Journal Publications

[33] W. Kelly, S. Veigne, X. Li, S. Subramanian, Z. Huang, E. Schaefer. Optimizing Performance of Semi-Continuous Cell Culture in an Ambr15TM Microbioreactor Using Dynamic Flux Balance Modelling. Biotechnology Progress, in press, 2017
[32] N. Ribaudo, X. Li, B. Davis, T.K. Wood, Z. Huang. A Genome-Scale Modeling Approach to Quantify Biofilm Component Growth of Salmonella Typhimurium. Journal of Food Science, 82(1), 154-166, 2017.
[31] X. Li, Z. Huang. An Inverted Classroom Approach to Educate MATLAB in Chemical Process Control. Education for Chemical Engineers, 19, 1-12, 2017. 
[30] Z. Xu, N. Ribaudo, X. Li, T.K. Wood, Z. Huang. A Genome-Scale Modeling Approach to Investigate the Antibiotics-Triggered Perturbation in the Metabolism of Pseudomonas aeruginosa. IEEE Life Science Letters, 2(3), 39-42, 2016.
[29] X. Li, Y. Liu, Q. Jia, V. LaMacchia, K. O'Donoghue, Z. Huang. A Systems Biology Approach to Investigate the Antimicrobial Activity of Oleuropein. Journal of Industrial Microbiology & Biotechnology, 43(12), 1705-1717, 2016.
[28] X. Li, N. Ribaudo, Z. Huang, A Kinetic Model-Based Approach to Identify Malfunctioned Components in Signal Transduction Pathways from Artificial Clinical Data. BioMed Research International, 415083, 1-19, 2015.
[27] Q. Ping, Z. Huang, C. Dosoretz, Z. He. Integrated Experimental Investigation and Mathematical Modeling of Brackish Water Desalination and Wastewater Treatment in Microbial Desalination Cells. Water Research, 77, 13-23, 2015.
[26] Z. Xu, S. Islam, T.K. Wood, Z. Huang. An Integrated Modeling and Experimental Approach to Study the Influence of Environmental Nutrients on Biofilm Formation of Pseudomonas aeruginosa. BioMed Research International, 506782, 1-12, 2015.
[25] K. Lee, N. Comolli, W.J. Kelly, Z. Huang. MATLAB Based Teaching Modules in Biochemical Engineering. Chemical Engineering Education, 49(2), 95-100, 2015.
[24] Z. Xu, J.O.M. Karlsson, Z. Huang. Modeling the Dynamics of Acute Phase Protein Expression in Human Hepatoma Cells Stimulated by IL-6. Processes, 3(1), 50-70, 2015.  
[23] Q. Ping*, C. Zhang*, X. Chen, B. Zhang, Z. Huang**, and Z. He**. A Mathematic Model of Dynamic Behavior of Microbial Desalination Cells. Environmental Science & Technology, 48, No. 21, pp. 13010–13019, 2014 (*equal contribution; ** joint corresponding authors)
[22] K. Lee, N. Comolli, V. Punzi, W.J. Kelly, Z. Huang. Survey: MATLAB & MathCAD Education in Biochemical Engineering. Chemical Engineering Education, 48(1), 59, 2014
[21] Z. Xu, X. Fang, T.K. Wood, Z. Huang. A Systems-Level Approach for Investigating Pseudomonas aeruginosa Biofilm Formation. PLoS One, 8(2): e57050, 2013.
[20] W. Kelly, G. Kamguia, P. Mullen, A. Ubiera, K. Goklen, Z. Huang, G. Jones. Using a Two Species Competitive Binding Model to Predict Expanded Bed Breakthrough of a Recombinant Protein Expressed in a High Cell Density Fermentation. Biotechnology and Bioprocess Engineering, 18, No. 3, pp. 546-559, 2013.
[19] O. Donaldson, Z. Huang, N. Comolli. An Integrated Experimental and Modeling Approach to Propose Biotinylated PLGA Microparticles as Versatile Targeting Vehicles for Drug Delivery. Progress in Biomaterials, 2:3, 2013.
[18] Z. Huang, Y. Chu, and J. Hahn. Computing Transcription Factor Distribution Profiles from Green Fluorescent Protein Reporter Data. Chemical Engineering Science , 68, No. 1, pp. 340-354, 2012
