Peer-reviewed articles & preprints

Rethinking the Choice Behavior of Sugar Metabolism in Bacteria

Varner JD (2026) · Submitted to PLoS ONE · arXiv 2607.07677

Continuous Hidden Markov Models for Equity Returns: Heavy-Tail Emission Families and Regime-Conditional Value-at-Risk

Alswaidan A, Jin C, Varner JD (2026) · arXiv 2606.23492

Synthetic American Option Pricing via Jump-HMM-Driven Heston Implied Volatility

Sun J, Jin Z, Zhang J, Varner JD (2026) · arXiv 2605.13998

Computational framework for multistep metabolic pathway design

Zhang PZ, Varner JD (2026) · arXiv 2604.13471

Validated Synthetic Patient Generation for Small Longitudinal Cohorts: Coagulation Dynamics Across Pregnancy

Varner JD, Bravo MC, McBride C, Orfeo T, Bernstein I (2026) · Accepted, npj Systems Biology and Applications

ParetoEnsembles.jl: A Julia Package for Multiobjective Parameter Estimation Using Pareto Optimal Ensemble Techniques

Varner JD (2026) · arXiv 2603.29986

Conditioning Protein Generation via Hopfield Pattern Multiplicity

Varner JD (2026) · arXiv 2603.20115

BSTModelKit.jl: A Julia Package for Constructing, Solving, and Analyzing Biochemical Systems Theory Models

Vadhin S, Varner JD (2026) · arXiv 2603.19115

Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention

Varner JD (2026) · Submitted to PNAS Nexus · arXiv 2603.14717

Hybrid Hidden Markov Model for Modeling Equity Excess Growth Rate Dynamics: A Discrete-State Approach with Jump-Diffusion

Alswaidan A, Varner JD (2026) · Submitted to Journal of Data and Information Quality

Stochastic Attention via Langevin Dynamics on the Modern Hopfield Energy

Alswaidan A, Varner JD (2026) · arXiv 2603.06875

MarketGPT: Developing a pre-trained transformer (GPT) for modeling financial time series

Wheeler A, Varner JD (2024) · arXiv 2411.16585

Scalable agent-based modeling for complex financial market simulations

Wheeler A, Varner JD (2024) · arXiv 2312.14903

Comparison of rapid-, kaolin-, and native-TEG parameters in burn patient cohorts with acute burn-induced coagulopathy and abnormal fibrinolytic function

Keyloun JW, Le TD, Moffatt LT, Orfeo T, McLawhorn MM, Bravo MC, et al., Varner JD (2024) · Journal of Burn Care & Research 45(1):70–79

Convergent approaches to delineate the metabolic regulation of tumor invasion by hyaluronic acid biosynthesis

Shimpi AA, Tan ML, Vilkhovoy M, Dai D, Roberts LDM, Kuo JCH, Huang L, et al., Varner JD (2023) · Advanced Healthcare Materials 12(14):2202224

Endothelial cells metabolically regulate breast cancer invasion toward a microvessel

Tan ML, Jenkins-Johnston N, Huang S, Schutrum B, Vadhin S, Adhikari A, et al., Varner JD, Fischbach C (2023) · APL Bioengineering 7(4):046116

Virtual high-throughput screening of vapor-deposited amphiphilic polymers for inhibiting biofilm formation

Feng Z, Cheng Y, Khlyustova A, Wani A, Franklin T, Varner JD, Hook AL, Yang R (2023) · Advanced Materials Technologies 8(13):2201533

Integrated constraint-based modeling of E. coli cell-free protein synthesis

Vilkhovoy M, Dammalapati S, Vadhin S, Adhikari A, Varner JD (2023) · bioRxiv 2023.02.10.528035

Modeling and analysis of a cell-free gluconate responsive biosensor

Adhikari A, Murti A, Narayanan AM, Lim HE, Varner JD (2023) · bioRxiv 2023.01.10.523462

Assessing factor V antigen and degradation products in burn and trauma patients

Keyloun JW, Le TD, Orfeo T, Brummel-Ziedins KE, Bravo MC, Kaye MD, et al., Varner JD (2022) · Journal of Surgical Research 274:169–177

Constructing cell-free expression systems for low-cost access

Guzman-Chavez F, Arce A, Adhikari A, Vadhin S, Pedroza-Garcia JA, et al., Varner JD, Federici F, Haseloff J (2022) · ACS Synthetic Biology 11(3):1114–1128

