For all of JV's publications visit his Google Scholar page

Gould R, Chakrabarti A, Varner J and J. Butcher (2015) Population heterogeneity in the epithelial to mesenchymal transition is controlled by NFAT and phosphorylated Sp1. BioRxiv DOI:10.1101/028993
Jensen HA, Yourish YB, Bunaciu RP, Varner JD and A. Yen (2015) Induced myelomonocytic differentiation in leukemia cells is accompanied by noncanonical transcription factor expression. FEBS Open Bio DOI:10.1016/j.fob.2015.09.008
Bunaciu RP, Jensen HA, MacDonald RJ, LaTocha DH, Varner JD and A. Yen (2015) 6-Formylindolo(3,2-b)Carbazole (FICZ) Modulates the Signalsome Responsible for RA-Induced Differentiation of HL-60 Myeloblastic Leukemia Cells. PLoS ONE. DOI:10.1371/journal.pone.0135668
Chelsea Y. Hu, J. Varner, and Julius B. Lucks (2015) Generating Effective Models and Parameters for RNA Genetic Circuits. ACS Synthetic Biology DOI: 10.1021/acssynbio.5b00077
Sagar A and J. Varner (2015) Dynamic Modeling of the Human Coagulation Cascade using Reduced Order Effective Kinetic Models. Processes DOI:10.3390/pr3010178
Coagulation model code (GitHub)
Wayman J, Sagar A and J. Varner (2015) Dynamic Modeling of Cell Free Biochemical Networks using Effective Kinetic Models. Processes DOI:10.3390/pr3010138
Jensen H, Bunaciu R, Varner J and A. Yen (2015) GW5074 and PP2 kinase inhibitors implicate nontraditional c-Raf and Lyn function as drivers of retinoic acid-induced maturation. Cell Signaling DOI: 10.1016/j.cellsig.2015.03.014
Jensen H, Bunaciu R, Ibabao C, Myers R, Varner J and A Yen (2014). Retinoic acid therapy resistance progresses from unilineage to bilineage in HL-60 leukemic blasts. PLoS ONE DOI: 10.1371/journal.pone.0098929
Portnoff A, Stephens E, Varner J and M. DeLisa (2014) Ubiquibodies: Synthetic E3 Ubiquitin Ligases Endowed with Unnatural Substrate Specificity for Targeted Protein Silencing. Journal of Biological Chemistry DOI:10.1074/jbc.M113.544825
Stephens, Erin A., Alyse D. Portnoff, Morgan R. Baltz, J. Varner and M. DeLisa (2014) Ubiquibodies: Engineered E3 Ubiquitin Ligases for Targeted Degradation. Protein Science DOI: 10.1002/pro.2504
Wayman J and J. Varner (2013) Systems Modeling in Biotechnology and Bioprocess Engineering, Current Opinion Chemical Engineering DOI:10.1016/j.coche.2013.09.001
Jensen HA, Styskal LE, Tasseff R, Bunaciu RP, Congleton J, Varner JD and A Yen (2013) The Src-Family Kinase Inhibitor PP2 Rescues Inducible Differentiation Events in Emergent Retinoic Acid-Resistant Myeloblastic Leukemia Cells. PLoS ONE DOI:10.1371/journal.pone.0058621
Verbridge S, Chakrabarti A, Varner J, Stroock A and C. Fischbach (2013) Physicochemical regulation of endothelial sprouting in a 3-D microfluidic angiogenesis model. Journal Biomedical Materials Research Part A DOI:10.1002/jbm.a.34587
Gould R, Aboulmouna L, Varner J and J. Butcher (2013) Hierarchical Approaches for Systems Modeling in Cardiac Development, Wiley Interdisciplinary Reviews: Systems Biology and Medicine DOI: 10.1002/wsbm.1217
Chakrabarti A, Verbridge S, Stroock AD, Fischbach C and J. Varner (2012) Multiscale models of breast cancer progression. Annals of Biomedical Engineering DOI:10.1007/s10439-012-0655-8
Sun S, Titushkin I, Varner J and M. Cho (2012) Millimeter Wave-induced Modulation of Calcium Dynamics in an Engineered Skin Co-Culture Model: Role of secreted ATP on Calcium Spiking. Journal of Radiation Research DOI: 10.1269/jrr.11037