[17] Y. Chu, Z. Huang, and J. Hahn. Global Sensitivity Analysis Procedure Accounting for Effect of Available Experimental Data . Industrial & Engineering Chemistry Research 50, No. 3, pp. 1294-1304, 2011
[16] C. Moya*, Z. Huang*, P. Cheng, A. Jayaraman, and J. Hahn. Investigation of IL-6 and IL-10 Signaling in Steatosis via Mathematical Modeling. IET Systems Biology, 5, No. 1, pp. 15-26, 2011 (*equal contribution)
[15] Z. Huang*, C. Moya*, J. Hahn, and A. Jayaraman. Using the Tet-On System to Develop a Procedure for Extracting Transcription Factor Activation Dynamics. Molecular Biosystems 6, pp. 1883-1889, 2010 (*equal contribution)
[14] Z. Huang, Y. Chu, B. Cunha, and J. Hahn. Generalization of a Procedure for Computing Transcription Factor Profiles. IET Systems Biology 4, No. 2, pp. 108-118, 2010
[13] R. Kaunas, Z. Huang, and J. Hahn. A Kinematic Model Coupling Stress Fiber Dynamics with JNK Activation in Response to Matrix Stretching. Journal of Theoretical Biology 264, No.2, pp. 593-603, 2010
[12] Z. Huang, Y. Chu, and J. Hahn. Model Simplification Procedure for Signal Transduction Pathway Models: An Application to IL-6 Signaling. Chemical Engineering Science 65, No.6, pp. 1964-1975, 2010
[11] Z. Huang and J. Hahn. Fuzzy Modeling of Signal Transduction Networks. Chemical Engineering Science 64, No. 9, pp. 2044-2056, 2009
[10] Y. Chu, Z. Huang, and J. Hahn. Improving Prediction Capabilities of Complex Dynamic Models via Parameter Selection and Estimation. Chemical Engineering Science 64, No.19, pp. 4178-4185, 2009
[9] Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn. Integrated Modeling and Experimental Approach for Determining Transcription Factor Concentrations from Fluorescent Reporter Profiles. BMC Systems Biology, 2 (64), 2008
[8] J. Brewer, Z. Huang, A.K. Singh, M. Misra, and J. Hahn. Sensor Network Design via Observability Analysis and Principal Component Analysis. Industrial & Engineering Chemistry Research 46, No.24, pp. 8026-8032, 2007
[7] Z. Huang, D. Li, X. Jiang, and L. Sun. Study on Bumpless Switching of Inverted Pendulum Control. Journal of Tsinghua University 44, No.2, pp.266-269, 2004 (in Chinese)
[6] Z. Huang, D. Li, X. Jiang, and L. Sun. Global Control for the Angle of Inverted Pendulum with Gain Scheduled. Electric Machines and Control 8, No.2, pp.130-133, 2004
[5] Z. Huang, D. Li, X. Jiang, and L. Sun. Gain Scheduled Servo System for Boiler-Turbine Unit. Proceedings of the CSEE (Chinese Society of Electrical Engineering) 23, No.10, pp.191-198, 2003
[4] Z. Huang, J. Chen, and D. Li. Simultaneous Identification of System Order and Parameters Based onRational Fraction Equality. Journal of Tsinghua University 43, No.6, pp. 794-797, 2003
[3] Z. Huang, and J. Chen. Identification of Output Error Model Based on Impulse Response. Control Theory and Application 20, No.5, pp.793-796, 2003
[2] Z. Huang, Y. Zhang, and Q. Li. Character of Convective Heat Transfer of Staggered Tube Bundles in the MSW Boiler. Proceedings of the CSEE (Chinese Society of Electrical Engineering) 23, No.4, pp.181-184, 2003
[1] Z. Huang. Characteristics of Fluid Resistance of the Crossing Staggered Tube Bundles of the MSW Boiler. Boiler Technology 34, No.1, pp. 72-75, 2003.

