Doctoral Student

Research Emphasis



Graduate Student

I am a sixth year doctoral student in the Bioengineering graduate program at the University of California, San Diego. My main research project involves the improvement and parameterization of ME-models of E. coli.

Google Scholar profile


2010 B.S. (Chemistry) California Institute of Technology


King, Z.A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J.A., Ebrahim, A., Palsson, B.O., and Lewis, N.E. (2015). BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res.

Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Dräger, A., Famili, I., Feist, A.M., Fleming, R.M., et al. (2015). Do genome-scale models need exact solvers or clearer standards? Mol. Syst. Biol. 11, 831.

Yang, L., Tan, J., O’Brien, E.J., Monk, J.M., Kim, D., Li, H.J., Charusanti, P., Ebrahim, A., Lloyd, C.J., Yurkovich, J.T., et al. (2015). Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc. Natl. Acad. Sci. U. S. A. 112, 10810–10815.

King, Z.A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N.E., and Palsson, B.O. (2015). Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput. Biol. 11, e1004321.

Guzmán, G.I., Utrilla, J., Nurk, S., Brunk, E., Monk, J.M., Ebrahim, A., Palsson, B.O., and Feist, A.M. (2015). Model-driven discovery of underground metabolic functions in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 112, 929–934.

LaCroix, R.A., Sandberg, T.E., O’Brien, E.J., Utrilla, J., Ebrahim, A., Guzman, G.I., Szubin, R., Palsson, B.O., and Feist, A.M. (2015). Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl. Environ. Microbiol. 81, 17–30.

Sandberg, T.E., Pedersen, M., LaCroix, R.A., Ebrahim, A., Bonde, M., Herrgard, M.J., Palsson, B.O., Sommer, M., and Feist, A.M. (2014). Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol. Biol. Evol. 31, 2647–2662.

Bordbar, A., Nagarajan, H., Lewis, N.E., Latif, H., Ebrahim, A., Federowicz, S., Schellenberger, J., and Palsson, B.O. (2014). Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol. Syst. Biol. 10, 737.

Federowicz, S., Kim, D., Ebrahim, A., Lerman, J., Nagarajan, H., Cho, B.-K., Zengler, K., and Palsson, B. (2014). Determining the control circuitry of redox metabolism at the genome-scale. PLoS Genet. 10, e1004264.

Nagarajan, H., Sahin, M., Nogales, J., Latif, H., Lovley, D.R., Ebrahim, A., and Zengler, K. (2013). Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microb. Cell Fact. 12, 118.

Schmidt, B.J., Ebrahim, A., Metz, T.O., Adkins, J.N., Palsson, B.Ø., and Hyduke, D.R. (2013). GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics 29, 2900–2908.

Ebrahim, A., Lerman, J.A., Palsson, B.O., and Hyduke, D.R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst. Biol. 7, 74.

Gong, Y., Ebrahim, A., Feist, A.M., Embree, M., Zhang, T., Lovley, D., and Zengler, K. (2013). Sulfide-driven microbial electrosynthesis. Environ. Sci. Technol. 47, 568–573.

Contact Information

Email Address: aebrahim at ucsd dot edu