Welcome Text

2018 / 21 February

Publications


Zhang XD*. 2011. 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).

64、 Chen X#, Wang D#, Lin J, Yu J, Deng S, Huang L, Zhang T, Zheng J, Sun B, Zhang XD*. 2018. Clinical Practice of Integrating CSII, CGM and Personalized Data Analysis to Treat a Pregnant Woman with Type 2 Diabetes. (Submitted)

63、 Zheng J, Zou J, Zhang W, Zhang H, Zhang XD, Bo Peng B. 2018. Studies on Aminoglycoside Susceptibility Identify a Novel Function of KsgA to Secure Protein Translational Fidelity during Antibiotic Stress. (Submitted)

62、 Huang C, Leng D, Sun S, Zhang XD*. 2018. 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. (Submitted)

61、  Sun S#, Jin Y#, Chen C, Sun B, Cao Z, Lo LL, Zhao Q, Zheng J, Shi Y*, Zhang XD*. 2018. entropy change of biological dynamics in asthma. (Submitted)

60、  Dong X#, Chen C#, Geng Q, Cao Z, Yu J, Shi Y, Zhang XD*. 2018. A method for handling with missing values in the analysis of sample entropy for physiological signals. (Under review)

59、  Xue M#, Wang D#, Cao Z*, Luo Z, Zheng Y, Lu J, Zhao Q, Zhang XD*. 2017. A study demonstrating the potential of using transcutaneous oxygen and transcutaneous carbon dioxide tensions to assess the risk of pressure injury. (Under review)

58、  Shi Y*, Zhang B, Cai M, Wang D, Zhang XHD*. 2017. Estimation method for functional residual capacity in mechanical ventilated patients. (Under review)

57、  Shi Y*, Ren S, Cai M, Zhang Z, Zhang XHD. 2017. Simulation and Experimental Study of the Mucus Clearance Effectiveness Using a New Simulated Cough Device based on the Pneumatic System. (Under review)

56、  Chen X#, Guan W#, Sun S, Zheng P, Sun L, Chen D, Wang D, Chen C, Sun B*, Zhang XHD*. Effects of intranasal cellulose powder on asthma control in children with mild-to-moderate persistent allergic rhinitis: A single-center, randomized, placebo-controlled trial. (Under review)

55、Zheng J, Xie R, Zhang XD, Zhao Q, Peng B. 2018. Analysis of Global Prevalence of Antibiotic Resistance in Acinetobacter baumannii Infections Disclosed a Faster Increase in OECD Countries. Emerging Microbes & Infections (Accepted)

54、Shi Y*, Ren S, Cai M, Zhang Z, Zhang XD. 2017. ANSYS-MATLAB co-simulation of mucus flow iistribution and clearance effectiveness of a new simulated cough device. International Journal for Numerical Methods in Biomedical Engineering (Revision)

53、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 (Accepted)

52、Zhang XD#*, Zhang Z#, Wang D. 2017. CGManalyzer: an R package for analyzing continuous glucose monitoring studies. Bioinformatics (DOI: 10.1093/bioinformatics/btx826)

51、  Nin J#, Shi Y#*, Cai M, Cao Z, Wang D, Zhang Z, Zhang XHD*. 2017. Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques. Bioinformatics (DOI: 10.1093/bioinformatics/btx652)

50、Wang Y#, Liu H#, Leng D, Gao W*, Cai M, Xu W, Zhang XD, Shi Y*. 2017. New advances in EMG control of anthropomorphic prosthetic hand. Science China Technological Sciences (DOI: 10.1007/s11431-017-9159-3)

49、  Ren S, Cai M, Shi Y, Xu W, Zhang XHD, 2017. Influence of Bronchial Diameter Change on the airflow dynamics Based on a Pressure-controlled Ventilation System. International Journal for Numerical Methods in Biomedical Engineering (doi: 10.1002/cnm.2929).

