Zuyi (Jacky) Huang, Chemical Engineering, Texas A&M University

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EDUCATION

Expected August 2010, Pursuing Ph.D.

Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA

Research interests: Mathemetical modeling and dynamics analysis for complex chemical reaction networks, with a a special emphasis on signal transduction pathways in the field of Systems Biology.

08/2005 ~ 05/2006, Pursuing Ph.D.
- Department of Electrical Engineering, Texas A&M University, College Station, Texas, USA.
- Research interests: Continuous wave laser photo-acoustic microscopy to detect cancers under the skin.
07/2004, M. S.
- Department of Thermal Engineering, School of Mechanical Engineering, Tsinghua University, Beijing, China.
- Master Thesis: Gain Scheduling and its Application on Tuning of Controller Parameters in Thermal System
07/2001, B. E.
- Department of Thermal Engineering, School of Mechanical Engineering, Tsinghua University, Beijing, China.

HONORS & SCHOLARSHIPS

Deisler fellowship (awarded to the two most outstanding Ph.D. students in Chemical Engineering), 2009
Graduate Travel Grant Award, Computing and Systems Technology Division (CAST), AIChE, 2008.
Excellent Master Degree Thesis, Tsinghua University, 2004.
Excellent Master Graduate, Tsinghua University, 2004.
“Dec. 9th” Outstanding Graduate-student Scholarship, Tsinghua University, 2002 ~ 2003.
First-prize Winner in the 21st “Challenge Cup” Students’ Scientific and Technological Contest at Tsinghua University, 2002 ~ 2003.
First-prize Scholarship for Scientific and Technical Competition, Tsinghua University , 2002 ~ 2003.
Dongs Orient Outstanding Graduate-student Scholarship of Tsinghua University, 2001 ~ 2002.
Jiang Nanxiang Outstanding Undergraduate Scholarship, Tsinghua University, 1999 ~ 2000.
Third-prize winner in the 18th “Challenge Cup” Students’ Scientific and Technological Contest at Tsinghua University, 1999 ~ 2000.
Third-prize Scholarship for Scientific and Technical Competition, Tsinghua University , 1999 ~ 2000.
Scholarship for Excellent Idea in the 18th “Challenge Cup” Students’ Scientific and Technological Contest, Thermal Engineering, Tsinghua University, 1999 ~ 2000.
Special Financial Assistance for outstanding undergraduate, Department of Thermal Engineering, Tsinghua University, 1998 ~ 1999.

RESEARCH EXPERIENCE

Graduate Research Assistant, Advisor: Juergen Hahn May 2006 ~ Present
Department of Chemical Engineering, Texas A&M University, College Station, Texas
- Dissertation Research (5 projects)
  - Mathematical modeling of complex chemical reaction networks
    - Derived ordinary differential equations (ODEs) for complex signal transduction pathways that included hundreds of components and parameters
    - Investigated mathematical models using Sensitivity Analysis, and performed parameter estimation with Nonlinear Least Squares Optimization techniques
    - Facilitated experiment design
  - Solution of inverse problems
    - Derived input profiles from limited and noisy output profiles
    - Inferred stochastic properties of the input from the distribution information of the output
  - Statistical multivariate data analysis
    - Performed image analysis to identify objects from images via Principal Component Analysis and Clustering
    - Reduced noise in images via Wavelet and Mathematical Morphology
    - Developed population balance model for the identified objects
  - Fuzzy modeling of signal transduction pathway
    - Used Fuzzy modeling to integrate the qualitative information into linguistic models so that fewer quantitative data are required for modeling
  - Model reduction for nonlinear models of signal transduction pathway
    - Performed Sensitivity Analysis and Observability Analysis to determine the structure of reduced models
- Sensor network design for chemical process systems
  - Determined sensor network structure to obtain the most information with the fewest number of sensors
Graduate Research Assistant Sep 2001 ~ Jul 2004
Institute of Control & Simulation for Thermal systems, Tsinghua University, Beijing, China
- Thesis Research (3 projects)
  - Gain scheduling control and its application to nonlinear systems
  - Investigated DCS control system for circulating fluidized-bed boiler
  - Simultaneous identification of system order and parameters from time series data

Please refer to Section Research for more details about my work.