Engineering orthogonal human O-linked glycoprotein biosynthesis in bacteria

Natarajan A, Jaroentomeechai T, Cabrera-Sánchez M, Mohammed JC, Cox EC, Young O, et al., Varner JD, Azadi P, DeLisa MP (2020) · Nature Chemical Biology 16(10):1062–1070

Effective biophysical modeling of cell-free transcription and translation processes

Adhikari A, Vilkhovoy M, Vadhin S, Lim HE, Varner JD (2020) · Frontiers in Bioengineering and Biotechnology 8:539081

The evolution of cell-free biomanufacturing

Vilkhovoy M, Adhikari A, Vadhin S, Varner JD (2020) · Processes 8(6):675

Genome scale sequence specific dynamic model of cell-free protein synthesis in E. coli

Horvath N, Vilkhovoy M, Wayman JA, Calhoun K, Swartz J, Varner JD (2020) · Metabolic Engineering Communications 10:e00113

Absolute quantification of cell-free protein synthesis metabolism by reversed-phase liquid chromatography–mass spectrometry

Vilkhovoy M, Dai D, Vadhin S, Adhikari A, Varner JD (2019) · Journal of Visualized Experiments (153):e60329

Improving designer glycan production in Escherichia coli through model-guided metabolic engineering

Wayman JA, Glasscock C, Mansell TJ, DeLisa MP, Varner JD (2019) · Metabolic Engineering Communications 9:e00088

Analysis of the role of thrombomodulin in all-trans retinoic acid treatment of coagulation disorders in cancer patients

Ghaffari H, Varner JD, Petzold LR (2019) · Theoretical Biology and Medical Modelling 16:3

Retinoic acid and FICZ combination therapy reveals putative targets for enhancing response in non-APL AML

Bunaciu RP, MacDonald RJ, Jensen HA, Gao F, Wang X, Johnson L, Varner JD, Yen A (2019) · Leukemia & Lymphoma 60(7):1697–1707

SEML: A Simplified English Modeling Language

Zhang Z, Varner JD (2019) · IFAC-PapersOnLine 52:121–128

Kinetic modeling of coagulation and fibrinolysis with platelets

LeCover R, et al., Varner JD (2019) · IFAC-PapersOnLine 52:94–100

Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors

Shan M, Dai D, Vudem A, Varner JD, Stroock AD (2018) · PLoS Computational Biology 14(12):e1006584

Sequence specific modeling of E. coli cell-free protein synthesis

Vilkhovoy M, Horvath N, Shih C-H, Wayman JA, Calhoun K, Swartz J, Varner JD (2018) · ACS Synthetic Biology 7(8):1844–1857

Src family kinase inhibitor bosutinib enhances retinoic acid-induced differentiation of HL-60 leukemia cells

MacDonald RJ, Bunaciu RP, Ip V, Dai D, Tran D, Varner JD, Yen A (2018) · Leukemia & Lymphoma 59(10):2458–2468

Potential for subsets of wt-NPM1 primary AML blasts to respond to retinoic acid treatment

Bunaciu RP, MacDonald RJ, Gao F, Johnson LM, Varner JD, Wang X, Nataraj S, Guzman ML, Yen A (2018) · Oncotarget 9(3):4134–4149

Dynamic constraint-based model of cell-free protein production

Dai D, Horvath N, Varner JD (2018) · Processes 6(8):132

Dynamic Optimization with Particle Swarms (DOPS)

Sagar A, LeCover R, Shoemaker C, Varner JD (2018) · BMC Systems Biology 12:87

Reduced order modeling and analysis of the human complement system

Sagar A, Dai W, Minot M, LeCover R, Varner JD (2017) · PLoS ONE 12(11):e0187373

An effective model of the retinoic acid induced HL-60 differentiation program

Tasseff R, Jensen HA, Congleton J, Dai D, Rogers KV, Sagar A, Bunaciu RP, Yen A, Varner JD (2017) · Scientific Reports 7:14327

JuPOETs: A constrained multiobjective optimization approach to estimate biochemical model ensembles in Julia

Bassen DM, Vilkhovoy M, Minot M, Butcher JT, Varner JD (2017) · BMC Systems Biology 11:10