48、  Xu T, Ying T, Wang L, Zhang XHD, Kang L, Huang T, Cheng L, Wang L*, Zhao Q*. 2017. A native-like bispecific antibody suppresses the inflammatory cytokine response by simultaneously neutralizing tumor necrosis factor-alpha and interleukin-17. Oncotarget (doi: 10.18632/oncotarget.19899)

47、  Wang Y, Jin Y, Chen C, Zheng W, Wang S, Ungvari G, Ng C, Zhang XD, Jia F, Xiang YT*. Meta-analysis of Adherence to Highly Active Antiretroviral Therapy in Patients with HIV Infection in China (under review)

46、  Jin Y#, Chen C#, Cao Z, Sun B, Lo IL, Liu T, Zheng J, Sun S, Shi Y, Zhang XD*. Entropy change of biological dynamics in COPD. International Journal of Chronic Obstructive Pulmonary Disease. ( doi:10.2147/COPD.S140636)

45、  Chen C#, Jin Y#, Lo IL, Zhao H, Sun B, Zhao Q, Zheng J, Zhang XHD*. 2017. Complexity Change in Cardiovascular Diseases. International Journal of Biological Sciences (doi: 10.7150/ijbs.19462)

44、  Zhang XHD#, Pechter D#, Yang L, Ping X, Yao Z, Zhang R, Shen X, Li N, Connick J, Hill D, Nawrocki AR, Li C*. 2017. Decreased complexity of glucose dynamics preceding the onset of diabetes in preclinical species. PloS ONE 12(9):e0182810 .( doi:10.1371/journal.pone.0182810)

43、  Shi Y*, Zhang B, Cai M, Zhang XHD*. 2017. Numerical Simulation of volume-controlled mechanical ventilated respiratory system with two different lungs. International Journal for Numerical Methods in Biomedical Engineering ( doi: 10.1002/cnm.2852 In press).

42、  He L, Liu S, Shan C, Tu Y, Li Z, Zhang XHD*. 2016. Demonstrating placebo effect in clinical trials of DPP-4 inhibiters conducted in China: Meta-analysis. BMC Pharmacology and Toxicology 17:40 (doi: 10.1186/s40360-016-0084-7)

41、  Cox KS, Wang IM, Nefedov A, Zhang XHD, Dubey S, Bett A, Casimiro D, Mandl J, Feinberg MB. 2016. Comparison of the TLR7 and TLR9 innate immune signaling pathways in african green monkeys and rhesus macaques. Journal of Immunology 196 (1 Supplement) 203.8

40、  Zhao G, Li Q, Wang IM, Li X, Fang X, Zhang XHD*. 2015. An effective analytic method for detecting tissue-specific genes from RNA-seq data. Pharmacogenomics 16 (16):1769-1779 (doi: 10.2217/pgs.15.118).

39、  Zhang XHD*. 2015. Precision medicine, personalized medicine, omics and Big Data: concepts and relationships. Journal of Pharmacogenomics and Pharmacoproteomics 6:2 (doi: 10.4172/2153-0645.1000e144doi: 10.4172/2153-0645.1000e144).

38、  Kang H, Cho KH, Zhang XHD, Zeng T*, Chen L*. 2015. Inferring sequential order of somatic mutations during tumorgenesis based on markov chain model. IEEE/ACM Transactions on Computational Biology and Bioinformatics 99 (doi: 10.1109/TCBB.2015.2424408)

37、  Camargo LM, Zhang XHD, Loerch P, Caceres M, Marine SD, Uva P, Ferrer M, Rinaldis E, Stone DJ, Majercak J, Ray WJ, Chen Y, Shearman MS, Mizuguchi K. 2015. Pathway-based analysis of genome-wide siRNA screens reveals the regulatory landscape of APP processing PLoS ONE 10(2): e0115369. (doi:10.1371/journal.pone.0115369)

36、  Gould AL, Zhang XHD. 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)

35、  Zhang XHD*, Zhang ZZ. 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).

34、  Yang R, Lacson RG, Castriota G, Zhang XHD, Liu Y, Zhao WQ, Einstein M; Camargo, Luiz CM, Qureshi S, Wong KK, Zhang BB, Ferrer M, Berger JP. 2012. A genome-wide siRNA screen to identify modulators of insulin sensitivity and gluconeogenesis. PLoS ONE 7(5): e36384. (doi:10.1371/journal.pone.0036384)

33、  Zhang XHD*, 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).

