2021-03-12T15:22:43+08:002019-11-29|
Contact Information
Research Team
Name Position Office Phone Email
Johnny Kuan Cheok LEIResearch AssistantE12-3039+853 8822 2914Johnnylei@um.edu.mo
Yusi LIResearch AssistantE12-3039+853 8822 2914yusili@um.edu.mo
Shixue SUNPhD StudentE12-3039+853 8822 2914
Teng ZHANGPhD StudentE12-3039+853 8822 2914
Guoliang WANGPhD StudentE12-3039+853 8822 2914
Min DENGPhD StudentE12-3039+853 8822 2914
Dandan WANGPhD StudentE12-3039+853 8822 2914
Dongliang LENGPhD StudentE12-3039+853 8822 2914
Xiangqing HOUPhD StudentE12-3039+853 8822 2914
Nam Ian WONGPhD StudentE12-3039+853 8822 2914
Xizhi LUOPhD StudentE12-3039+853 8822 2914
Education
EMBA (2017) Guanghua School of Management, Peking University
Beijing, China
PhD (2002) Carnegie Mellon University
Pittsburgh, PA
PhD student (ABD) (1997-1998) Texas A & M University
College Station,TX
MS (1996) Beijing Normal University
Beijing, China
BS (1990) Beijing Normal University
Beijing, China
Positions
2016-present Professor, Faculty of Health Sciences, University of Macau
2015-2016 Senior Principal Scientist, Merck Research Laboratories, West Point, PA.
2012-2014 Director of BARDS and Head of Early Development Statistics – Asian Pacific, Merck Research Laboratories, West Point, PA.
2008-2012 Associate Director, Merck Research Laboratories, West Point, PA.
2005-2008 Senior Biometrician, Merck Research Laboratories, West Point, PA.
2002-2005 Biometrician, Merck Research Laboratories, West Point, PA.
Research Interests
Prof. Zhang’s lab focuses on research in digital health/medicine, artificial intelligence and big data analysis. Current research in this area includes, but not limited to, conducting studies in continuous monitoring of physiological signals (such as blood glucose, respiratory signals, cardiovascular signals) and high-throughput genomics (such as CRISPR/CAS9 HTS and RNA-seq) to address medical questions in diabetes, respiratory diseases, cardiovascular diseases, neuro-diseases, cancers and so on. Critical research also includes the development of novel experimental designs, analytic methodology and software (including R packages) for analyzing big data in digital health/medicine and precision medicine. Prof. Zhang has worked in quantitative high-throughput genotyping/phenotyping for about 20 years. The novel methods developed by him and his colleagues along with their applications have a high impact on the high-throughput screening research field, especially in RNAi high-throughput screening (HTS) research.
Representative Publications
  1. Zhang XD*#, Wang D#, Sun S, Zhang H*. 2020. Issues of z-factor and an approach to avoid them for quality control in high-throughput screening studies. Bioinformatics (Accepted)
    + 5yr IF=9.853, ranked as the 3rd in Mathematical & Computational Biology by Clarivate Analytics
  2. Luo W#, Wang D#, Zhang T, Zheng P, Leng D, Li L, Liu Y, Sun B*, Zhang XD*. 2020. Prevalence patterns of allergen sensitization by region, gender, age and season among patients with allergic symptoms in mainland China: A four-year multicenter study. Allergy (in press) (DOI: https://doi.org/10.1111/all.14597)
    + Ranked as the 2nd in Allergy by Clarivate Analytics
  3. Zhang XD#*, Zhang Z#, Wang 2018. CGManalyzer: an R package for analyzing continuous glucose monitoring studies. Bioinformatics 34(9): 1609–1611 (DOI: 10.1093/bioinformatics/btx826)
    + 5yr IF=9.853, ranked as the 3rd in Mathematical & Computational Biology by Clarivate Analytics
  4. Niu J#, Shi Y#*, Cai M, Cao Z, Wang D, Zhang Z, Zhang XD*. 2018. Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques. Bioinformatics 34(5): 820-827 (DOI: 10.1093/bioinformatics/btx652)
    + 5yr IF=9.853, ranked as the 3rd in Mathematical & Computational Biology by Clarivate Analytics
  5. Zhang XD*, Santini F, Lacson R, Marine SD, Wu Q, Benetti L, Yang R, McCampbell A, Berger JP, Toolan DM, Stec EM, Holder DJ, Soper KA, Heyse JF and Ferrer M. 2011. cSSMD: Assessing collective activity of multiple siRNAs in genome-scale RNAi screens. Bioinformatics 27(20): 2775-2781 (doi: 10.1093/bioinformatics/BTR474).