TEACHING EXPERIENCE

Assisted with Process Dynamics and Control for about 80 students (2008 Fall and 2009 Spring)
Supervised and trained 4 undergraduate students (including one REU student) in their research (2007 ~ Present)

PUBLICATIONS

Book Chapters
- 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 (Series Editors: Martin L. Yarmush and Robert S. Langer ), Artech House, Boston, Massachusetts, pp. 33-56 (2009)
Journal Publications
- Z. Huang, Y. Chu and J. Hahn, “Deriving the Concentration Distribution of Transcription Factors by Identifying Individual Cells from Fluorescent Miscroscopy Images,” submitted to Automatica (2010)
- Z. Huang*, C. Moya*, J. Hahn, and A. Jayaraman, “Modeling of Artificial Transcription Factor Dynamics by Solving an Inverse Problem,” submitted to Molecular Biosystems (2010). (*equal contribution)
- C. Moya*, Z. Huang*, P. Cheng, A. Jayaraman, and J. Hahn, “Investigation of IL-6 and IL-10 Signaling in Steatosis Via Mathematical Modeling,” submitted to IET Systems Biology (2009). (*equal contribution)
- 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, in Revision (2009)
- Z. Huang, Y. Chu, and J. Hahn, “Model Simplification Procedure for Signal Transduction Pathway Models: An Application to IL-6 Signaling,” Chemical Engineering Science, in Press (2009).
- Z. Huang, Y. Chu, B. Cunha., and J. Hahn, “Generalization of a Procedure for Computing Transcription Factor Profiles,” IET Systems Biology, 2009, In Press.
- 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, 4178-4185 (2009)
- Z. Huang, and J. Hahn, “Fuzzy Modeling of Signal Transduction Networks”, Chemical Engineering Science, 64(9), 2044-2056, 2009.
- 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, 2008, 2 (64) (Highly Accessed).
- J. Brewer,Z. Huang,A.K. Singh, M. Misra, and J. Hahn, “Sensor Network Design via Observability Analysis and Principal Component Analysis,” Ind. Eng. Chem. Res., 2007, 46 (24), 8026 -8032.
Earlier Journal Publications (In China)
- Z. Huang, D. Li, X. Jiang and L. Sun, “Study on Bumpless Switching of Inverted Pendulum Control,” Journal of Tsinghua University, 2004, 44(2), 266-269. (In Chinese)
- Z. Huang, D. Li, X. Jiang and L. Sun, “Global Control for the Angle of Inverted Pendulum with Gain Scheduled,” Electric Machines and Control, 2004, 8(2), 130-133. (In Chinese)
- 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), 2003, 23(10), 191-198. (In English, cited by 21)
- Z. Huang, J. Chen and D. Li, “Simultaneous Identification of System Order and Parameters Based on Rational Fraction Equality,” Journal of Tsinghua University, 2003, 43(6), 794-797. (In Chinese)
- Z. Huang, and J. Chen, “Identification of Output Error Model Based on Impulse Response,” Control Theory and Application, 2003, 20(5), 793-796. (In Chinese)
- 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), 2003, 23(4), 181-184. (In Chinese)
- Z. Huang, “Characteristics of Fluid Resistance of the Crossing Staggered Tube Bundles of the MSW Boiler,” Boiler Technology, 2003, 34(1), 72-75. (In Chinese)
Peer-reviewed Conference Papers in Proceedings
- Z. Huang, Y. Chu, and J. Hahn. “Model Simplification Procedure for Signal Transduction Pathway Models: An Application to IL-6 Signaling”, accepted in 2010 American Control Conference
- 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 2009, Denver, Colorado,28-31.
- Z. Huang, Y. Chu, and J. Hahn, “Derivation of a Reduced IL-6 Signal Transduction Model,” Proceedings Foundations of Systems Biology 2009, Denver, Colorado,32-35.
- Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn, “Solution of Inverse Problem for Obtaining Protein Concentrations from Fluorescent Microscopy,” 2009 American Control Conference, St. Louis, Missouri, 2009, 1688-1693.
- Z. Huang, and J. Hahn, “Fuzzy Modeling of Signal Transduction Networks,” Proceedings of the 2008 IFAC World Congress, Seoul, Korea, 2008, 15867-15872 (Invited Presentation).
- 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, Stuttgart, Germany, 45-50 (Plenary Presentation).
Conference Presentations: (excluding the ones with proceedings)
- Z. Huang, C. Moya, P. Cheng, A. Jayaraman, and J. Hahn. Mathematical Modeling for IL6 and IL10 Signal Transduction in Steatosis. AIChE 2009 Annual Meeting, Nashville, Tennessee (2009)
- 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 (2009)
- R. Kaunas, Z. Huang, and J. Hahn. A Kinematic Model Coupling Stress Fiber Dynamics with JNK Activation in Response to Matrix Stretching. 2009 Summer Bioengineering Conference, Lake Tahoe, California (2009)
- Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn,“Quantitative Measurement Technique for Transcription Factor Profiles,” AIChE 2008, Philadelphia, Pennsylvania.
- Y. Chu, Z. Huang, and J. Hahn, “Analysis Procedure for Signal Transduction Pathways by Clustering Parameters According to Their Sensitivity Profiles,” AIChE 2008, Philadelphia, Pennsylvania.
- Y. Chu, Z. Huang, and J. Hahn, “Sensitivity Analysis for Parameter Estimation of Signal Transduction Networks,” SIAM Conference on the Life Sciences 2008, Montreal, Canada (Invited Presentation).
- 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, Salt Lake City, Utah.