32、  Zhang XHD*, 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

31、  Zhang XHD*. 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).
#listed among the 50 most-frequently cited articles in Journal of Biomolecular Screening since 2014

30、  Zhang XHD*, 2010. Contrast variable potentially providing a consistent interpretation to effect sizes. Journal of Biometrics & Biostatistics 1:108 (doi:10.4172/2155-6180.1000108).

29、  Zhang XHD*, Lacson R, Yang R, Marine SD, McCampbell, Toolan DM, Hare TR, Kajdas J, Berger JP, Holder DJ, Heyse JF, Ferrer M. 2010. The use of SSMD-based false discovery and false non-discovery rates in genome-scale RNAi screens. Journal of Biomolecular Screening 15: 1123 – 1131 (doi: 10.1177/1087057110381919).

28、  Zhang XHD*, 2010. An effective method controlling false discoveries and false non-discoveries in genome-scale RNAi screens. Journal of Biomolecular Screening 15: 1116 – 1122 (doi: 10.1177/1087057110381783).

27、  Zhao WQ, Santini F, Breese R, Ross D, Zhang XHD, 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:10.1074/jbc.M109.057182).

26、  Zhang XHD*. 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)

25、  Zhang XHD*. 2010. Strictly standardized mean difference, standardized mean difference and classical t-test for the comparison of two groups. Statistics in Biopharmaceutical Research 2(2): 292-299 (doi: 10.1198/sbr.2009.0074)

24、  Klinghoffer RA, Frazier J, Annis J, Berndt JD, Roberts BS, Arthur WT, Lacson R, Zhang XHD*, Ferrer M, Moon, RT, Cleary MA. 2009. A lentivirus-mediated genetic screen identifies dihydrofolaste reductase (DHFR) as a modulator of -actenin/GSK3 signaling. PLoS ONE 4(9): e6892 (doi: 10.1371/journal.pone.0006892)

23、  Zhang XHD*, Heyse JF. 2009. Determination of sample size for hit selection in genome-scale RNAi screens. Bioinformatics 25: 841-844 (doi:10.1093/bioinformatics/btp082)

22、  Zhang XHD*, Shane SD, Ferrer M. 2009. Error rates and power in genome-scale RNAi screens. Journal of Biomolecular Screening 14:230-238 (doi:10.1177/1087057109331475)

21、  Zhang XHD*. 2009. A method effectively comparing gene effects in multiple conditions in RNAi and expression profiling research. Pharmacogenomics 10(3):345-358 (doi:10.2217/14622416.10.3.345)

20、  Zhou H, Xu M, Huang Q, Gates AT, Zhang XHD, 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:10.1016/j.chom.2008.10.004).
#listed by Nature Medicine in 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

19、  Zhang XHD*, 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:10.1093/nar/gkn435).

18、  Zhang XHD*. 2008. Genome-wide screens for effective siRNAs through assessing the size of siRNA effects. BMC Research Notes 1:33 (doi:10.1186/1756-0500-1-33).

17、  Zhao WQ, Breese R, Wolfe AA, Ross DA, Santini F, Zhang XHD, Ferrer M, Stone D, Seabrook GR, Stulovici B, Kinney GG, Ray WJ, Shughrue PJ. 2008. Targeting synaptic AMPA receptors by oligomers. Alzheimers & Dementia 4 (4):T197 (doi: http://dx.doi.org/10.1016/j.jalz.2008.05.548).

