1. Chakrabarti A, Chen AW and J. Varner (2011) A Review of the Mammalian Unfolded Protein Response. Biotechnol. Bioeng., in-press.
2. 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, in-press. 
3. Nayak S, Siddiqui J and J. Varner (2011) Modeling and Analysis of an Ensemble of Eukaryotic Translation Initiation Models. IET Syst. Biol. 5:2-14.
4. 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 9:1-8
5. 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 & Lymphoma, 51:1734 - 1747
6. 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. Mol. BioSys. 6:2272 - 2286
7. Song S, Chakrabarti A, and J. Varner (2010) Identifying ensembles of signal transduction models using
   Pareto Optimal Ensemble Techniques (POETs). Biotechnol. J. 5:757 - 769
8. 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 5:e8864.
9. 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. Thromb. Res., 125:432 - 437
10. Song S, Varner J (2009) Modeling and Analysis of the Molecular Basis of Pain in Sensory Neurons. PLoS ONE 4: e6758 - e6772.
11. Kim JI, Varner J, and Ramkrishna D. (2008) A hybrid model of anaerobic E.coli GJT001: Combination of elementary flux modes and cybernetic variables. Biotechnol. Prog., 24:993-1006.
12. Conrado RJ, Varner J, and DeLisa MP (2008) Macromolecular compartmentation and multienzyme organization in natural and synthetic metabolic pathways. Curr. Opin. Biotechnol., 19:492-499 
13. Nayak S, Saniya S, Luan D, Zai M, and Varner J. (2008)  A test of highly optimized tolerance reveals fragile cell-cycle mechanisms are molecular targets in clinical cancer trials. PLoS ONE, 3:e2016.
14. Luan D, Zai M, and Varner J. (2007) Computationally Derived Points of Fragility of a Human Cascade are Consistent with Current Therapeutic Strategies. PLoS Comp. Biol., 3: 1347 - 1359.
15. Conrado RJ, Mansell TJ, Varner JD, and DeLisa MP. (2007) Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for an engineered bacterial propanediol pathway. Metab. Eng., 9: 355-363.
16. Srivastava R, and Varner J,  (2007) Emerging Technologies: Systems Biology. Biotechnol. Prog., 23: 24-27.
17. Varner J, (2005) Systems Biology and the Mathematical Modeling of Antibody Directed Enzyme Prodrug Therapy (ADEPT). IEE Systems Biology, 152:291-302.
18. Gadkar KG, Varner J, and Doyle FJ III. (2005) Model Identification of Signal Transduction Networks from Data Using a State Regulator Problem. IEE Systems Biology, 2:17-30.
19. Gupta A, Varner JD, and Maranas CD. (2005)  Large-scale Inference of the Transcriptional Regulation of Bacillus subtilis. Comp. Chem. Eng., 29:565-576.
20. Dasika MS, Gupta A, Maranas CD, and Varner J. (2004) A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. Pac. Symp. Biocomput, 474-485.
21. Lee L-Q, Varner J, and Ko K. (2004) Parallel Extreme Pathway Computation for Metabolic Networks. Proceedings IEEE Computational Systems Bioinformatics, 2:636-639.
22. Gadkar KG, Doyle FJ III, Crowley TJ, and Varner JD. (2003) Cybernetic Model Predictive Control of a Continuous Bioreactor with Cell Recycle. Biotechnol. Prog., 19:1487-1497.
23. Fussenegger M, Bailey JE, and Varner J. (2000) A Mathematical Model of Caspase Function in Apoptosis. Nat. Biotechnol., 18:768-74.
24. Varner J. (2000) Toward the Large-Scale Prediction of Phenotype: Concept. Biotechnol. Bioeng. 69:664-78.
25. Varner J. and Ramkrishna D. (1999) Mathematical Models of Metabolic Pathways. Curr. Opin. Biotechnol., 10:146-150.
26. Varner J, and Ramkrishna D. (1999) Metabolic Engineering from a Cybernetic Perspective-I. Theoretical Preliminaries. Biotechnol. Prog., 15:407-425.
27. Varner, J, and Ramkrishna D. (1999) Metabolic Engineering from a Cybernetic Perspective-II. Qualitative Investigation of Nodal Architectures and their response to Genetic Perturbation. Biotechnol. Prog., 15:426-438.
28. Varner J, and Ramkrishna D. (1999) Metabolic Engineering from a Cybernetic Perspective. Aspartate Family of Amino Acids. Metabol. Eng., 1:88-116.
29. Varner J, and Ramkrishna D. (1999) Nonlinear Analysis of Cybernetic Models. Guidelines for Model Formulation. J. Biotechnol., 71:67-103.
30. Varner J, and Ramkrishna D. (1998) The Application of Cybernetic Models to Metabolic Engineering. Investigation of Storage Pathways. Biotechnol. Bioeng., 58:112-121.

Book chapters

1. Varner J, and Fussenegger M, (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.
2. Varner J,  (2007) Multi-scale modeling of metabolic regulation. Smolke, C.D., editor. In: Handbook for Metabolic Pathway Engineering. San Diego: CRC Press.