Shen M, Bunaciu R, Fabi M, Congleton J, Jensen H, Varner J, Sayam L and A. Yen (2011) The interferon regulatory factor-1 binds c-Cbl, enhances MAPK signaling and promotes retinoic acid-induced differentiation of HL-60 human myelo-monoblastic leukemia cells. Leukemia and Lymphoma DOI: 10.3109/10428194.2011.603449
Lequieu J ,Chakrabarti A , Nayak S and J.Varner (2011) Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation. PLoS Computational Biology DOI: 10.1371/journal.pcbi.1002263
Chakrabarti A, Chen AW and J. Varner (2011) A Review of the Mammalian Unfolded Protein Response. Biotechnology and Bioengineering DOI: 10.1002/bit.23282
Tasseff R, Nayak S, Song S, Yen A, and J. Varner (2011) Modeling and Analysis of Retinoic Acid Induced Differentiation of Uncommitted Precursor Cells. Integrative Biology DOI: 10.1039/C0IB00141D
Nayak S, Siddiqui J and J. Varner (2011) Modeling and Analysis of an Ensemble of Eukaryotic Translation Initiation Models. IET Systems Biology DOI: 10.1049/iet-syb.2009.0065
Luan D, Szlam F, Tanaka K.A, Barie P.S, and J. Varner (2010) Ensembles of uncertain mathematical models can identify network response to therapeutic interventions. Molecular BioSystems DOI: 10.1039/b920693k
Song S, Chakrabarti A, and J. Varner (2010) Identifying ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs). Biotechnology Journal DOI: 10.1002/biot.201000059
Tasseff R, Nayak N, Salim S, Kaushik P, Rizvi N and J. Varner (2010) Analysis of the Molecular Networks in Androgen Dependent and Independent Prostate Cancer Revealed Fragile and Robust Subsystems. PLoS ONE DOI: 10.1371/journal.pone.0008864
Reiterer G, Chen L, Tasseff R, Varner J, Chen C-Y and A. Yen (2010) RAF associated with phosphorylated nuclear BudR1 during endoreduplication induced by JAK inhibition. Cell Cycle DOI: 0.4161/cc.9.16.12631
Nayak S, Shen M, Bunaciu R, Bloom S, Varner J and A. Yen (2010) Arsenic trioxide cooperates with all trans retinoic acid to enhance mitogen-activated protein kinase activation and differentiation in PML-RARa negative human myeloblastic leukemia cells. Leukemia and Lymphoma DOI: 10.3109/10428194.2010.501535
Szlam F, Luan D, Bolliger D, Szlam A.D, Levy J.H, Varner J, and K. A. Tanaka (2010) Anti-factor IXa Aptamer reduces propagation of thrombin generation in plasma anticoagulated with warfarin. Thrombin Research DOI: 10.1016/j.thromres.2009.11.018
Song S and J. Varner (2009) Modeling and Analysis of the Molecular Basis of Pain in Sensory Neurons. PLoS ONE DOI: 10.1371/journal.pone.0006758
Kim JI, Varner J, and D Ramkrishna (2008) A hybrid model of anaerobic E.coli GJT001: Combination of elementary flux modes and cybernetic variables. Biotechnology Progress DOI: 10.1002/btpr.73
Conrado RJ, Varner J, and MP DeLisa (2008) Macromolecular compartmentation and multienzyme organization in natural and synthetic metabolic pathways. Current Opinion Biotechnology DOI: 10.1016/j.copbio.2008.07.006
Nayak S, Saniya S, Luan D, Zai M, and J. Varner (2008) A test of highly optimized tolerance reveals fragile cell-cycle mechanisms are molecular targets in clinical cancer trials. PLoS ONE DOI: 10.1371/journal.pone.000201
Luan D, Zai M, and J. Varner (2007) Computationally Derived Points of Fragility of a Human Cascade are Consistent with Current Therapeutic Strategies. PLoS Computational Biology DOI: 10.1371/journal.pcbi.0030142
Conrado RJ, Mansell TJ, Varner J, and MP DeLisa (2007) Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for an engineered bacterial propanediol pathway. Metabolic Engineering DOI:10.1016/j.ymben.2007.05.002
