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
Although life science research has entered the post-genomic era, we still understand little about the diversity of microbial life on earth. Information is particularly lacking on microbial extremophiles, which thrive at the limits of life. Extremophiles can be found in deep-sea hydrothermal vents under high pressure and temperature, saturated salt lakes, and polar icecaps. Many of these organisms are members of the third domain of life, the archaea. How do these microorganisms cope with an extreme and changing environment? How do they alter their genetic programs and metabolic pathways to adapt and survive changes in their unique habitats on earth? Central to this process are gene regulatory networks (GRNs) composed of groups of regulatory proteins that switch genes on and off in response to environmental stimuli. Upon sensing a change in the environment, the GRN increases the production of genes encoding proteins that repair damage, restore the cell to a healthy state and prepare for future stress. The organism studied in the current research, called Halobacterium salinarum, thrives in high salt environments. The long-term aim of our work is to determine the underlying mechanisms by which regulatory factors interact in the GRN of H. salinarum enable survival during environmental perturbations. We are using a systems biology approach, which combines cutting-edge high throughput experimental techniques with computational or statistical modeling. Research toward these goals will lay the foundation for rational re-engineering of cellular physiology for desired outcomes such as targeted industrial, environmental and medical purposes.


  • Ph.D., University of Washington 2004

  • B.S., Marquette University 1997

Schmid, AK, and Baliga, NS. "Prokaryotic Systems Biology." In Systems Biology,edited by M Al-Rubeai and M Fussenegger, 395-423. Springer, December 7, 2006. (Chapter)

Martin, JH, Sherwood Rawls, K, Chan, JC, Hwang, S, Martinez-Pastor, M, McMillan, LJ, Prunetti, L, Schmid, AK, and Maupin-Furlow, JA. "GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii." Journal of Bacteriology 200, no. 17 (September 2018). Full Text

Dulmage, KA, Darnell, CL, Vreugdenhil, A, and Schmid, AK. "Copy number variation is associated with gene expression change in archaea." Microbial Genomics 4, no. 9 (September 2018). Full Text

Eun, YJ, Ho, PY, Kim, M, Larussa, S, Robert, L, Renner, LD, Schmid, A, Garner, E, and Amir, A. "Archaeal cells share common size control with bacteria despite noisier growth and division." Nature Microbiology 3, no. 2 (February 1, 2018): 148-154. Full Text

McDowell, IC, Manandhar, D, Vockley, CM, Schmid, AK, Reddy, TE, and Engelhardt, BE. "Clustering gene expression time series data using an infinite Gaussian process mixture model." Plos Computational Biology 14, no. 1 (January 16, 2018): e1005896-null. Full Text

Martinez-Pastor, M, Tonner, PD, Darnell, CL, and Schmid, AK. "Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks." Annual review of genetics 51 (November 2017): 143-170. Full Text

Darnell, CL, Tonner, PD, Gulli, JG, Schmidler, SC, and Schmid, AK. "Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis." Msystems 2, no. 5 (September 19, 2017). Full Text

Martinez-Pastor, M, Lancaster, WA, Tonner, PD, Adams, MWW, and Schmid, AK. "A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea." Nucleic acids research 45, no. 17 (September 2017): 9990-10001. Full Text

Tonner, PD, Darnell, CL, Engelhardt, BE, and Schmid, AK. "Detecting differential growth of microbial populations with Gaussian process regression." Genome research 27, no. 2 (February 2017): 320-333. Full Text

Darnell, CL, and Schmid, AK. "Systems biology approaches to defining transcription regulatory networks in halophilic archaea." Methods (San Diego, Calif.) 86 (September 2015): 102-114. Full Text

Tonner, PD, Pittman, AMC, Gulli, JG, Sharma, K, and Schmid, AK. "A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea." Plos Genetics 11, no. 1 (January 8, 2015): e1004912-null. Full Text


Schmid, A, Dulmage, KA, Darnell, CL, and Vreugdenhil, A. "Data and scripts from: Copy number variation is associated with gene expression change in archaea." (May 4, 2018). Full Text

Selected Grants

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 2019

Understanding gene regulatory networks in hypersaline-adapted achaea: toward synthetic biology for industrial applicatio awarded by National Science Foundation (Principal Investigator). 2014 to 2018

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