Book Chapter

[2] Z. Huang, Q. Jia and T.K. Wood. Use of Omic Technologies for in Silico Modeling to UnderstandE. coliPhysiology and to Develop Novel therapeutics. Pathogenic E. coli: Evolution, Omics, Detection, and Control, Caister Academic Press/ Horizon Scientific Pres, in press, 2017
[1] Z. Huang and J. Hahn. Algorithms for Analysis of Fluorescence Microscopy Images for Studying Signal Transduction Pathways and Computation of Transcription Factor Profiles. Methods in Bioengineering, Artech House, Boston, Massachusetts, pp.33-56, 2009

Peer-reviewed Conference Papers in Proceedings

[14] Z. Xu, N. Ribaudo, L. Huang, Z. Huang. A Systems Biology Approach to Study the Uncertainty in the Growth Rate of Escherichia coli. Foundations of Systems Biology in Engineering 2015 (FOSBE 2015), Boston, MA, 2015
[13]  Z. Xu, N. Ribaudo, Z. Huang. A Genome-Scale Modeling Approach to Investigate the Antibiotics-Triggered Perturbation in the Metabolism of Pseudomonas aeruginosa. Foundations of Systems Biology in Engineering 2015 (FOSBE 2015), Boston, MA, 2015
[12] J.J. Elmer, N.K. Comolli, W.J. Kelly, Z. Huang. “Preparation of Biology Review and Virtual Experiment/Training Videos to Enhance Learning in Biochemical Engineering Courses,” 2015 ASEE Annual Conference and Exposition, Seattle, Washington, June 2015.
[11] Z. Xu and Z. Huang.Drug Target Screening for Acute Phase Response from Kinetic Models. 54th Annual Conference of the Society of Instrument and Control Engineers of Japan (SICE), Hangzhou, China, 2015.
[10] X. Li and Z. Huang. Development of a Model-Based Inference Approach to Detect Malfunctioned Components in Biological Systems from Clinical Data. 54th Annual Conference of the Society of Instrument and Control Engineers of Japan (SICE), Hangzhou, China, 2015.
[9] C. Ekaputra, and Z. Huang. Educating High School Students in Process Simulation and Control with a Simulink-Based Controller Design for Microbial Fuel Cells. ASEE-SE 2015, University of Florida, Gainesville, FL, 2015.
[8] Z. Xu, X. Fang, T.K. Wood, Z. Huang. Modeling Framework for investigating the Influence of Amino Acids on the Planktonic-Biofilm Transition of Pseudomonas aeruginosa. The International Federation of Automatic Control (IFAC) World Congress 2014, Cape Town, South Africa, 2014.
[7] Z. Xu, X. Fang, T.K. Wood, Z. Huang. Gene target identification for biofilm-associated pathogens: an application to Pseudomonas aeruginosa . Proceedings of the 2013 American Control Conference, Washington, DC, pp. 3765 - 3770
[6] Z. Huang, Y. Chu, and J. Hahn. Derivation of Simplified Signal Transduction Pathway Models: Application to IL-6 Signaling. Proceedings of the 2010 American Control Conference, Baltimore, Maryland, pp. 5131-5136 (Invited Presentation)
[5] Z. Huang, C. Moya, P. Cheng, A. Jayaraman, and J. Hahn. In Silico Investigation of IL-6 and IL-10 Signaling in Steatosis. Proceedings Foundations of Systems Biology in Engineering 2009 (FOSBE 2009), Denver, Colorado, pp. 28-31
[4] Z. Huang, Y. Chu, and J. Hahn. Derivation of a Reduced IL-6 Signal Transduction Model. Proceedings Foundations of Systems Biology in Engineering 2009 (FOSBE 2009), Denver, Colorado, pp. 32-35
[3] Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn. Solution of Inverse Problems for Obtaining Protein Concentrations from Fluorescent Microscopy Images. Proceedings of the 2009 American Control Conference (ACC 2009), St. Louis, Missouri, pp. 1688-1693
[2] Z. Huang and J. Hahn, Fuzzy Modeling of Signal Transduction Networks. Proceedings of the 2008 IFAC World Congress, Seoul, Korea, pp. 15867-15872 (Invited Presentation)
[1] Z. Huang, Y. Chu, F. Senocak, A. Jayaraman, and J. Hahn, Model Update of Signal Transduction Pathways in Hepatocytes based upon Sensitivity Analysis. Proceedings Foundations of Systems Biology 2007 (FOSBE 2007), Stuttgart, Germany, pp. 45-50 (Plenary Presentation)

