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Matthew Brooks

Profile picture for Matthew Brooks

Contact Information

161 ERML
1201 W. Gregory Dr.
1201 W Gregory Dr
M/C 051
Urbana, IL 61801
Adjunct Assistant Professor

Research Interests

Integrating transcriptomic and physiological measurements to reveal gene regulatory networks coordinating photosynthesis and nitrogen use.       

A relationship between photosynthesis and nitrogen use has been recognized at a physiological level for decades, but how these two important metabolic pathways are coordinated is poorly understood. Advances in DNA-sequencing technologies now present opportunities to revisit how these two processes interact at a regulatory level. Using a systems biology approach that combines genomics, phenotyping, and computational biology, the three main objectives driving my research are to: 

  1. Define the molecular factors involved in coordinating photosynthesis with nitrogen availability.
  2. Identify natural genetic variation influencing crosstalk between photosynthesis and nitrogen use.
  3. Bridge basic and applied research by transferring knowledge from data-rich model species to crops. 

Improving our understanding of how genetic and environmental factors influence the coordination of photosynthesis and nitrogen assimilation will help identify strategies for improving nitrogen use efficiency. This is an important goal because nitrogen fertilizer production is a significant source of greenhouse gas emissions, and climate change will in turn impact photosynthesis and crop yield. At a fundamental level, this work will also contribute to understanding the basic principles underlying how cellular networks process complex environmental signals. 


B.S. Michigan State University
Ph.D. University of California-Berkeley
NIH-NRSA Postdoctoral Fellow, Center for Genomics and Systems Biology, New York University          

selected publications

Brooks MD, Juang C-L, Katari MS, Alvarez JM, Pasquino A, Shih H-J, Huang J, Shanks C, Cirrone J, Coruzzi GM (2020) ConnecTF: A platform to build gene networks by integrating transcription factor-target gene interactions. bioRxiv: 2020.07.07.191627

Li Y, Brooks M, Yeoh-Wang J, McCoy RM, Rock TM, Pasquino A, Moon CI, Patrick RM, Tanurdzic M, Ruffel S, Widhalm JR, McCombie WR, Coruzzi GM (2020) SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling. Plant Physiology: pp.00682.02019

Alvarez JM, Schinke AL, Brooks MD, Pasquino A, Leonelli L, Varala K, Safi A, Krouk G, Krapp A, Coruzzi GM (2020) Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade. Nature Communications 11: 1157

Cirrone J, Brooks MD, Bonneau R, Coruzzi GM, Shasha DE (2020) OutPredict: multiple datasets can improve prediction of expression and inference of causality. Scientific Reports 10: 6804

Brooks MD, Cirrone J, Pasquino AV, Alvarez JM, Swift J, Mittal S, Juang C-L, Varala K, Gutiérrez RA, Krouk G, Shasha D, Coruzzi GM (2019) Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nature Communications 10: 1569

Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM (2018) Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proceedings of the National Academy of Sciences 115: 6494-6499

Leonelli L, Brooks MD, Niyogi KK (2017) Engineering the lutein epoxide cycle into Arabidopsis thaliana. Proceedings of the National Academy of Sciences 114: E7002-E7008

Clausen CH, Brooks MD, Grob P, Kemalyan G, Nogales E, Niyogi KK, Fletcher DA (2014) Dynamic mechanical responses of Arabidopsis thylakoid membranes during PSII-specific illumination. Biophysical Journal 106: 1864-1870

Brooks MD, Jansson S, Niyogi KK (2014) PsbS-dependent non-photochemical quenching. In Non-photochemical quenching and energy dissipation in plants, algae and cyanobacteria. Springer, Dordrecht, pp 297-314

Onoa B, Schneider AR, Brooks MD, Grob P, Nogales E, Geissler PL, Niyogi KK, Bustamante C (2014) Atomic force microscopy of photosystem II and its unit cell clustering quantitatively delineate the mesoscale variability in Arabidopsis thylakoids. PloS one 9: e101470

Brooks MD, Sylak-Glassman EJ, Fleming GR, Niyogi KK (2013) A thioredoxin-like/β-propeller protein maintains the efficiency of light harvesting in Arabidopsis. Proceedings of the National Academy of Sciences 110: E2733-E2740