    + listed among the 50 most-frequently cited articles in Bioinformatics in 2013
  6. Zhang XD*, Zhang Z. 2013. displayHTS: a R package for displaying data and results from high-throughput screening experiments. Bioinformatics 29 (6): 794–796 (doi: 10.1093/bioinformatics/btt060).
    + 5yr IF=9.853, ranked as the 3rd in Mathematical & Computational Biology by Clarivate Analytics
  7. Zhang XD, Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi Research. Cambridge University Press, Cambridge, UK (ISBN: 9780521734448 or 9780521517713, amazon.com).
  8. Zhang XD*, Heyse JF. 2009. Determination of sample size for hit selection in genome-scale RNAi screens. Bioinformatics 25: 841-844 (doi:1093/bioinformatics/btp082)
    + 5yr IF=9.853, ranked as the 3rd in Mathematical & Computational Biology by Clarivate Analytics
  9. Zhang XD*, Kuan PF, Ferrer M, Shu X, Liu YC, Gates AT, Kunapuli P, Stec EM, Xu M, Marine SD, Holder DJ, Stulovici B, Heyse JF, Espeseth AS. 2008. Hit selection with false discovery rate control in genome-scale RNAi screens. Nucleic Acids Research 36 (14):4667-4679 (doi:1093/nar/gkn435).
    + 5yr IF=11.797
  10. Zhou H, Xu M, Huang Q, Gates AT, Zhang XD, Stec EM, Ferrer M, Hazuda DJ, Espeseth AS. 2008. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host & Microbe 4(5):495-504 (doi:1016/j.chom.2008.10.004).
    + listed by Nature Medicinein its year end review on Notable advances in 2008  (http://www.nature.com/nm/journal/v14/n12/full/nm1208-1302.html)
    + selected to appear in the cover page of the November issue of Cell Host & Microbe
    + 5yr IF=17.766
  11. Zhang XD*. 2007. A pair of new statistical parameters for quality control in RNA interference high throughput screening assays. Genomics 39: 552-561 (doi: 1016/j.ygeno.2006.12.014).
  12. Lei KC, Zhang XD*. 2020. Conservation analysis of SARS-CoV-2 spike suggests complicated viral adaptation history from bat to human. Evolution, Medicine and Public Health (Accepted)
  13. Xue M#, Zeng Y#, Qu H# , Zhang T, Li N, Huang H, Zheng P, Hu H, Zhou L, Duan Z, Zhang Y, Bao W, Tian L, Hakonarson H, Nanshan Zhong*, Zhang XD*, Sun B*. 2020. Heparin-binding protein levels correlated with aggravation and multi-organ damage in severe COVID-19. European Respiratory Journal Open Research (Accepted)
  14. Zheng P#, Huang C#, Dongliang Leng, Sun B*, Zhang XD*. 2020. Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma. BMC Medical Genomics 13 (1): 136 (doi: https://doi.org/10.1186/s12920-020-00785-y)
  15. Huang C#, Leng D#, Lei KC, Sun S, Zhang XD*. 2019. Transcriptome analysis reveals lncRNA-mediated complex regulatory network response to DNA damage in the liver tissue of Rattus norvegicus. Journal of Cellular Physiology 234:23216–23231 (doi:10.1002/jcp.28889)
  16. Sun X, Liu X, Xia M, Shao Y, Zhang XD*. 2019. Multicellular gene network analysis identifies a macrophage-related gene signature predictive of therapeutic response and prognosis of gliomas. Journal of Translational Medicine 17 (1), 159
  17. Huang C, Leng D, Sun S, Zhang XD*. 2019. Re-analysis of the coral Acropora digitifera transcriptome reveals the a complex lncRNAs-mRNAs interaction network implicated in response of transcript repertoire to Symbiodinium infection. BMC Genomics 20:48 (doi: 10.1186/s12864-019-5429-3)
  18. Dong X#, Chen C#, Geng Q, Cao Z, Chen X, Lin J, Yu J, Zhang Z, Shi Y, Zhang XD*. 2019 An improved method of handling missing values in the analysis of sample entropy for continuous monitoring of physiological signals. Entropy 21(3), 274 (doi: 3390/e21030274)
  19. Xie R, Zhang XD, Zhao Q, Peng B, Zheng J*. 2018. Analysis of global prevalence of antibiotic resistance in acinetobacter baumannii infections disclosed a faster increase in OECD countries. Emerging Microbes & Infections 7:31. (DOI 10.1038/s41426-018-0038-9)
  20. Shi Y#, Wang G#, Niu J*, Zhang Q, Cai M, Sun B, Wang D, Xue M, Zhang XD*. 2018. Classification of sputum sounds using artificial neural network and wavelet transform. International Journal of Biological Sciences 2018; 14(8): 938-945 (DOI: 10.7150/ijbs.23855)
  21. Gould AL*, Zhang XD. 2014. Bayesian adaptive determination of the sample size required to assure acceptably low adverse event risk. Statistics in Medicine 33(6): 940-957 (DOI: 10.1002/sim5993)
  22. Zhang XD*, Heyse JF. 2012. Contrast variable for comparing groups in biopharmaceutical research. Statistics in Biopharmaceutical Research 4 (3): 228 – 239 (DOI: 10.1080/19466315.2011.646905).
