1. Moya, C., Huang, Z., Cheng, P., Jayaraman, A# and Hahn, J#. Investigation of IL-6 and IL-10 Signaling via Mathematical Modeling. IET Systems Biology. Accepted (2010). #: Joint corresponding authors
  2. Huang, Z., Moya, C., Jayaraman, A# and Hahn, J#. Using the Tet-On system to develop a procedure for extracting transcription factor activation dynamics. Molecular BioSystems. Accepted doi:10.1039/C003229H (2010). #: Joint corresponding authors
  3. Kim, J., Hegde, M. and Jayaraman, A. Microfluidic co-culture of epithelial cells and bacteria for investigating soluble signal-mediated interactions. Journal of Visualized Experiments, 38: pii: 1749.doi: 10.3791/1749 (2010).
  4. Englert, D. L., Manson, M. D. and Jayaraman, A. A microfluidic device for quantifying bacterial chemotaxis in stable concentration gradients. Journal of Visualized Experiments, 38: pii: 1779. doi: 10.3791/1779 (2010).
  5. Englert, D. L*., Manson, M. D. and Jayaraman, A. “A Microfluidic (µFlow) method for quantifying bacterial chemotaxis”. Nature Protocols. 5: 864-72 (2010).
  6. Englert, D. L*, Adase, C, Jayaraman, A. and Manson, M. D. “Repellent Taxis to Nickel Ion Requires Neither Ni2+ Transport nor the PeriplasmicNikA Binding Protein”. Journal of Bacteriology. 192: 2633-7 (2010).
  7. Bansal, T*., Alaniz, R., Wood, T. K. and Jayaraman, A. “The bacterial signal indole increasestransepithelial resistance and attenuates epithelial cell inflammation”. Proceedings of the National Academy of Sciences. 107: 228-33 (2010).
  8. Kim, J*., Hegde, M*. and Jayaraman, A. “Co-culture of bacteria and epithelial cells for investigating signal-mediated interactions in the GI tract”. Lab Chip 10: 43-50 (2010). Featured article



  1. Huang, J. H., Kim, J., Agrawal, N., Sudarsan, A., Maxim, J., Jayaraman, A#. and Ugaz, V#. “Rapid fabrication of branched 3-D microvascular networks using electric discharge”. Advanced Materials 21: 1-5 (2009). #: Joint corresponding authors
  2. Hegde, M., Wood, T. K. and Jayaraman, A. “The neuroendocrine hormone norepinephrine increasesPseudomonas aeruginosa PA14 virulence through the las quorum sensing pathway”. Applied Microbiology and Biotechnology. 84: 763-6 (2009).
  3. Newton, B., Russell, W. K., Russell, D. H., Ramaiah, S. K. and Jayaraman, A. “Liver proteome analysis in a rodent model of alcoholic steatosis”. Journal of Proteome Research. 8: 1663-71 (2009).
  4. Englert, D. L*., Jayaraman, A. and Manson, M. D. “Microfluidic techniques for the analysis of bacterial chemotaxis”. Methods in Molecular Biology. 571: 1-23 (2009).
  5. Wang, S., Chen, P. C., Berthiaume, F., Toner, M., Jayaraman, A. and Yarmush, M. L. “Dynamic effect of heat shock pre-treatment on apoptotic responses to TNF-α in liver cells”.Journal of Biomechanical Engineering. 131: 071003(2009).
  6. Englert, D. L., Manson, M. D. and Jayaraman, A. “Using a microfluidic device to investigate interactions between signaling molecules on Escherichia coli chemotaxis”. Applied and Environmental Microbiology. 75: 4557-64 (2009).
  7. Englert, D. L*.,Janakiraman, V., Jayaraman, A#. and Baskaran, H#. “Modeling growth and quorum sensing in biofilms grown in microfluidic chambers”. Annals of Biomedical Engineering. 37: 1206-16 (2009). #: Joint corresponding authors



