School of
Integrative Biology
Amy Marshall-Colon

193 ERML
Office: 217-300-1430

Mail: 1201 W. Gregory Dr. Urbana, IL. 61801
Lab Page

Amy Marshall-Colon
Assistant Professor


NIH-NRSA Fellow, 2010-2013, New York University, New York, NY
Ph.D. 2009, Purdue University, West Lafayette, IN
M.S. 2002, University of Florida, Gainesville, FL
B.S. 2000, Lipscomb University, Nashville, TN

Teaching Interests

IB 204 Genetic (every fall)
IB 502 Biological Networks (every other spring)
IB 512 Plant Metabolomics (every other spring)

Integrative modeling to investigate the multi-scale regulation of crop response to genetic and environmental perturbations.

A critical problem facing crop science today is determining and predicting the effects of environmental stress on important plant traits. Nitrogen use efficiency (NUE) is an important crop trait defined as the ratio between the amount of N fertilizer removed from the field by a crop and the amount of N fertilizer applied. Currently, major crops in managed systems only take up 30-50% of the applied N fertilizer, and the rest is lost to evaporation and leaching leading to both air and water pollution. Recent studies have shown that crop NUE will decline even further due to factors associated with global climate change such as higher temperatures and atmospheric CO2 and extremes in water availability (drought and floods). To fully understand and manage environmental impacts on NUE and other important crop traits such as biomass and yield, integrative approaches are needed to identify the underlying genetics contributing to NUE and explore the molecular mechanisms by which it is regulated. To address these questions and better understand how plant genotype translates to observed molecular phenotypes and traits, I apply a systems biology approach to explore two distinct but connected focus areas: i) cross-communication among signaling pathways; and ii) integrative and multiscale modeling to analyze gene-by-environment interactions.


List of Teachers Ranked as Excellent by Their Students
Teaching Tools in Plant Biology Competition winner
Joseph B. Hawkes Research Award, University of Illinois
National Center for Supercomputing Applications (NCSA) Faculty Fellowship, University of Illinois

Representative Publications

Heerah, S., Katari, M., Penjor, R., Coruzzi, G, Marshall-Colon, A.†. WRKY1 mediates transcriptional regulation of light and nitrogen signaling pathways in Arabidopsis thaliana. bioRxiv. doi:

Marshall-Colon, A, Kliebenstein, D. Plant networks as traits and hypotheses; moving beyond description. Trends in Plant Science (Invited review). ACCEPTED 06/04/19.

Kannan, K, Wang, Y, Challa, GS, Lang, MM, Srinivasan, V, Long, SP, Marshall-Colon, A†. Combining gene network, metabolic, and leaf-level models show means to future-proof soybean photosynthesis under rising CO2. in silico Plants. ACCEPTED. bioRxiv link: doi:

Assmann, Sarah, Cris Argueso, Kenneth Birnbaum, Sixue Chen, Jose Dinneny, Colleen Doherty, Andrea Eveland, Joanna Friesner, Vanessa Greenlee, Julie Law, Amy Marshall-Colon, Grace Mason, Ruby O'Lexy, Scott Peck, Robert Schmitz, Liang Song, David Stern, Marguerite Varagona, Justin Walley, and Cranos Williams. 2019. Directions for Research and Training in Plant Omics: Big Questions and Big Data. Plant Direct Journal.

Challa, G, Marshall-Colon, A†. 2019. in silico crops and multi-omic approaches to meet agricultural challenges. CAB Reviews, DOI: 10.1079/PAVSNNR201914005; CABI Wallingford UK

Safi, A, Medici, A, Szponarski, W, Marshall-Colon, A, Ruffel, S, Gaymard, F, Coruzzi, G, and Lacombe, B, Krouk, G. 2018. HRS1/HHOs GARP transcription factors and reactive oxygen species are regulators of Arabidopsis nitrogen starvation response. Pre-print:

Varala, K., Williams, M., Marshall-Colon, A†*. (Oct 17, 2018). A Bioinformatics Pipeline to Explore Transcriptional Regulation in Plants. Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online).

Varala K.*, A. Marshall-Colon*, J. Cirrone*, M. Brooks, A.V. Pasquino, S. Leran, S. Mittal, T. Rock, M.B. Edwards, G.J. Kim, S. Ruffel, W.R. McCombie, D. Shasha, and G.M. Coruzzi. 2018. The temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. PNAS.

Christensen, A.J., Srinivasan, V., Hart, J., Marshall-Colon, A.*† 2017. Computational modeling combined with advanced visualization can direct strategies for crop ideotype design to address future food security issues. Nutrition Reviews. doi:10.1093/nutrit/nux076 (Invited Review)

Singh, V., Perraki, A., Kim, S.Y., Shrivastava, S., Lee, J.H., Zhao, Y., Schwessinger, B., Oh, M.-H., Marshall-Colon, A., Zipfel, C., Huber, S.C. 2017. Tyrosine-610 in the receptor kinase BAK1 does not play a major role in brassinosteroid signaling or innate immunity. Frontiers in Plant Science. 8:1273. doi: 10.3389/fpls.2017.01273

Marshall-Colon, A.†, Long Stephen P., Allen Douglas K., Allen Gabrielle, Beard Daniel A., Benes Bedrich, von Caemmerer Susanne, Christensen A. J., Cox Donna J., Hart John C., Hirst Peter M., Kannan Kavya, Katz Daniel S., Lynch Jonathan P., Millar Andrew J., Panneerselvam Balaji, Price Nathan D., Prusinkiewicz Przemyslaw, Raila David, Shekar Rachel G., Shrivastava Stuti, Shukla Diwakar, Srinivasan Venkatraman, Stitt Mark, Turk Matthew J., Voit Eberhard O., Wang Yu, Yin Xinyou, Zhu Xin-Guang. Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform. 2017. Frontiers in Plant Systems and Synthetic Biology. 8: 786. 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

Para, A*, Li, Y*, Marshall-Colon, A*, Varala, K*, Francoeur, NJ, Moran, TM, Edwards, M, Hackley, C, Bargmann, BOR, Birnbaum, KD, McCombie, RW, Krouk, G, and Coruzzi, GM. 2014. Hit-and-run" transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. PNAS. EE 2014-04657R. *Equal contribution.

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. *Equal contribution.

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-?-oxidative pathway to benzenoid compounds. Plant Cell 18(12): 3458-3475. *Equal contribution.

Complete Publications List