  23. Zhang XD*. 2011. Illustration of SSMD, z-score, SSMD*, z*-score and t-statistic for hit selection in high-throughput screens. Journal of Biomolecular Screening 16 (7): 775 – 785 (doi: 10.1177/1087057111405851).
  24. Zhao WQ, Santini F, Breese R, Ross D, Zhang XD, Stone DJ, Ferrer M, Townsend M, Wolfe AL, Seager MA, Kinney GG, Shughrue PJ, Ray WJ. 2010. Inhibition of calcineurin-mediated endocytosis and AMPA receptor prevent amyloid β oligomer-induced synaptic disruption. Journal of Biological Chemistry 285(10): 7619-7632 (doi:1074/jbc.M109.057182).
  25. Zhang XD*. 2010. Assessing the size of gene or RNAi effects in multi-factor high-throughput experiments. Pharmacogenomics 11(2): 199 – 213 (doi:10.2217/PGS.09.136)
  26. Zhang XD*, Espeseth AS, Johnson E, Chin J, Gates A, Mitnaul L, Marine SD, Tian J, Stec EM, Kunapuli P, Holder DJ, Heyse JF, Stulovici B, Ferrer M. 2008. Integrating experimental and analytic approaches to improve data quality in genome-wide RNAi screens. Journal of Biomolecular Screening 13(5): 378-389 (doi: 1177/1087057108317145).
    + selected to appear in the cover page of the June issue
  27. Zhang XD*, 2008. Novel analytic criteria and effective plate designs for quality control in genome-wide RNAi screens. Journal of Biomolecular Screening 13(5): 363-377 (doi:1177/1087057108317062)
  28. Zhang XD*. 2007. A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high throughput screening assays. Journal of Biomolecular Screening 12 (5): 645-655 (doi:1177/1087057107300645)
  29. Johnson TE, Zhang XD, Shu S, Umbenhauer DR. 2005. Statins and PPARagonists induce myotoxicity in differentiated rat skeletal muscle cultures but do not exhibit synergy with co-treatment. Toxicology and Applied Pharmacology 208 (3) 210-221 (PMID: 16239165).
  30. Zhang XD, Roeder K*, Wallstrom G, Devlin B. 2003. Integration of association statistics over genomic regions using Bayesian adaptive regression splines. Human Genomics 1: 20-29 (doi:1186/1479-7364-1-1-20; PMID: 15601530 link).

