Peer-Reviewed Journal Articles

(Dr. He’s students are indicated by *, correspondence authors are indicated by #.)


1. Cheng, F., He, Q. P.#, & Zhao, J. # (2019). A novel process monitoring approach based on variational recurrent autoencoder. Computers & Chemical Engineering, 129, 106515.

2. Shah D.*, Wang J. & He Q.P.# (2019), A feature-based soft sensor for spectroscopic data analysis, Journal of Process Control, 78, 98-107.

3. Angajala A., Mothershed E., Davis M.B., Tripathi S., He Q.P., Bedi D., Dean-Colomb W., Yates C.# (2019). Quadruple Negative Breast Cancers (QNBC) Demonstrate Subtype Consistency among Primary and Recurrent or Metastatic Breast Cancer. Translational oncology. 12(3):493-501.

4. Lee J.* & He Q.P.# (2019), Understanding the Effect of Specialization on Hospital Performance Through Knowledge-Guided Machine Learning, Computers & Chemical Engineering, 125, 490-498.

5. Stone K.*, He Q.P.#, & Wang J.# (2019), Two Experimental Protocols for Accurate Measurement of Gas Component Uptake and Production Rates in Bioconversion Processes, Nature Scientific Report, 9(1), 5899. (citation: 1)

6. Suthar, K.*, Shah, D.*, Wang, J., & He, Q. P.# (2019). Next-generation virtual metrology for semiconductor manufacturing: A feature-based framework. Computers & Chemical Engineering, 127, 140-149.

7. He Q.P.#, Wang J.#, & Shah D.* (2019), Feature Space Monitoring for Smart Manufacturing via Statistics Pattern Analysis, Computers and Chemical Engineering, 126, 321-331. (citation: 1)

8. Bahr K., Hilliard M., Roberts N., He Q.P. and Wang J. (2019), Photoautotroph-Methanotroph Coculture – A Flexible Platform for Efficient Biological CO2-CH4 Co-utilization, IFAC-PapersOnLine, 52 (1), 916-921;

9. Hilliard M., He Q.P. and Wang J. (2019), Dynamic Transcriptomic Data Reveal Unexpected Regulatory Behavior of Scheffersomyces stipitis, IFAC-PapersOnLine, 52(1), 538-543;

10. Hilliard M., He Q.P. and Wang J. (2019), Interplay of Shadow Price, Phenotype and Alternative Optimal Solutions in Flux Balance Analysis, IFAC-PapersOnLine, 52(1), 76-81;

11. Shah D.*, Wang J. and He Q.P.# (2019), An Internet-of-things Enabled Smart Manufacturing Testbed, IFAC-PapersOnLine, 52(1), 562-567;


1. He Q.P.# & Wang J. (2018), Statistics process monitoring as a Big Data analytics tool for smart manufacturing, Journal of Process Control, 67, 35-43 (citation: 25)

2. He Q.P.#, 2018. Information Entropy based Indices for Variable Selection Performance Assessment. Computer Aided Chemical Engineering, 44, 2281-2286.

3. Hilliard M., He Q. P.#, & Wang J.# (2018). Dynamic Transcriptomic Data Analysis by Integrating Data-driven and Model-guided Approaches. IFAC-PapersOnLine, 51(19), 104-107.

4. Hilliard M., Damiani A., He Q.P., & Wang J.# (2018). Using a System Identification based Framework to Elucidate How Scheffersomyces stipitis Shifts Redox in Response to Reduced Oxygen Supply. IFAC-PapersOnLine, 51(19), 110-111.

5. Hilliard, M., He, Q. P., & Wang, J.# (2018). Revealing the Biological Meaning of Alternative Optimal Solutions of an E. coli Core Model through a System Identification Based Framework. IFAC-PapersOnLine, 51(19), 42-43.

6. Lee J.* & He Q.P.# (2018) Evaluating Hospital Performance Using Process Systems Engineering Tools, Computer Aided Chemical Engineering, 44, 2155-2160.

