I’m a computational systems biologist and my research involves analyses of complex biological networks at different levels of detail.  I use dynamic and steady state models to examine systems biology of microbial communities, multi-cellular organisms, and host-pathogen interactions.  I work with microbiologists in assessing the phenotypic capabilities of biofuel producing organisms (such as Rhodopseudomonas palustris) and designing new strains for improved production of desired compounds.

I am also interested in systems pharmacology.   I develop and use physiology-based pharmacokinetic and pharmacodynamic models to predict the transient outcome of drug metabolism and therapeutic or toxic outcomes.

Ph.D., Theoretical physical biochemistry, 2004, Indiana University, Bloomington, IN

M.S., Inorganic Physical Chemistry, 1998, University of North Dakota, Grand Forks, ND

B.S., Chemistry, 1992, University of Maryland, College Park, MD

• Georgouli, K., Yeom, J.S., Blake, R.C., Navid, A., Multi-scale models of whole cells: progress and challenges (2023), Frontiers in Cell and Developmental Biology, 11, 1260507.
• Griesemer, M., Navid, A., Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites, (2023), Microorganisms, 11(9), 2149.
• Vanarsdale, E., Navid, A., Chu, M. J., Halvorsen, T. M., Payne, G.F., Jiao, Y., Bentley, W.E., Yung, M.C. Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis. (2023), Biotechnology and Bioengineering, 120(5), 1366.
• Windler, M., Stuart, R., Deutzmann, J. S., Mayali, X., Navid, A., D'haeseleer, P., Marcu, O. E., Lipton, M., Nicora, C., Spormann, A.M., Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity. (2022), FEMS Microbiology Ecology, 98(9), p. fiac091, 2022.
• Yeom, J-S., Georgouli, K., Blake, R., Navid, A., Towards Dynamic Simulation of a Whole Cell Model. (2021), Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 1.
• Hackenberg, K.A.M., Rajabzadeh-Oghaz, H., Dreier, R., Buchholz, B.A., Navid, A., Rocke, D.M., Abdulazim, A., Hanggi, D., Siddiqui, A., Macdonald, R.L., Meng, H., Etminan, N., Collagen Turnover in Relation to Risk Factors and Hemodynamics in Human Intracranial Aneurysms. (2020) Stroke, 51, 1624.
• Navid, A., Jiao, Y.Q., Wong, S.E., Pett-Ridge, J., System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris (2019), BMC Bioinformatics, 20, 233.
• Griesemer, M., Kimbrel, J.A., Zhou, C.E., Navid, A., D’haeseleer, P., Combining Multiple Functional Annotation Tools Increases Coverage of Metabolic Annotation (2018), BMC Genomics, 19, 948.
• Navid, A., Ng, D.M., Wong, S.E., Lightstone, F.C., Application of a Physiologically Based Pharamacokinetic Model to Study Theophylline Metabolism and Its Interactions With Ciprofloxacin and Caffeine. (2016) CPT: Pharmacometrics & Systems Pharmacology, 5(2), 74-81.
• Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Drager, A., Famili, I., Feist, A.M., Fleming, R.M.T.; Fong, S.S., Hatzimanikatis, V., Herrgard, M.J., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S.Y., Le Novere, N., Lerman, J.A., Lewis, N.E., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L.K., Nogales, J., Noronha, A., Pal, C., Palsson, B.O., Papin, J.A.; Patil, K.R.; Price, N.D., Reed, J.L., Saunders, M., Senger, R.S., Sonnenschein, N., Sun, Y., Thiele, I., Do Genome-scale Models Need Exact Solvers or Clearer Standards? (2015) Molecular Systems Biology, 11(10), 831.
• Navid, A., Ng, D.M., Stewart, B.J., Wong, S.E., Lightstone, F.C., Quantitative In Silico Analysis of Transient Metabolism of Acetaminophen and Associated Causes of Hepatotoxicity in Humans (2013), In Silico Pharmacology, 1, 14.
• Chaudhury, S., Abdulhameed, M.D.M., Singh, N., Tawa, G.J., D’haeseleer, P.M., Zemla, A.T., Navid, A., Zhou, C.E., Franklin, M.C., Cheung, J., Rudolph, M.J., Love, J., Graf, J.F., Rozak, D.A., Dankmeyer, J.L, Amemiya, K., Daefler, S., Wallqvist, A., Rapid Countermeasure Discovery Against Francisella tularensis Based on a Metabolic Network Reconstruction (2013), PLOS One, 5, e63369.
• Stewart, B.J., Navid, A., Kulp, K.S., Knaack, J.L.S., Bench, G., D-Lactate Production as a Function of Glucose Metabolism in Saccharomyces cerevisiae (2013), Yeast, 30, 81-91.
• Navid, A., Almaas, E., Genome-Level Transcription Data of Yersina Pestis Analyzed With A New Metabolic Constraint-Based Approach (2012), BMC Systems Biology, 6(1), 150.
• Jiao, Y.Q., Navid, A., Stewart, B.J., McKinlay, J.B., Thelen, M.P., Pett-Ridge, J., Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum and Rhodopseudomonas palustris for hydrogen production (2012), International Journal of Hydrogen Energy, 37, 11719-11726.
• Navid, A., Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets (2012), Briefings in Functional Genomics, 10, 354-364.
• Stewart, B.J., Navid, A., Turteltaub, K.W., Bench, G., Yeast Dynamic Metabolic Flux Measurement in Nutrient-Rich Media by HPLC and Accelerator Mass Spectrometry (2010), Analytical Chemistry, 82, 9812-9817.
• Navid, A., Almaas, E., Genome-scale Reconstruction of Metabolic Network Yersinia Pestis, strain 91001 (2009), Molecular Biosystems, 5, 368-375.
• Navid, A., Nicholas, S.C., Hamer, R.D., A Proposed Role for all-trans Retinal in Regulation of Rhodopsin Regeneration in Human Rods, (2006), Vision Research, 46, 4449-4463.
• Navid, A., Ortoleva, P.J., Simulated Complex Dynamics of Glycolysis in the Protozoan Parasite Trypanosoma brucei. (2004), Journal of Theoretical Biology, 228, 449-458.
• Ortoleva, P., E. Berry, J. Fan, M. Fontus, A. Navid, A. Sayyed-ahmad, Z. Shreif, F. Stanley, K. Tuncay, L. Wu, E. Weitzke., Karyote Physico-Chemical Genome, Proteome, Metabolome Cell Modeling System. (2003), Omics A Journal of Integrative Biology , 7(3), 269-283.
• Navid, A., Tyapochkin, E.M., Archer, C.J., Kozliak, E.I., UV-vis and Binding Studies of cobalt terasulphophthalocyanine-thiolate Complexes as intermediates of the Merox Process. (1999),Journal of Porphyrins and Phthalocyanines, 3(6-7), 654-666.