Population heterogeneity in the epithelial to mesenchymal transition is controlled by NFAT and phosphorylated Sp1

Gould R, Bassen DM, Chakrabarti A, Varner JD, Butcher J (2016) · PLoS Computational Biology 12(12):e1005251

Differential contributions of intrinsic and extrinsic pathways to thrombin generation in adult, maternal and cord plasma samples

Rice NT, Szlam F, Varner JD, Bernstein PS, Szlam AD, Tanaka KA (2016) · PLoS ONE 11(5):e0154127

Hybrid cybernetic modeling with flux balance analysis

Vilkhovoy M, Minot M, Varner JD (2016) · bioRxiv 047316

Prostate signal transduction model

Rogers K, Wayman J, Tasseff R, Gee C, DeLisa M, Varner JD (2016) · bioRxiv 058552

Induced myelomonocytic differentiation in leukemia cells is accompanied by noncanonical transcription factor expression

Jensen HA, Yourish HB, Bunaciu RP, Varner JD, Yen A (2015) · FEBS Open Bio 5:789–800

FICZ modulates the signalsome responsible for RA-induced differentiation of HL-60 myeloblastic leukemia cells

Bunaciu RP, Jensen HA, MacDonald RJ, LaTocha DH, Varner JD, Yen A (2015) · PLoS ONE 10(8):e0135668

Generating effective models and parameters for RNA genetic circuits

Hu CY, Varner JD, Lucks JB (2015) · ACS Synthetic Biology 4(8):914–926

GW5074 and PP2 kinase inhibitors implicate nontraditional c-Raf and Lyn function as drivers of retinoic acid-induced maturation

Jensen HA, Bunaciu RP, Varner JD, Yen A (2015) · Cell Signalling 27(6):1198–1207

Reduced order extrinsic coagulation model

Sagar A, Varner JD (2015) · Processes 3(1):178–203

Retinoic acid therapy resistance progresses from unilineage to bilineage in HL-60 leukemic blasts

Jensen HA, Bunaciu RP, Ibabao CN, Myers R, Varner JD, Yen A (2014) · PLoS ONE 9(6):e98929 · Paper →

Ubiquibodies, synthetic E3 ubiquitin ligases endowed with unnatural substrate specificity for targeted protein silencing

Portnoff AD, Stephens EA, Varner JD, DeLisa MP (2014) · Journal of Biological Chemistry 289(11):7844–7855 · Paper →

Physicochemical regulation of endothelial sprouting in a 3D microfluidic angiogenesis model

Verbridge SS, Chakrabarti A, DelNero P, Kwee B, Varner JD, Stroock AD, Fischbach C (2013) · J. Biomed. Mater. Res. A 101(10):2948–2956 · Paper →

The Src-family kinase inhibitor PP2 rescues inducible differentiation events in emergent retinoic acid-resistant myeloblastic leukemia cells

Jensen HA, Styskal LE, Tasseff R, Bunaciu RP, Congleton J, Varner JD, Yen A (2013) · PLoS ONE 8(3):e58621 · Paper →

Hierarchical approaches for systems modeling in cardiac development

Gould RA, Aboulmouna LM, Varner JD, Butcher JT (2013) · WIREs Systems Biology and Medicine 5(3):289–305 · Paper →

Multiscale models of breast cancer progression

Chakrabarti A, Verbridge S, Stroock AD, Fischbach C, Varner JD (2012) · Annals of Biomedical Engineering 40(11):2488–2500 · Paper →

Computational modeling and analysis of insulin induced eukaryotic translation initiation

Lequieu J, Chakrabarti A, Nayak S, Varner JD (2011) · PLoS Computational Biology 7(11):e1002263 · Paper →

A review of the mammalian unfolded protein response

Chakrabarti A, Chen AW, Varner JD (2011) · Biotechnology and Bioengineering 108(12):2777–2793 · Paper →

Interferon regulatory factor-1 binds c-Cbl, enhances MAPK signaling and promotes retinoic acid-induced differentiation of HL-60 cells

Shen M, Bunaciu RP, Congleton J, Jensen HA, Sayam LG, Varner JD, Yen A (2011) · Leukemia & Lymphoma 52(12):2372–2379 · Paper →

Modeling and analysis of retinoic acid induced differentiation of uncommitted precursor cells