16、  Zhang XHD*, 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: 10.1177/1087057108317145).
#selected to appear in the cover page of the June issue

15、  Zhang XHD*, 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:10.1177/1087057108317062)
#listed among the 50 most-frequently cited articles in Journal of Biomolecular Screening since 2013 (http://jbx.sagepub.com/reports/most-cited)

14、  Chung N, Zhang XHD, Kreamer A, Locco L, Kuan PF, Bartz S, Linsley PS, Ferrer M, Strulovici B. 2008. Median absolute deviation to improve hit selection for genome-scale RNAi screens. Journal of Biomolecular Screening 13: 149-158 (doi: 10.1177/1087057107312035).
#listed among the 50 most-frequently cited articles in Journal of Biomolecular Screening since 2011

13、  Clodfelter KH, Miles GD, Wauthier V, Holloway MG, Zhang XHD, Hodor P, Ray WJ, Waxman DJ. 2007. Role of STAT5a in Regulation of Sex-specific Gene Expression in Female but not Male Mouse Liver Revealed by Microarray Analysis. Physiological Genomics 31:63-74 (PMID: 17536022).

12、  Zhang XHD*. 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:10.1177/1087057107300645)
#listed among the 50 most-frequently cited articles in Journal of Biomolecular Screening since April 2009

11、  Zhang XHD*, Ferrer M, Espeseth AS, Marine SD, Stec EM, Crackower MA, Holder DJ, Heyse JF, Strulovici B. 2007. The use of strictly standardized mean difference for hit selection in primary RNA interference high throughput screening experiments. Journal of Biomolecular Screening 12 (4): 497-509 (doi:10.1177/1087057107300646).
#listed among the 50 most-frequently cited articles in Journal of Biomolecular Screening since 2008

10、  Zhang XHD*. 2007. A pair of new statistical parameters for quality control in RNA interference high throughput screening assays. Genomics 39: 552-561 (doi: 10.1016/j.ygeno.2006.12.014).

9、  Kim JJ, Shirts BH, Dayal M, Bacanu S, Wood J, Xie W, Zhang X, Chowdari KV, Yolken R, Devlin B, Nimgaonkar VL. 2007. “Are exposure to cytomegalovirus and genetic variation on chromosome 6p as joint risk factors for schizophrenia?” Annals of Medicine 39(2):145-53 (doi: 10.1080/07853890601083808).

8、  Espeseth AS, Huang Q, Gates AT, Xu M, Yu Y, Simon AJ, Shi X, Zhang XHD, Hodor PG, Stone D, Burchard J, Cavet GL, Bartz S, Linsley PS, Ray WJ, Hazuda DJ. 2006. A genome wide analysis of ubiquitin ligases in APP processing identifies a novel regulator of BACE1 mRNA levels. Molecular and Cellular Neuroscience 33(3): 227-235.

7、  Zhang XHD*, Yang XC, Chung N, Gates AT, Stec EM, Kunapuli P, Holder DJ, Ferrer M, Espeseth AS. 2006. Robust statistical methods for hit selection in RNA interference high throughput screening experiments. Pharmacogenomics 7 (3) 299-309 (doi: 10.2217/14622416.7.3.299).

6、  Johnson TE, Zhang X, Shu S, Umbenhauer DR. 2005. Statins and PPAR agonists 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).

5、  Roeder K, Bacanu S, Sonpar V, Zhang X, Devlin B. 2005. Analysis of Single-Locus Tests to Detect Gene/Disease Associations. Genetic Epidemiology 28 (3) 207-219 (PMID: 15637715)

4、  Johnson TE, Zhang X, Bleicher KB, Dysart G, Loughlin AF, Schaefer WH, Umbenhauer DR. 2004. Statins induce apoptosis in rat and human myotube cultures by inhibiting protein geranylgeranylation but not ubiquinone. Toxicology and Applied Pharmacology 200 (3): 237-250 (PMID: 15504460). 

3、  Parrish ML, Wei N, Duenwald S, Tokiwa GY, Wang Y, Holder DJ, Dai H, Zhang X, Wright C, Hodor P, Cavet G, Phillips R, Sun BI, Fare TL. 2004. A microarray platform comparison for neuroscience applications. Journal of Neuroscience Methods 132: 57-68 (PMID: 14687675).

2、  Zhang X, 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:10.1186/1479-7364-1-1-20; PMID: 15601530 link).

1、  Mao SX and Zhang X. 1999. Gene diversity, gene differentiation coefficients of parent populations and prediction of their F1 heterosis. Journal of Biomathematics 14: 7-11