress response, and archaeal molecular biology. My lab group and I are also actively involved in developing microbiology and bioinformatics workshops for various communities (K-12, teachers, researchers).


  • Ph.D., University of Washington 2004

  • B.S., Marquette University 1997

Schmid, A. K., and N. S. Baliga. “Prokaryotic Systems Biology.” In Systems Biology, edited by M. Al-Rubeai and M. Fussenegger, 5:395–423. Springer, 2006.

Tonner, Peter D., Cynthia L. Darnell, Francesca M. L. Bushell, Peter A. Lund, Amy K. Schmid, and Scott C. Schmidler. “A Bayesian non-parametric mixed-effects model of microbial growth curves.Plos Computational Biology 16, no. 10 (October 26, 2020): e1008366. Full Text

Darnell, Cynthia L., Jenny Zheng, Sean Wilson, Ryan M. Bertoli, Alexandre W. Bisson-Filho, Ethan C. Garner, and Amy K. Schmid. “The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.Mbio 11, no. 4 (August 11, 2020). Full Text

Hwang, Sungmin, Nikita E. Chavarria, Rylee K. Hackley, Amy K. Schmid, and Julie A. Maupin-Furlow. “Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen.International Journal of Molecular Sciences 20, no. 19 (September 26, 2019). Full Text

Hackley, Rylee K., and Amy K. Schmid. “Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.Journal of Molecular Biology 431, no. 20 (September 2019): 4147–66. Full Text

Zaretsky, Marianna, Cynthia L. Darnell, Amy K. Schmid, and Jerry Eichler. “N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility.Frontiers in Microbiology 10 (January 2019): 1367. Full Text

Schmid, Amy K. “Conserved principles of transcriptional networks controlling metabolic flexibility in archaea.Emerging Topics in Life Sciences 2, no. 4 (December 2018): 659–69. Full Text

Martin, Jonathan H., Katherine Sherwood Rawls, Jou Chin Chan, Sungmin Hwang, Mar Martinez-Pastor, Lana J. McMillan, Laurence Prunetti, Amy K. Schmid, and Julie A. Maupin-Furlow. “GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii.Journal of Bacteriology 200, no. 17 (September 2018). Full Text

Dulmage, Keely A., Cynthia L. Darnell, Angie Vreugdenhil, and Amy K. Schmid. “Copy number variation is associated with gene expression change in archaea.Microbial Genomics 4, no. 9 (September 2018). Full Text

Eun, Ye-Jin, Po-Yi Ho, Minjeong Kim, Salvatore LaRussa, Lydia Robert, Lars D. Renner, Amy Schmid, Ethan Garner, and Ariel Amir. “Archaeal cells share common size control with bacteria despite noisier growth and division.Nature Microbiology 3, no. 2 (February 2018): 148–54. Full Text

McDowell, Ian C., Dinesh Manandhar, Christopher M. Vockley, Amy K. Schmid, Timothy E. Reddy, and Barbara E. Engelhardt. “Clustering gene expression time series data using an infinite Gaussian process mixture model.Plos Comput Biol 14, no. 1 (January 2018): e1005896. Full Text


Eun, Y., M. Kim, S. A. LaRussa, K. Dulmage, A. K. Schmid, and E. C. Garner. “How archaeal cells generate their cell shape.” In Molecular Biology of the Cell, Vol. 26. AMER SOC CELL BIOLOGY, 2015.

Schmid, Amy, Keely A. Dulmage, Cynthia L. Darnell, and A. Vreugdenhil. “Data and scripts from: Copy number variation is associated with gene expression change in archaea,” May 4, 2018. Full Text

Selected Grants

Genetic and Genomics Training Grant awarded by National Institutes of Health (Mentor). 2020 to 2025

Causes and consequences of regulatory network rewiring under extreme environmental selection awarded by National Science Foundation (Principal Investigator). 2019 to 2023

CAREER: Elucidating cell cycle regulatory networks across the tree of life awarded by National Science Foundation (Principal Investigator). 2017 to 2022

Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Mentor). 2005 to 2021

Modeling the function and evolution of metabolic networks across hypersaline-adapted archaea awarded by National Science Foundation (Principal Investigator). 2016 to 2020

Genetics Training Grant awarded by National Institutes of Health (Mentor). 1979 to 2020

Organization and Function of Cellular Structure awarded by National Institutes of Health (Mentor). 1975 to 2020

Understanding Gene Regulatory Network Function During Stress Response Adaptation of an Archaeal Extremophile awarded by National Science Foundation (Principal Investigator). 2011 to 2015