Graduate Student
I am a doctoral candidate in Bernhard Palsson's Systems Biology Research Group at the University of California, San Diego. My main interests lie in both innovating new computational methods and applying them to systems biology of human metabolism, particularly hematopoetic cells, with focuses on biomarkers and understanding infection and inflammation. I am the former president of the Bioengineering Graduate Society (BEGS) at UCSD.
Education
2008 B.S. (Bioengineering: Biotechnology) University of California San Diego
Some of my work
- Bordbar A., Mo M.L., Nakayasu E.S., Schrimpe-Rutledge A.C., Kim Y.M., Metz T.O., Jones M.B., Frank B.C., Smith R.D., Peterson S.N., Hyduke D.R., Adkins J.N., Palsson, B.O. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation Mol Syst Biol, 8:588 (2012)
- Bordbar A. and Palsson, B.O. Using the reconstructed genome-scale human metabolic network to study physiology and pathology J Intern Med, 271(2):131-41 (2012)
- Bordbar A., Feist A.M., Usaite-Black R., Woodcock J., Palsson, B.O., Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology BMC Syst Biol, 5:180 (2011) *Highly Accessed
- Bordbar A., Jamshidi N., Palsson, B.O. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states BMC Syst Biol, 5:110 (2011)
- Bordbar A., Lewis N.E., Schellenberger J., Palsson B.O., Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol, 6:422 (2010).
Some work I've been lucky to be involved in
- Thiele I., Fleming R.M.T., Que R., Bordbar A., Diep D., Palsson B.O. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage PLoS ONE 7(9):e45635 (2012).
- Schellenberger J., Que R., Fleming R.M.T., Thiele I., Orth J.D., Feist A.M., Zielinski D.C., Bordbar A., Lewis N.E., Rahmanian S., Kang J., Hyduke D.R., Palsson B.O. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v 2.0 Nat Protocols 6:1290-1307 (2011).
- Lewis N.E., Schramm G., Bordbar A., Schellenberger J., Andersen M.P., Cheng J.K., Patel N., Yee A., Lewis R.A., Eils R., König R., Palsson B.O. Large-scale in silico modeling of metabolic interactions between cell types in the human brain, Nat Biotech, 28:1279-1285 (2010).
- Thiele I., Fleming R.M.T., Bordbar A., Schellenberger J., Palsson B.O. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery Biophys J 98(10):2072-2081 (2010).
Book Chapters
- Jamshidi N., Bordbar A., Palsson B.O. Modeling Mycobacterium tuberculosis H37Rv In Silico in Systems Biology of Tuberculosis (2013).
- Bordbar A. and Palsson B.O. Moving Toward Genome-Scale Kinetic Models: The Mass Action Stoichiometric Simulation Approach in Functional Coherence of Molecular Networks in Bioinformatics (2012).
Contact Information
Email Address: aabordba at ucsd dot edu
Phone: (858) 534-9717
Mailing Address: 9500 Gilman Drive, Mail Code 0412 , La Jolla, CA 92093-0412
