VARNERLAB Publication Respositories

This page links to the GitHub repositories associated with VARNERLAB publications. We are commited to OpenScience, for on-going projects (not published yet, or in process) check out our experimental page.
2015
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)
2016
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)
2017
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)
2018
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)
2019
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)
2020
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)