Reduced order extrinsic coagulation model Sagar A and J. Varner (2015) Dynamic Modeling of the Human Coagulation Cascade using Reduced Order Effective Kinetic Models. Processes, 3:178 - 203 (python)
Hybrid cybernetic modeling with flux balance analysis Vilkhovoy M, Minot M and J. Varner (2016) Effective Dynamic Models of Metabolic Networks. bioRxiv 047316; doi: https://doi.org/10.1101/047316 (julia)
Prostate signal transduction model Rogers K, Wayman J, Tasseff R, Gee C, DeLisa M and J. Varner (2016) Modeling and Analysis of Hormone and Mitogenic Signal Integration in Prostate Cancer. bioRxiv 058552; doi: http://dx.doi.org/10.1101/05855 (octave/sundials)
Reduced order epithelial-to-mesenchymal transition (EMT) model Gould R, Bassen DM, Chakrabarti A, Varner JD, Butcher J (2016) Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1. PLoS Comput Biol 12(12): e1005251. https://doi.org/10.1371/journal.pcbi.10052 (julia)
Reduced order complement model Sagar A, Dai W, Minot M, LeCover R, Varner JD (2017) Reduced order modeling and analysis of the human complement system. PLoS ONE 12(11): e0187373. https://doi.org/10.1371/journal.pone.0187373 (julia)
Sequence specific constraint based modeling of cell free reactions Vilkhovoy et al (2017) Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis. bioRxiv 139774; doi: https://doi.org/10.1101/139774 (julia)
Effective HL60 ATRA-induced signal transduction model Tasseff et al (2017) An Effective Model of the Retinoic Acid Induced HL-60 Differentiation Program. Sci Reports, 7, Article number: 14327 doi:10.1038/s41598-017-14523-5 (available at bioRxiv 138784; doi: https://doi.org/10.1101/138784) (julia)
JuPOETs: Pareto Optimal Ensemble Technique in the Julia programming language Bassen et al (2017) JuPOETs: A Constrained Multiobjective Optimization Approach to Estimate Biochemical Model Ensembles in the Julia Programming Language. BMC Systems Biology 11:10 https://doi.org/10.1186/s12918-016-0380-2 (julia)
Dynamic constraint based model of cell free protein production Dai D, Horvath H and J. Varner (2018) Dynamic Sequence Specific Constraint-based Modeling of Cell-free Protein Synthesis. Processes 6, 132; doi: https://doi.org/10.3390/pr6080132 (julia)
Dynamic Optimization with Particle Swarms (DOPS) Sagar A at al (2018) Dynamic Optimization with Particle Swarms (DOPS): A meta-heuristic for parameter estimation in biochemical models. BMC Systems Biol., 12:87 https://doi.org/10.1186/s12918-018-0610-x (matlab)
Designer glycan production in Escherichia coli Wayman et al (2019) Improving designer glycan production in Escherichia coli through model-guided metabolic engineering. Metabolic Engineering Communications, 9, e00088; doi: https://doi.org/10.1016/j.mec.2019.e00088 (matlab)
SEML: A Simplified English Modeling Language Zhang Z and J. Varner (2019) SEML: A Simplified English Modeling Language for Constructing Biological Models in Julia. IFAC-PapersOnLine, 52, 121-128; doi: https://doi.org/10.1016/j.ifacol.2019.12.246 (julia)
Effective Kinetc Modeling of Fibrinolysis with Platelets LeCover R et al (2019) Kinetic Modeling of Coagulation and Fibrinolysis. IFAC-PapersOnLine, 52, 94-100; doi: https://doi.org/10.1016/j.ifacol.2019.12.242 (julia)
Sequence specific dynamic model of cell-free protein synthesis in Escherichia coli N Horvath et al (2020) Toward a genome scale sequence specific dynamic model of cell-free protein synthesis in Escherichia coli. Metabolic Engineering Communications 10, e00113 (julia)