  1. Huang, Z., Senocak, F*., Jayaraman, A#. and Hahn, J#. “Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data”. BMC Systems Biology. 2: 64 (2008). #: Joint corresponding authors. “Highly accessed
  2. Lai, N., Jayaraman, A. Lee, K. “Vascular endothelial cell growth factor receptor-2 mediates synergistic proliferation and differentiation of adipocytes and endothelial cells in co-culture”. Tissue Engineering.Epub ahead of print. (2008).
  3. Jayaraman, A. and Wood, T. K. “Bacterial quorum sensing: Signals, circuits, and implications for biofilms and disease”. Annual Reviews of Biomedical Engineering. 10: 145-167 (2008). “Top 10 downloaded articles”
  4. Banerjee, A., Jayaraman, A., Russell, W. K. and Ramaiah, S. K. “Identification of proteins to predict the molecular basis for observed gender susceptibility in a rat model of alcoholic steatohepatitis by 2-D gel proteomics”. Proteomics. 8: 4327-37 (2008).
  5. Lee, J., Zhang, X. S., Hegde, M*., Bentley, W. E., Jayaraman, A. and Wood, T. K. “Indole cell signaling occurs primarily at low temperatures in Escherichia coli”. ISME Journal. 2: 1007-23 (2008).
  6. Jayaraman, A., Maguire, T, Vemula, M., Kwon, D. W., Vannucci, M., Berthiaume, F. and Yarmush, M. L. “Gene expression profiling of long-term changes in rat liver following burn injury”. Journal of Surgical Research. Epub ahead of press, Aug 28, 2008.
  7. Bansal, T*., Jesudhasan, P., Pillai, S, Wood, T. K. and Jayaraman, A. “Temporal regulation ofenterohemorrhagicEscherichia coli virulence mediated by autoinducer-2”. Applied Microbiology & Biotechnology. 78: 811-9 (2008).
  8. Soni, K., Jesudhasan, P., Cepeda, M., Williams, B., Hume, M., Russell, W. K., Jayaraman, A. and Pillai, S. D. “Autoinducer-2 is involved in regulating a variety of cellular processes in Salmonellatyphimurium.” Foodborne Pathogens and Disease. 5: 147-53 (2008).
  9. King, K. R., Wang, S., Jayaraman, A., Yarmush, M. L. and Toner, M. “Microfluidic flow-encoded switching for parallel control of dynamic cellular microenvironments”. Lab Chip 8: 107-16 (2008).



  1. Bansal, T., Englert, D., Lee, J., Hegde, M., Wood, T. K. and Jayaraman, A. “Differential effects of epinephrine, norepinephrine, and indole on Escherichia coli O157:H7 chemotaxis, colonization, and gene expression”. Infection & Immunity. 75: 4597-607 (2007).
  2. Senocak, F., Si, Y., Lee, K. and Jayaraman, A. “Effect of forced uncoupling protein-1 expression on 3T3-L1 adipocyte gene expression”. FEBS Letters 581: 5865-71 (2007). “Cover article”
  3. Si, Y., Palani, S., Jayaraman, A. and Lee, K. “Effects of forced uncoupling protein 1 expression in 3T3-L1 cells on mitochondrial function and lipid metabolism”. Journal of Lipid Research 48: 826-36 (2007).
  4. Lee, J., Bansal, T., Jayaraman, A., Bentley, W. E. and Wood, T. K. “Enterhemorrhagic Escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin”. Applied and Environmental Microbiology 73: 4100-9 (2007).
  5. Lee, J., Jayaraman, A. and Wood, T. K. “Indole is an inter-species signal mediated by SdiA”. BMC Microbiology 7: 42 (2007).
  6. Singh, A., Jayaraman, A. and Hahn, J. “A case study of representing signal transduction in liver cells as a feedback control problem”. Chemical Engineering Education. 41: 177-182 (2007).
  7. Y. Chu, A. Singh, A. Jayaraman, and J. Hahn, 2007. Parameter Sensitivity Analysis of IL-6 Signaling Pathways IEEE Trans Sys Biol. 1: 342-52 (2007).
  8. King, K. R., Wang, S., Jayaraman, A., Toner, M. and Yarmush, M. L. “A High-throughput Microfluidic Real-time Gene Expression Living Cell Array”. Lab-on-Chip 7: 77-85 (2007).
  9. Soni, K., Jesudhasan, P., Cepeda, M., Williams, B., Hume, M., Russell, W. K., Jayaraman, A. and Pillai, S. D. “Proteomic analysis to identify the role of LuxS/AI-2 mediated protein expression inEscherichia coli O157:H7”. Foodborne Pathogens and Disease. 4: 463-71 (2007).
  10. Banta, S., Vemula, M., Yokoyoma, T., Jayaraman, A., Berthiaume, F. and Yarmush, M. L. “Contribution of gene expression to metabolic fluxes in hypermetabolic livers induced through burn injury and polymicrobial sepsis in rats”. Biotechnology & Bioengineering 97: 118-37. (2007).



  1. Singh, A, Jayaraman, A., and Hahn, J. “Modeling regulatory mechanisms in IL-6 signal transduction in hepatocytes”. Biotechnology & Bioengineering. 95: 850-62 (2006).



  1. Wieder, K. J., King, K. R., Thompson, D. M., Toner, M., Yarmush, M. L. and Jayaraman, A. “Optimization of reporter cells for expression profiling in a microfluidic device”. BiomedicalMicrodevices. 7: 213-22 (2005).
  2. Jayaraman, A., Roberts, K. A., Yoon, J., Yarmush, D. M., Duan, X., Lee, K. and Yarmush, M. L. ”Identification of neutrophilgelatinase-associated lipocalin (NGAL) as a discriminant marker of thehepatocyte secreted protein response to IL-1β: a proteomic analysis,” Biotechnology Bioengineering.91: 502-15 (2005).
  3. Duan, X, Yarmush, D. M, Berthiaume, F, Jayaraman, A., and Yarmush, M. L. “Evaluation ofimmunoprecipitation-based depletion of albumin for two-dimensional gel separation of normal and inflamed mouse plasma”. Proteomics. 5: 3391-4000 (2005).
  4. Jayaraman, A, Roth, C.M. and Yarmush, M.L. “Comprehensive evaluation of an in vitro model of hepatic inflammatory response by gene expression profiling”. Tissue Engineering. 11: 50-63. (2005).