Srivastava R, and J. Varner (2007) Emerging Technologies: Systems Biology. Biotechnology Progress DOI: 10.1021/bp060352v
J. Varner (2005) Systems Biology and the Mathematical Modeling of Antibody Directed Enzyme Prodrug Therapy (ADEPT). IEE Proceedings Systems Biology DOI: 10.1021/bp060352v
Gadkar KG, Varner J, and Doyle FJ III. (2005) Model Identification of Signal Transduction Networks from Data Using a State Regulator Problem. IEE Proceedings Systems Biology DOI: 10.1049/sb:20045029
Gupta A, Varner JD, and Maranas CD. (2005) Large-scale Inference of the Transcriptional Regulation of Bacillus subtilis. Computers and Chemical Engineering DOI:10.1016/j.compchemeng.2004.08.030
Lee L-Q, Varner J, and Ko K. (2004) Parallel Extreme Pathway Computation for Metabolic Networks. Proceedings IEEE Computational Systems Bioinformatics DOI:10.1109/CSB.2004.1332526
Dasika MS, Gupta A, Maranas CD, and J. Varner (2004) A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. Pacific Symposium on Biocomputing Research Gate (Open Access)
Gadkar KG, Doyle FJ III, Crowley TJ, and J. Varner (2003) Cybernetic Model Predictive Control of a Continuous Bioreactor with Cell Recycle. Biotechnology Progress DOI: 10.1021/bp025776d
Fussenegger M, Bailey JE, and J. Varner (2000) A Mathematical Model of Caspase Function in Apoptosis. Nature Biotechnology DOI:10.1038/77589
Varner J (2000) Toward the Large-Scale Prediction of Phenotype: Concept. Biotechnology and Bioengineering DOI: 10.1002/1097-0290(20000920)69:6<664::AID-BIT11>3.0.CO;2-H
Varner J, and D. Ramkrishna (1999) Metabolic Engineering from a Cybernetic Perspective. Aspartate Family of Amino Acids. Metabolic Engineering DOI:10.1006/mben.1998.0104
Varner J. and D. Ramkrishna (1999) Mathematical Models of Metabolic Pathways. Current Opinion Biotechnology DOI:10.1016/S0958-1669(99)80025-1
Varner J and D. Ramkrishna (1999) Metabolic Engineering from a Cybernetic Perspective-I. Theoretical Preliminaries. Biotechnology Progress DOI: 10.1021/bp990017p
Varner J and D. Ramkrishna (1999) Metabolic Engineering from a Cybernetic Perspective-II. Qualitative Investigation of Nodal Architectures and their response to Genetic Perturbation. Biotechnology Progress DOI: 10.1021/bp990018h
Varner J and D. Ramkrishna (1999) Nonlinear Analysis of Cybernetic Models. Guidelines for Model Formulation. Journal of Biotechnology DOI: 10.1016/S0168-1656(99)00016-4
Varner J and D. Ramkrishna (1998) The Application of Cybernetic Models to Metabolic Engineering. Investigation of Storage Pathways. Biotechnology and Bioengineering DOI: 10.1002/(SICI)1097-0290(19980420)58:2/3<282::AID-BIT24>3.0.CO;2-D
Book chapters
M.L. Shuler and J. Varner (2011) Cell Growth Dynamics. Editor: Moo-Young, M., In: Comprehensive Biotechnology, 2nd Edition. Oxford UK: Elsevier DOI:10.1016/B978-0-08-088504-9.00021-0
R. Tasseff and J. Varner (2011) Mathematical Models in Biotechnology Editor: Moo-Young, M., In: Comprehensive Biotechnology, 2nd Edition. Oxford UK: Elsevier DOI:10.1016/B978-0-08-088504-9.00075-1
C. A. Leclerc and J. Varner (2007) Multiscale modeling of metabolic regulation. Editor: Smolke, C.D., In: Handbook for Metabolic Pathway Engineering. San Diego: CRC Press eBook ISBN: 978-1-4398-0297-7
Varner J and M. Fussenegger (2004) A Systems View of Cell Death. Cell Engineering Series Vol. 4, Eds. Mohamed Al-Rubeai, Martin Fussenegger, Biomedical Unit, Kluwer Academic Publishers, The Netherlands ISBN: 978-1-4020-2216-6 (Print) 978-1-4020-2217-3 (Online)