7. Hilliard M., Damiani A., He Q.P., Jeffries T.W. & Wang J.# (2018), Elucidating the Redox Balance Shift in Scheffersomyces stipitis’ Fermentative Metabolism Using A Modified Genome-Scale Metabolic Model, Microbial Cell Factories, 17(1):140. doi: 10.1186/s12934-018-0983-y. (citation: 2)

8. Hilliard M., Damiani A., He Q.P. & Wang J.# (2018), A System Identification Enhanced Phenotype Phase Plane Analysis, Computer Aided Chemical Engineering, 44, 2503-2508 (citation: 2)

9. He Q.P.# and Wang J. (2018), Statistics Pattern Analysis: a Statistical Process Monitoring Tool for Smart Manufacturing, Computer Aided Chemical Engineering, 44, 2071-2076;

10. Suthar K.*, Shah D.*, Wang J. & He Q.P.# (2018), Feature-based Virtual Metrology for Semiconductor Manufacturing, Computer Aided Chemical Engineering,44, 2083-2088 (citation: 1)

11. Davis, M., Tripathi, S., Hughley, R., He, Q.P. , Bae, S., Karanam, B., … & Yates, C.# (2018). AR negative triple negative or “quadruple negative” breast cancers in African American women have an enriched basal and immune signature. PloS one, 13(6), e0196909.

12. Shah D., He Q.P.#, Wang J.# (2018), A spectroscopic chemometric modeling approach based on statistics pattern analysis. IFAC-PapersOnLine. 51(18):369-74.


1. Tripathi S., Davis M.B., Hughley R., He Q.P., Bae S., Grizzle W.E., Karanam B., Marini R., Colomb W.D., Yates C.# (2017) Quadruple Negative Breast Cancers in African American women have an enriched Basal and Immune signature. The Journal of Immunology 198 (1) 76.5;

2. Stone K.A., Shah D.*, Kim M.H., Roberts N.R., He Q.P.# and Wang J.#, (2017). A novel soft sensor approach for estimating individual biomass in mixed cultures. Biotechnology progress, 33(2), pp.347-354 (citation: 4)

3. Stone S.A., Hilliard M.*, He Q.P., Wang J. # (2017), A mini review on bioreactor configurations and gas transfer enhancements for biochemical methane conversion, Biochemical Engineering Journal, Vol. 128, 83-92. (citation: 9)

4. He Q. P.#, Wang J., Shah D., & Vahdat N. (2017). Statistical process monitoring for IoT-Enabled cybermanufacturing: opportunities and challenges. IFAC-PapersOnLine, 50(1), 14946-14951. (citation: 4)

5. Damiani A., He Q.P., & Wang J.# (2017). A System Identification Based Framework for Genome-Scale Metabolic Model Validation and Refinement. IFAC-PapersOnLine, 50(1), 12502-12507.

2016 and before

1. He Q.P. #, Wang J., Johnson D., Knight A., Polala R., Zhang R. (2016), A Modular Approach of Integrating Biofuels Education into Chemical Engineering Curriculum: Part I – Learning Materials, Chemical Engineering Education, Vol 50(2), 9-17. (citation: 2)

2. Kim M., Liang M., He Q.P.# & Wang J.# (2016), A Novel Bioreactor to Study the Dynamics of Co-culture Systems, Biochemical Engineering Journal, Vol 107, 52-60. (citation: 1)

3. Wang H., Liu W., Turner O., Black S., Daniels J., He Q.P., Davis M. & Yates C. #, (2016) Kaiso, a transcriptional repressor, promotes cell migration of prostate cancer cells through regulation of miR-31 expression, Onco-Targets, 7(5), 5677. (citation: 30)

4. Damiani A., He Q.P., Jeffries T.W. & Wang J.# (2015), Comprehensive evaluation of two genome-wide metabolic network models of Scheffersomyces stipitis, Biotechnology and Bioengineering, 112(6), 1250-1262 (citation: 13)