Conference Presentations excluding the ones with proceedings

[22] X. Li, Z. Huang. “Educate Matlab in Chemical Process Control Using Flipped-Classroom Modules,” AIChE 2016 Annual Meeting, San Francisco, CA.
[21] X. Li, Y. Liu, Q. Jia, V. LaMacchia, K. O'Donoghue, Z. Huang. “A Systems-Biology Approach to Investigate the Antimicrobial Activity of Oleuropein,” AIChE 2016 Annual Meeting, San Francisco, CA.
[20] X. Li and Z. Huang. “Educate MATLAB in Chemical Process Control Using an Inverted-Classroom Approach,” STEM Education section, 2016 International Education Conference, Orlando, FL, 2016
[19]  Z. Xu, N. Ribaudo, Z. Huang. Investigation of the Antibiotics-Triggered Perturbation in the Metabolism of Pseudomonas aeruginosa via a Metabolic Modeling Approach. American Institute of Chemical Engineering Annual Meeting, Salt Lake City, UT, Nov 2015
[18] X. Li, N. Ribaudo, Z. Huang. A Kinetic Model-Based Approach to Identify Malfunctioned Components in Signal Transduction Pathways from Data. American Institute of Chemical Engineering Annual Meeting,  Salt Lake City, UT, Nov 2015
[17] Q. Ping, C. Zhang, X. Chen, B. Zhang, Z. Huang, and Z. He. Development of a Mathematical Model for Microbial Desalination Cells. American Institute of Chemical Engineering Annual Meeting, Atlanta, GA, Nov 2014 
[16] K. Lee, Z. Huang. A Systems Biology Approach to Quantify the Metabolism of Escherichia Coli for Generating 3-Hydroxypropionic Acid From Glycerol. American Institute of Chemical Engineering Annual Meeting, San Francisco, CA, Nov 2013
[15] Z. Xu, X. Fang, T.K. Wood, and Z. Huang. A Systems Biology Approach for Investigation of the Influence of Environmental Nutrients On the Biofilm Formation of P. Aeruginosa. American Institute of Chemical Engineering Annual Meeting, San Francisco, CA, Nov 2013
[14] C. Zhang, N. Giraldo-Wingler, Z. Xu, and Z. Huang. Modeling the Dynamics of Acute Phase Proteins During the Heat Shock Response. American Institute of Chemical Engineering Annual Meeting, San Francisco, CA, Nov 2013
[13] Z. Xu, X. Fang, T.K. Wood, and Z. Huang. A systems biology approach to investigate environmental infl uence on Pseudomonas aeruginosa biofilm formation. 2nd International Conference and Exhibition on Metabolomics & Systems Biology, Chicago, IL, April 2013.
[12] Z. Xu, F. Xin, T.K. Wood, and Z. Huang. A Systems-level Analysis Approach for Identifying Genetic Targets to Treat Biofilm-forming Pathogens: an Application to Pseudomonas aeruginosa. AIChE 2012 Annual Meeting, Pittsburgher, PA
[11] J.O.M. Karlsson, Z. Xu, A. Plakkat, H. Li, and Z. Huang. Modeling Dynamics of Acute Phase Protein Expression in HepG2 Cells Stimulated by IL-6. AIChE 2012 Annual Meeting, Pittsburgher, PA
[10] R. Kaunas, Z. Huang, and J. Hahn. Derivation of a Kinematic Model Coupling Stress Fiber Dynamics with JNK Activation In Response to Matrix Stretching. AIChE 2011 Annual Meeting, Minneapolis, MN
[9] Z. Huang, Y. Chu, L. Bansal, and J. Hahn, Derivation of Transcription Factor Distribution Profiles From Green Fluorescent Protein Reporter Data. AIChE 2010 Annual Meeting, Salt Lake City, Utah (Invited Presentation)
[8] Y. Chu, Z. Huang, M. Serpas, and J. Hahn, Global Sensitivity Analysis Procedure Accounting for Effect of Available Experimental Data. AIChE 2010 Annual Meeting, Salt Lake City, Utah
[7] C. Moya, Z. Huang, J. Hahn, and A. Jayaraman. Quantitative Determination of Transcription Factor Profiles From Reporter Data. AIChE 2010 Annual Meeting, Salt Lake City, Utah
[6] Z. Huang, C. Moya, P. Cheng, A. Jayaraman, and J. Hahn. Mathematical Modeling of IL-6 and IL-10 Signal Transduction in Steatosis. AIChE 2009 Annual Meeting, Nashville, Tennessee
[5] Z. Huang, Y. Chu, and J. Hahn. Derivation of Reduced Models for Signal Transduction Pathways Via Sensitivity and Observability Analysis. AIChE 2009 Annual Meeting, Nashville, Tennessee
[4] Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn,Quantitative Measurement Technique for Transcription Factor Profiles. AIChE 2008 Annual Meeting, Philadelphia, Pennsylvania
[3] Y. Chu, Z. Huang, and J. Hahn. Analysis Procedure for Signal Transduction Pathways by Clustering Parameters According to their Sensitivity Profiles. AIChE 2008 Annual Meeting, Philadelphia, Pennsylvania
[2] Y. Chu, Z. Huang, and J. Hahn. Sensitivity Analysis for Parameter Estimation of Signal Transduction Networks. SIAM Conference on the Life Sciences, Montreal, Canada (Invited Presentation)
[1] Z. Huang and J. Hahn. Development and Comparison of Algorithms for Analysis of Fluorescent Images for Studying the Dynamics of Signal Transduction Pathways. AIChE 2007 Annual Meeting, Salt Lake City, Utah