2000 – 2004

  1. Vemula, M., Berthiaume, F., Jayaraman, A., and Yarmush, M. L. “Expression profiling analysis of the metabolic and inflammatory changes following burn injury in rats”. Physiological Genomics. 18: 87-98. (2004).
  2. Thompson, D., Toner, M., Yarmush, M. L. and Jayaraman, A. “Dynamic gene expression profiling using a living cell array”. Analytical Chemistry.76: 4098-4103. (2004).
  3. Duan, X, Berthiaume, F, Yarmush, D. M, Jayaraman, A., and Yarmush, M. L. “A mouse serum two-dimensional gel map: Application to profiling burn injury and infection”. Electrophoresis. 25: 3055-3065. (2004).
  4. Duan, X., Yarmush, M. L., Jayaraman, A. and Yarmush M. L. “Dispensable role for interferon gamma in the acute phase response: A proteomics analysis”.  Proteomics. 4: 1830-1839. (2004).
  5. Yarmush, M. L. and Jayaraman, A. “Advances in Proteomics Technologies”. Annual Reviews of Biomedical Engineering. 4: 349-373. (2002).
  6. Jayaraman, A., Yarmush, M. L. and Roth, C. M. “Molecular Bioengineering”. Industrial & Engineering Chemistry Research. 44:441-455. (2002).
  7. Jayaraman, A., Walton, S. P. and Roth, C. M. “Rational selection and quantitative evaluation of antisense oligonucleotides”. Biochimica Biophysica Acta.1520: 105-114 (2001).
  8. Jayaraman, A., Yarmush, M. L. and Roth, C. M. “Dynamics of gene expression in rat hepatocytes under stress”. Metabolic Engineering. 2: 239-251. (2000).


1992 – 1998

  1. Jayaraman, A., Duarte, D. D. and Wood, T. K.  “Inhibition of anaerobic corrosion of copper and aluminum by protective bacterial biofilms”. Applied Microbiology & Biotechnology. 52: 787-790. (1999).
  2. Jayaraman, A., Carson, R. M., Hallock, P. J, and Wood, T. K. “Inhibiting anaerobic corrosion of steel by excluding sulfate-reducing bacteria with in situ generated antimicrobials”. Applied Microbiology & Biotechnology. 52: 267-275. (1999).
  3. Ismail, K. M., Jayaraman, A., Wood, T. K. and Earthman, J. C. “The Influence of Bacteria on the Passive Film Stability of 304 Stainless Steel”. Electrochimica Acta. 44: 4685-4692. (1999).
  4. Jayaraman, A., Duarte, D. D, Lee, C-C., Chen, M. W, Mansfeld, F, and Wood, T. K.  “Cloning the antimicrobial peptides indolicidin and bactenecin to inhibit sulfate-reducing bacteria on stainless steel”.Journal of Industrial Microbiology & Biotechnology. 22: 167-175. (1999).
  5. Jayaraman, A., Sun, A. K., Earthman, J. C. and Wood, T. K.  “Characterization of axenic P. fragi andE. coli biofilms that inhibit corrosion of SAE 1018 steel”.  Journal of Applied Microbiology. 84: 485 – 492. (1998).
  6. Jayaraman, A., Earthman, J. C. and Wood, T. K.  “Corrosion inhibition of SAE 1018 steel by aerobic biofilms”. Applied Microbiology and Biotechnology. 47: 62-68. (1997).
  7. Jayaraman, A., Cheng, E T., Earthman, J. C. and Wood, T. K.  “Importance of biofilm formation for corrosion inhibition of SAE 1018 steel by axenic aerobic biofilms” Journal of Industrial Microbiology and Biotechnology. 18: 396-401. (1997).
  8. Jayaraman, A., Cheng, E T., Earthman, J. C. and Wood, T. K.  “Axenic aerobic biofilms inhibit corrosion of SAE 1018 steel through oxygen depletion”.  Applied Microbiology and Biotechnology.  48: 11-17. (1997).
  9. Jayaraman, A., DeBernardez, E. and Goldberg, E. B. “Thermal unfolding of bacteriophage T4 short tail fibers”.  Biotechnology Progress. 13: 837 – 843. (1997).
  10. Kumar, R. A., Jayaraman, A., Lakshmanan, M. and Gunasekaran, P. G. “Bioconversion of gallic acid into pyrogallol by immobilized Citrobacter freundii TB3”. Journal of Fermentation and Bioengineering74:159-162 (1992).