5. Wang Z., He Q.P. # & Wang J.# (2015), Comparison of variable selection methods for PLS-based soft sensor modeling, Journal of Process Control, 26, pp 56-72. (citation: 46)

6. Wang J.#, He Q.P. and Edgar T.F. (2014), State estimation for integrated moving average processes in high-mix semiconductor manufacturing, Industrial & Engineering Chemistry Research, 2014, 53 (13), pp 5194–5204, DOI: 10.1021/ie401537d. (citation: 2)

7. He Q.P.# & Wang J. (2014), Valve Stiction Quantification Method Based on a Semiphysical Valve Stiction Model, Ind. Eng. Chem. Res., 2014, 53 (30), pp 12010–12022. (citation: 12)

8. Liang M., He Q.P. & Wang J.# (2014), Elucidating Xylose Metabolism of Scheffersomyces stipitis by Integrating Principal Component Analysis with Flux Balance Analysis, Advanced Chemical Engineering Research, 3(1):8-17.

9. Yoo W.#, Mayberry R., Bae S., Singh K., He Q.P., Lillard J.W., (2014) A Study of Effects of MultiCollinearity in the Multivariable Analysis. International Journal of Applied Science and Technology, 2014;4(5):9-19. (citation: 151)

10. Liang, M., Damiani, A., He, Q.P., & Wang, J.# (2014). Elucidating xylose metabolism of Scheffersomyces stipitis for lignocellulosic ethanol production. ACS Sustainable Chemistry & Engineering, 2(1), 38-48. (citation: 13)

11. Liang M., Kim M.H., He Q.P. & Wang J. # (2013), Impact of pseudo-continuous fermentation on the ethanol tolerance of Scheffersomyces stipitis, Journal of Bioscience and Bioengineering, Vol. 116 (3), 319-326. DOI: 10.1016/j.jbiosc.2013.03.016 (citation: 9)

12. Otali, D., He, Q.P., & Grizzle, W. E. # (2013). The Effect of Antigen Retrieval on Cells Fixed in 10% Neutral Buffered Formalin Followed by Transfer to 70% Ethanol. PloS one, 8(12), e82405. (citation: 6)

13. Otali, D., He, Q.P., Stockard, C.R., & Grizzle, W.E.# (2013). Preservation of immunorecognition by transferring cells from 10% neutral buffered formalin to 70% ethanol. Biotechnic & Histochemistry, 88(3-4), 170-180. (citation: 8)

14. Galicia H.J., He Q.P., Wang J. (2012), Comparison of the performance of a reduced-order dynamic PLS soft sensor with different updating schemes for digester control, Control Engineering Practice, 20(8), 747–760. (citation: 41)

15. Wang H., Jones J., Turner T., He Q.P., Hardy S., Grizzle W.E., Welch D., & Yates C. (2012), Clinical and Biological Significance of KISS1 Expression in Prostate Cancer, The American Journal of Pathology, Vol. 180(3):1170-8. (citation: 39)

16. Jones J., Wang H., Zhou J., Hardy S., Austin D., Turner T., He Q.P., Wells, A., Grizzle W., Yates C. (2012) Nuclear Kaiso Indicates Aggressive Prostate Cancers and Promotes Migration and Invasiveness of Prostate Cancer Cells, The American Journal of Pathology, Vol. 181(5): 1836–1846. (citation: 47)

17. Grunda J.M., Steg A.D., He Q.P., Steciuk M.R., Parker S.B., Johnson M.R., Grizzle W.E. (2012) Differential expression of breast cancer-associated genes between stage- and age-matched tumor specimens from African- and Caucasian-American Women diagnosed with breast cancer, BMC Research Notes, 5:248. (citation: 25)

18. Galicia H., He Q.P., Wang J. (2011), A reduced order soft sensor approach and its application to a continuous digester, Journal of Process Control, Vol. 21(4), 489-500 (citation: 57)

19. He Q.P., Wang J., Mobley J.A., Richman, J. & Grizzle W. E. (2011), Self-Calibrated Warping for Spectrum Alignment, Cancer Informatics, Vol. 10, 65-82 (citation: 20)

