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Pienaar Computational Systems Pharmacology Lab

Publications

Selected publications are listed below. Please see google scholar for an up-to-date list.

 

  • Catherine Weathered, Kelly Pennington, Patricio Escalante, Elsje Pienaar. The role of biofilms, bacterial phenotypes, and innate immune response in Mycobacterium avium colonization to infection. J. Theor. Biol. 2021 Oct 27, 110949 (2021)
  • Jonathan W. Cody, Amy Ellis, Shelby L. O’Connor, Elsje Pienaar. Mathematical modeling of N-803 treatment in SIV-infected non-human primates. PLoS Computational Biology. 17, e1009204, doi:10.1371/journal.pcbi.1009204 (2021).
  • Sarathy J, Blanc L, Alvarez-Cabrera N, O'Brien P, Dias-Freedman I, Mina M, Zimmerman M, Kaya F, Liang HH, Prideaux B, Dietzold J, Salgame P, Savic R, Linderman J, Kirschner D, Pienaar E, Dartois V. Fluoroquinolone efficacy against tuberculosis is driven by penetration into lesions and activity against resident bacterial populations. Antimicrob Agents Chemother. 2019 Feb 25. pii: AAC.02516-18.
  • Elkington P, Lerm M, Kapoor N, Mahon R, Pienaar E, Huh D, Kaushal D, Schlesinger L. In vitro granuloma models of tuberculosis: potential and challenges. Journal of Infectious Diseases. jiz010, 2019.
  • Joslyn, L. R., Pienaar, E., DiFazio, R. M., Suliman, S., Kagina, B. M., Flynn, J. L., Kirschner, D. E. Integrating Non-human Primate, Human, and Mathematical Studies to Determine the Influence of BCG Timing on H56 Vaccine Outcomes. 2018. Front Microbiol, 9, 1734.
  • Pienaar E. Multi-fidelity analysis for predicting rare events in stochastic computational models of complex biological systems. Biomedical Engineering and Computational Biology, 9:1179597218790253, 2018.
  • Pienaar E, Linderman JJ, Kirschner DE. Emergence and selection of isoniazid and rifampin resistance in tuberculosis granulomas. PLoS One. 2018;13(5):e0196322.
  • Warsinske HC, Pienaar E, Linderman JJ, Mattila JT, Kirschner DE. Deletion of TGF-β1 Increases Bacterial Clearance by Cytotoxic T Cells in a Tuberculosis Granuloma. Frontiers in Immunology. 2017; 8:1843
  • Cicchese J, Pienaar E, Kirschner D, Linderman JJ. Applying optimization algorithms to tuberculosis antibiotic treatment regimens. Cellular and Molecular Bioengineering. Aug 2017. DOI: 10.1007/s12195-017-0507-6
  • Kirschner DE, Pienaar E, Marino S, Linderman JJ . A review of computational model contributions to our understanding of M. tuberculosis within-host infection and treatment. Current Opinion in Systems Biology. 2017; 3:170-185.
  • Pienaar E, Sarathy J, Prideaux B, Dartois V, Kirschner DE and Linderman JJ. Systems Pharmacology Evaluation of Fluoroquinolone Spatial Distribution And Efficacy In Tuberculosis Granulomas. PLoS Computational Biology. 2017;13(8):e1005650.
  • Pienaar E, Matern W, Linderman JJ, Bader JS, Kirschner DE. Multi-scale model of Mycobacterium tuberculosis infection maps metabolite and gene perturbations to granuloma sterilization predictions. Infection and Immunity. 2016;84(5):1650.
  • Pienaar E, Dartois V, Linderman JJ, Kirschner DE. In silico evaluation and exploration of antibiotic tuberculosis treatment regimens. BMC Systems Biology. 2015;9:79.
  • Linderman JJ, Cilfone N, Pienaar E, Gong C, and Kirschner DE. A Multi-scale Approach to Designing Therapeutics for Tuberculosis. Integrative biology. 2015; 7:591-609.
