Experience

Staff scientist, 2009-present
Lawrence Livermore National Laboratory, Livermore, CA

Postdoctoral researcher, 2006-2009
Lawrence Livermore National Laboratory, Livermore, CA

Postdoctoral fellow, 2004- 2006
Smith-Kettlewell Eye Research Institute, San Francisco, CA

Research Interests

• Computational modeling of complex biological systems.
• Systems biology of microbial communities
• System-level identification of drug targets and analyses of drug metabolism
• Cancer metabolism
• Modeling host-pathogen interactions

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

• 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, BMC Bioinformatics (2019), in press.
• 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 Pharmacokinetic Model to Study Theophylline Metabolism and Its Interactions with Ciprofloxacin and Caffeine (2016), CPT: Pharmacometrics and Systems Pharmacology, 5, 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), Mol. Syst. Biol., 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.

Book Chapters

• 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, Methods in Molecular Biology, Vol. 881, Springer, New York, NY, USA, ISBN:  9781617798269.

For a full list of publications, see my Google Scholar or ResearchGate Profiles