Profile – Amy Marshall-Colon

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Amy Marshall-Colon

Job Title:

Assistant Professor


Phone Number:



Google Scholar Profile


I am studying the regulatory mechanisms that underlie nitrogen metabolism in response to combinations of abiotic stress, in particular climate related stress. My group uses a systems biology approach to examine the regulation of cross-talk between signaling pathways that influence nitrogen uptake and assimilation. Data from the transcriptome and metabolome are incorporated into multi-scale models to predict system-wide response to perturbations and generate testable hypotheses. Our aim is to enhance plant nitrogen use efficiency through directed engineering of influential gene targets.
Research Areas:

  • Systems Biology
  • Modeling
  • Metabolomics
  • Transcriptomics

Current N-related Projects:

  • Regulation of long distance nitrogen signaling


Marshall-Colon, A.†, et al. Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform. 2017. Frontiers in Plant Systems and Synthetic Biology. doi: 10.3389/fpls.2017.00786

Long, S.P., Marshall-Colon, A., and Zhu, X.-G. Meeting the global food demand of the future by engineering crop photosynthesis and yield potential. Cell (2015) 161(1): 56-66.

Varala, K, Li, Y, Marshall-Colon, A, Para, A, and Coruzzi, G. 2015. “Hit-and-Run” leaves its mark: Catalyst transcription factors and chromatin modification. BioEssays 37(8): 851-856. Doi: 10.1002/bies.201400205

Anna Medici, Amy Marshall-Colon, Elsa Ronzier, Wojciech Szponarski, Rongchen Wang, Alain Gojon, Nigel M. Crawford, Sandrine Ruffel, Gloria M. Coruzzi & Gabriel Krouk. 2015. AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nature Communications. 6: 6274. DOI: 10.1038/ncomms7274

Alessia Para*, Ying Li*, Amy Marshall-Colón*, Kranthi Varala*, Nancy J. Francoeur, Tara M. Moran, Molly B. Edwards, Christopher Hackley, Bastiaan O. R. Bargmann, Kenneth D. Birnbaum, W. Richard McCombie, Gabriel Krouk, and Gloria M. Coruzzi. Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis PNAS 2014 111 (28) 10371-10376; published ahead of print June 23, 2014,doi:10.1073/pnas.1404657111.

Krouk, G, Lingeman, J, Marshall-Colon, A, Coruzzi, G, and Shasha, D. 2013. Gene regulatory networks in plants: Learning causality from time and perturbation. Genome Biology, 14: 123.

Bargmann, B., Marshall-Colon, A., Efroni, I., Ruffel, S., Birnbaum, K., Coruzzi, G., and Krouk, G. 2013. TARGET, a transient transformation system for genome-wide transcription factor target discovery. Molecular Plant, 6:978-980.

Marshall-Colón, A., Sengupta, N., Rhodes, D. and Morgan, J.A. 2014. Simulating labeling to estimate kinetic parameters for flux control analysis. In “Plant Metabolic Flux Analysis,” A. Alonso and M. Duide-Noubani Eds. Springer, NY. Pp 211-222.

Marshall-Colón, A., Sengupta, N., Rhodes, D., Dudareva, N., and Morgan, J.A. 2010. A kinetic model describes metabolic response to perturbations and distribution of flux control in the benzenoid network of Petunia hybrida. Plant Journal 62: 64-76.

Marshall-Colón, A.J., Morgan, J.A., Dudareva, N., and Rhodes, D. Application of Dynamic Flux Analysis in Plant Metabolic Networks. In “Plant Metabolic Networks,” J. Schwender Ed. Springer, NY, 2009, pp. 285-305.

Orlova, I.*, Marshall-Colón, A.*, Schnepp, J., Wood, B., Varbanova, M., Fridman, E., Blakeslee, J., Peer, W.A., Murphy, A., Rhodes, D., Pichersky, E., Dudareva, N. 2006. Reduced synthesis of benzylbenzoate in petunia flowers increases contribution from the non-β-oxidative pathway to benzenoid compounds. Plant Cell 18(12): 3458-3475.