  • Cilfone N, Pienaar E, Thurber GM, Kirschner DE, Linderman JJ. Systems pharmacology approach towards the design of inhaled formulations of rifampicin and isoniazid for treatment of tuberculosis. CPT Pharmacometrics Syst Pharmacol. 2015;4:e22.
  • Pienaar E, Cilfone NA, Lin PL, Dartois V, Mattila JT, Butler JR, Flynn JL, Kirschner DE, Linderman JJ. A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment. J Theor Biol. 2015;367:166-179.
  • Raffetseder J*, Pienaar E*, Blomgran R, Eklund D, Patcha Brodin V, Andersson H, Stendahl O, Welin A, Lerm M. Replication Rates of Mycobacterium tuberculosis in Human Macrophages Do Not Correlate with Mycobacterial Antibiotic Susceptibility. PLoS One. 2014;9(11):e112426. *: Shared first authorship.
  • Pienaar E, Lerm M. A Mathematical Model of the Initial Interaction between Mycobacterium tuberculosis and Macrophages. J Theor Biol. 2014; 342:23-32.
  • Abuzeid N, Kalsum S, Koshy RJ, Larsson M, Glader M, Andersson H, Raffetseder J, Pienaar E, Eklund D, Alhassan MS, AlGadir HA, Koko WS, Schön T, Mesaik MA, Abdalla OM, Khalid A and Lerm M. Antimycobacterial activity of selected medicinal plants traditionally used in Sudan to treat infectious diseases. J Ethnopharmacol. 2014;157:134-139.
  • Viljoen S, Pienaar E, Viljoen HJ. A state-time epidemiology model of tuberculosis: Importance of re-infection. Computational Biology and Chemistry. 2012;36(0):15-22.
  • Louw TM, Booth CS, Pienaar E, Termaat JR, Whitney SE, Viljoen HJ. Experimental Validation of a Fundamental Model for PCR Efficiency. Chem Eng Sci. Apr 15 2011;66(8):1783-1789.
  • Booth CS, Pienaar E, Termaat JR, Whitney SE, Louw TM, Viljoen HJ. Efficiency of the Polymerase Chain Reaction. Chem Eng Sci. Sep 2010;65(17):4996-5006.
  • Pienaar E, Fluitt AM, Whitney SE, Freifeld AG, Viljoen HJ. A model of tuberculosis transmission and intervention strategies in an urban residential area. Comput Biol Chem. 2010;34(2):86-96.
  • TerMaat JR, Mamedov TG, Pienaar E, Whitney SE, Subramanian A. Automated two-column purification of iminobiotin and BrdU-labeled PCR products for rapid cloning: application to genes synthesized by polymerase chain assembly. J Chromatogr Sci. 2010;48(2):120-124.
  • TerMaat JR, Pienaar E, Whitney SE, Mamedov TG, Subramanian A. Gene synthesis by integrated polymerase chain assembly and PCR amplification using a high-speed thermocycler. J Microbiol Methods. 2009;79(3):295-300.
  • Valente W, Pienaar E, Fast A, et al. A Kinetic Study of In Vitro Lysis of Mycobacterium smegmatis. Chem Eng Sci. May 2009;64(9):1944-1952.
  • Pienaar E, Whitney SE, Viljoen HJ, van Rensburg NF. A model of the complex response of Staphylococcus aureus to methicillin. J Theor Biol. Apr 2009;257(3):438-445.
  • Mamedov TG, Pienaar E, Whitney SE, et al. A fundamental study of the PCR amplification of GC-rich DNA templates. Comput Biol Chem. Dec 2008;32(6):452- 457.
  • Pienaar E, Viljoen HJ. The tri-frame model. J Theor Biol. Apr 2008;251(4):616-627.
  • Fluitt A, Pienaar E, Viljoen H. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem. Oct 2007;31(5-6):335-346.
  • Pienaar E, Theron M, Nelson M, Viljoen HJ. A quantitative model of error accumulation during PCR amplification. Comput Biol Chem. Apr 2006;30(2):102-111.