Tasseff R, Nayak S, Song SO, Yen A, Varner JD (2011) · Integrative Biology 3(5):578–591 · Paper →

Modelling and analysis of an ensemble of eukaryotic translation initiation models

Nayak S, Siddiqui JK, Varner JD (2011) · IET Systems Biology 5(1):2–14 · Paper →

Ensembles of uncertain mathematical models can identify network response to therapeutic interventions

Luan D, Szlam F, Tanaka KA, Barie PS, Varner JD (2010) · Molecular BioSystems 6(11):2272–2286 · Paper →

RAF associates with phosphorylated nuclear BubR1 during endoreduplication induced by JAK inhibition

Reiterer G, Chen L, Tasseff R, Varner JD, Chen CY, Yen A (2010) · Cell Cycle 9(16):3297–3304 · Paper →

Ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs)

Song SO, Chakrabarti A, Varner JD (2010) · Biotechnology Journal 5(7):768–780 · Paper →

Arsenic trioxide cooperates with all-trans retinoic acid to enhance MAPK activation and differentiation in PML-RARα negative human myeloblastic leukemia cells

Nayak S, Shen M, Bunaciu RP, Bloom SE, Varner JD, Yen A (2010) · Leukemia & Lymphoma 51(9):1734–1747 · Paper →

Analysis of the molecular networks in androgen dependent and independent prostate cancer revealed fragile and robust subsystems

Tasseff R, Nayak S, Salim S, Kaushik P, Rizvi N, Varner JD (2010) · PLoS ONE 5(1):e8864 · Paper →

Anti-factor IXa aptamer reduces propagation of thrombin generation in plasma anticoagulated with warfarin

Szlam F, Luan D, Bolliger D, Szlam AD, Levy JH, Varner JD, Tanaka KA (2010) · Thrombosis Research 125(5):e252–e258 · Paper →

A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables

Kim JI, Varner JD, Ramkrishna D (2008) · Biotechnology Progress 24(5):993–1006 · Paper →

Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy

Conrado RJ, Varner JD, DeLisa MP (2008) · Current Opinion in Biotechnology 19(5):492–499 · Paper →

A test of highly optimized tolerance reveals fragile cell-cycle mechanisms are molecular targets in clinical cancer trials

Nayak S, Salim S, Luan D, Zai M, Varner JD (2008) · PLoS ONE 3(4):e2016 · Paper →

Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies

Luan D, Zai M, Varner JD (2007) · PLoS Computational Biology 3(7):e142 · Paper →

Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway

Conrado RJ, Mansell TJ, Varner JD, DeLisa MP (2007) · Metabolic Engineering 9(4):355–363 · Paper →

Systems biology and the mathematical modelling of antibody-directed enzyme prodrug therapy (ADEPT)

Varner JD (2005) · IEE Proceedings – Systems Biology 152(4):291–302 · Paper →

Cybernetic model predictive control of a continuous bioreactor with cell recycle

Gadkar KG, Doyle FJ III, Crowley TJ, Varner JD (2003) · Biotechnology Progress 19(5):1487–1497 · Paper →

A mathematical model of caspase function in apoptosis

Fussenegger M, Bailey JE, Varner JD (2000) · Nature Biotechnology 18(7):768–774 · Paper →

Large-scale prediction of phenotype: concept

Varner JD (2000) · Biotechnology and Bioengineering 69(6):664–678 · Paper →

Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries

Varner J, Ramkrishna D (1999) · Biotechnology Progress 15(3):407–425 · Paper →

Metabolic engineering from a cybernetic perspective. 2. Qualitative investigation of nodal architectures and their response to genetic perturbation

Varner J, Ramkrishna D (1999) · Biotechnology Progress 15(3):426–438 · Paper →

Metabolic engineering from a cybernetic perspective: aspartate family of amino acids

Varner J, Ramkrishna D (1999) · Metabolic Engineering 1(1):88–116 · Paper →

Mathematical models of metabolic pathways

Varner J, Ramkrishna D (1999) · Current Opinion in Biotechnology 10(2):146–150 · Paper →

Application of cybernetic models to metabolic engineering: investigation of storage pathways

Varner J, Ramkrishna D (1998) · Biotechnology and Bioengineering 58(2-3):282–291 · Paper →

Metabolic engineering from a cybernetic perspective: a conceptual framework

Varner JD (1997) · PhD Dissertation, Purdue University · Thesis →