*: corresponding author
#: co-first authors

Full Publications List
Awards
  • Elected as Fellow of American Statistical Association, 2014
  • Elected as Member of International Statistical Institute, 2014
  • Charlie Sampson Poster Award, 2001
  • Second-Place Medal for the Development of Science & Technology, Jiangxi, China, 1994
Professional Activities
Expert for Professional Evaluation

  • 2014 Expert for evaluation of Horizon 2020 grant proposals on topic “development of new diagnostic tools and technologies: in vitro devices, assays and platforms”, remotely
  • 2011(November) Expert for evaluation of grant proposals for – omics for rare diseases Panel for the European Union 7th Framework Programme Health Theme, Brussels, Belgium
  • 2011(March) Expert for evaluation of grant proposals for Large-Scale Data Gathering Panel for the EU 7th Framework Programme Health Theme, remotely
  • 2011 Expert for evaluation in NIH Assay Development for High Throughput Molecular Screening Study Section, Santa Monica, California,USA
  • 2009 Expert for evaluation of grant proposals for the EU 7th Framework Programme Health Theme, remotely
  • 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014 Student Paper Competition Committee member and evaluator, ASA Biopharmaceutical Section
Editorial Services for Peer-Reviewed Professional Journals

  • 2012, Guest Editor, special issue in Journal of Probability and Statistics
  • December 2010 – Present, Editorial Board Member, Journal of Biometrics & Biostatistics
  • June 2010 – Present, Editorial Board Member, Journal of Pharmacogenomics and Pharmcoproteomics
Referee for Peer-Reviewed Professional Journals

  • November 2017, January 2013, November 2012, October, September & January 2011, October 2008, Bioinformatics
  • August 2017, Statistical Methods in Medical Research
  • July 2017, Mathematical Problems in Engineering
  • June 2017, The FASEB journal
  • January 2016, August 2015, International Journal of Biological Sciences
  • June 2015, Computer Methods and Programs in Biomedicine
  • March 2014, Advances in Genomics and Genetics
  • February 2014, December 2013, Methods
  • August 2013, PLOS ONE
  • June & January 2013, PLOS Computational Biology
  • January 2013, November 2012, October, September & January 2011, October 2008, Bioinformatics
  • November & September 2013, January 2012, December, July 2010, Journal of Biomolecular Screening
  • May 2011, Current Chemical Genomics
  • January 2013, November 2010, December 2008, November 2007, IMECS Proceeding
  • January 2010, November 2009, BMC Bioinformatics
  • October 2009, January 2009, Statistics in Biopharmaceutical Research
  • August 2009, Nature
  • April 2009, Nature Methods
  • January 2009, BMC Genomics
  • January 2008, April 2007, Journal of American Statistical Association
  • January 2005, Biometrical Journal
  • September 2003, Annals of Human Genetics
Professional Meeting Services

  • 2016, 2015, 2014, 2013, 2012, 2011, 2010, Program Committee member for International Conference on Information Science and Applications, Seoul, Korea
  • 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007, Program Committee member for the International MultiConference of Engineers and Computer Scientists, Hong Kong
  • 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007, Conference Committee member for the IAENG International Conference on Bioinformatics, Hong Kong
  • 2013, Organizer, Special session, “Statistics in biopharmaceutical research”, the 59th World Statistics Congress, Hong Kong
  • 2010, Chair and organizer, Roundtable session ‘High-throughput screening and data analysis’, The Joint Statistical Meetings, Vancouver, Canada
  • 2010, Chair and organizer, Special session ‘Data Analysis in Genome-scale RNAi Researches’, International Conference on Intelligent Systems for Molecular Biology, Boston, MA, USA.
  • July 2008, chaired a session “Omics and System Biology for Antiviral Drug Discovery” in BIT’s 1st Annual World Summit of Antivirals. Kunming, China
  • June 2008, organized and chaired invited session “Statistics for Biotechnology” in the First Symposium of The International Society for Biopharmaceutical Statistics, Shanghai, China
  • August 2007, organized invited session “Data analysis in High Throughput Screening Assays”
    in the Joint Statistical Meetings, Salt Lake City, UT
  • June 2006, chaired session “SESSION 8-BIOCOMP: INTELLIGENT DRUG DESIGN” in the International Conference on Bioinformatics & Computational Biology, Las Vegas, Nevada
  • August 2005, organized and chaired invited session “Pharmacogenomics” in the Joint Statistical Meetings, Minneapolis, MN, USA
  • August 2005, organized and chaired luncheon roundtable “Pharmacogenomics: the Critical path to Personalized Medical Products” in the Joint Statistical Meetings, Minneapolis, MN
  • August 2004, organized contributed session “Microarray” for the Joint Statistical Meetings, Toronto, Ontario
  • August 2003, organized and chaired contributed session “Genetics Data Analysis I” in the Joint Statistical Meetings, San Francisco, CA
Society Memberships
2016 – Present IEEE
2015 – Present American Association for the Advancement of Science
2014 – Present Executive Committee Member, Functional Genomics and System Biology,
Chinese Society for Cell Biology
2014 – Present Chairperson, Biopharmaceutical Section,Functional Genomics and System Biology, Chinese Society for Cell Biology
2014 – Present Vice Chairperson, Specialty Committee of Reproductive Medicine,World Federation of Chinese Medicine Society
2002 – Present American Statistical Association
2012 – 2015 Core member of the DIA China Statistics SIAC
2012-2014 Committee Member, Functional Genomics and System Biology,
Chinese Society for Cell Biology