20. He Q.P.# & Wang J. (2011), Statistics Pattern Analysis – A New Process Monitoring Framework and Its Application to Semiconductor Batch Processes, AIChE journal, 57(1), 107–121 (citation: 95)

21. Wang J.#, He Q.P. (2010), Multivariate process monitoring based on statistics pattern analysis, Industrial & Engineering Chemistry Research, Vol. 49 (17), 7858-7869 (citation: 108)

22. He Q.P. & Wang J. (2010), Large-scale Semiconductor Process Monitoring Using a Fast Pattern Recognition Based Method, IEEE Transactions on Semiconductor Manufacturing, Vol. 23(2),194-200 (citation: 53)

23. Wang J., He Q.P. and Qin S.J. (2010), Stability analysis and optimal tuning of EWMA controllers: Gain adaptation vs. intercept adaptation, Journal of Process Control, Vol. 20 (2), 134-142, nominated for the Annual Best Paper Award. (citation: 14)

24. Wang J., He Q.P. & Edgar T.F. (2009), State estimation in high-mix semiconductor manufacturing, Journal of Process Control, Vol. 19, 443-456. (citation: 33)

25. He Q.P. & Wang J. (2007), Fault detection using k-nearest neighbor rule for semiconductor manufacturing processes (invited), IEEE Transactions on Semiconductor Manufacturing, Vol. 20(4), 345-354. (citation: 285)

26. He Q.P., Wang J., Pottmann M. & Qin S.J. (2007), A Curve fitting method for detecting valve stiction in oscillating control loops, Industrial & Engineering Chemistry Research, Vol. 46 (13), 4549 -4560. (citation: 157)

27. Wang J. & He Q.P. (2007), A Bayesian approach for fast disturbance detection and classification in microelectronics manufacturing, IEEE Transactions on Semiconductor Manufacturing, Vol. 20(2), 126 – 136. (citation: 30)

28. Bode, C.A., Wang J., He Q.P. & Edgar T.F. (2007), Run-to-run control and state estimation in semiconductor manufacturing (invited), Annual Reviews in Control, Vol. 31(2), 241 – 253. (citation: 27)

29. He Q.P., Wang J. & Qin S. J. (2005), A new fault diagnosis method using fault directions in Fisher discriminant analysis, AIChE Journal, Vol. 51(2), 555 – 571. (citation: 230)

30. Wang J., He Q.P., Qin S.J., Bode C. & Purdy M. (2005), Recursive least squares estimation for run-to-run control with metrology delay and its application to STI etch process, IEEE Transactions on Semiconductor Manufacturing, Vol. 18(2), 309 – 319. (citation: 66)

31. He Q.P., Qin S.J. & Toprac A.J. (2003), Computationally efficient modeling of wafer temperatures in a low pressure chemical vapor deposition furnace. IEEE Transactions on Semiconductor Manufacturing, Vol. 16 (2), 342 – 350. (citation: 9)

32. Wang J., Liu, Z., Luo J., He Q.P., Ding F. & Yuan N. (2000). Determination of zeta-potential by measuring electroosmotic flux in an alternating electric field and its application in the study of membrane fouling. Separation Science and Technology, 35(8), 1195 – 1206. (citation: 13)

33. Yin G., He Q.P., Liu Z., Ding F. & Yuan N. (1999) Isolation and characterization of biliproteins and polysaccharides from Spirulina. Fine Chemicals (China), 16(2), 10 – 13. (citation: 9)

34. Wang J., Liu Z., He Q.P., Luo J. & Yuan N. (1999). Characterization of membrane fouling process using zeta-potential. Huagong Xuebao (China), 50(5), 687 – 691.

35. Mu F., Fan Y., He Q.P., Wang Q., Hu H., Ding F. & Yuan N. (1998). Gas holdup and liquid circulation velocity of the external-loop airlift reactor. Journal of Chemical Engineering of Chinese Universities (China) 12(4), 345 – 349.