Book Chapters

• Navid, A., A Beginner's Guide to the COBRA Toolbox, Microbial Systems Biology, 2^nd ed., Methods in Molecular Biology, Vol. 2349, Navid, A., (ed.), Springer, ISBN: 978-1-0716-1585-0, Ch. 15, 339-365.
• Navid, A., Curating COBRA Models of Microbial Metabolism, Microbial Systems Biology, 2^nd ed., Methods in Molecular Biology, Vol. 2349, Navid, A., (ed.), Springer, ISBN: 978-1-0716-1585-0, Ch. 14, 321-338.
• Navid, A, Almaas, E., Yersinia pestis Metabolic Network, Yersinia:  Systems Biology and Control, Carniel, E., Hinnebusch, B.J. (eds), Caister Academic Press, ISBN: 978-1-908230-05-8, Ch. 6, 83-108.
• Navid, A., Development of constraint-based system-level models of microbial metabolism, Microbial Systems Biology, Methods in Molecular Biology, Vol. 881, Navid, A. (ed.), Springer, ISBN:  9781617798269, Ch. 18, 531-549.
• Navid, A., Ghim, C-M., Fenley, A., Yoon, S., Lee, S., Almaas, E., Systems Biology of Microbial Communities., Methods in Molecular Biology, Systems Biology, Maly, I.V. (ed.), Humana press, ISBN: 978-1-934115-64-0, Ch. 16. 469-494.

Books Edited

• Microbial Systems Biology, 2^nd ed., Methods in Molecular Biology, Vol. 2349, Springer, New York, NY, USA, ISBN: 978-1-0716-1585-0.
• Microbial Systems Biology, Methods in Molecular Biology, Vol. 881, Springer, New York, NY, USA, ISBN:  9781617798269.