Contact information Lawrence Livermore National Laboratory 7000 East Avenue, L-776 Livermore, CA 94550 email: navid1@llnl.gov phone: 925 424 3564

Education

B.S., University of Maryland.

M.S., University of North Dakota.

Ph.D., Indiana University

Research interests

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.   

Publications

• 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.