You are here: Home Faculty Pages Xiang Zhang, Ph.D.

Xiang Zhang, Ph.D.

by Andres,Sarah A. last modified Oct 04, 2013 03:23 PM

Associate Professor of Chemistry

Zhang

Email Xiang Zhang

Phone Number: 502-852-8878

Address: University of Louisville

Department of Chemistry

Louisville, KY  40292

Ph.D. Purdue University

 

 


Research Interests:

We exploit practical and efficient high throughput technologies for the analyses of complex mixtures derived from living systems. This will facilitate the development of preventive, predictive, personalized and participatory medicine for specific diseases and will promote health and wellness. We use a number of high throughput analytical platforms including multidimensional liquid chromatography - mass spectrometry (MDLC-MS) for proteomics, multidimensional liquid chromatography - mass spectrometry (MDLC-MS) and two dimensional gas chromatography - mass spectrometry (GC×GC-MS) for metabolomics. Using the high information content data generated from these analytical platforms, we develop advanced bioinformatic algorithms and data analysis tools for the discovery of molecular expression, correlation, and interaction networks in biological systems.

 

Investigators:

  • Dr. Jun Zhang, Post-doc
  • Dr. Bing Wang, Post-doc
  • Dr. Imhoi Koo, Post-doc
  • Dr. Xiaoli Wei, Post-doc
  • Yiaping Zhao, visiting student
  • Shiwen Wu, visiting student
  • Wenlong Sun, visiting student
  • Jiayuan Zhang, visiting student
  • Zijun Wang, visiting student
  • Aiqin Fang, Ph.D. student
  • Xue Shi, Ph.D. student
  • Yuan Zhang, MS student
  • Xinmin Yin, Senior technologist

 Recent Publications:

  1. Phillips, M.; Cataneo, R.N.; Chaturvedi, A.; Kaplan, P.D.; Libardoni, M.; Mundada, M.; Patel, U.; Zhang, X. Detection of an extended human volatome with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. Plos One 2013, accepted on Aug. 15.
  2. Kim, S.; Zhang, X. Comparative analysis of mass spectral similarity measures on peak alignment for two-dimensional gas chromatography mass spectrometry. Computational and Mathematical Methods in Medicine. 2013, 509761.
  3. Schmidt, R.H.; Jokinen, J.D.; Massey, V.L.; Falkner, K.C.; Shi, X.; Yin, X.; Zhang, X.; Beier, J.I.; Arteel, G.E. Olanzapine activates hepatic mammalian target of rapamycin (mTOR): new mechanistic insight into metabolic dysregulation with a typical antipsychotic drugs. J. Pharmacol. Exp. Ther. 2013, DOI:10.1124/jpet.113.207621.
  4. Laulhé, S.; Geers, T.E.; Shi, X.; Zhang, X.; Nantz, M.H. Electron ionization–induced release of coded isotopic reporter ions in an m/z zone of minimal interference for quantifiable, multiplexed GC-MS analyses. Analytical Methods 2013, 5 (18), 4701 - 4706.
  5. Wei, X.; Shi, X.; Koo, I.; Kim, S.; Schmidt, R.H.; Arteel, G.E.; Watson, W.H.; McClain, C.; Zhang, X. MetPP: A computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics. Bioinformatics 2013, 29, 1786-1792.
  6. Wei, X.; Shi, X.; Merrick, M.; Willis, P.; Alonso, D.; Zhang, X. A method of aligning peak lists generated by gas chromatography high-resolution mass spectrometry. Analyst 2013, 138, 5453-5460.
  7. Koo, I.; Kim, S.; Zhang, X. Comparative analysis of mass spectral matching-based compound identification in gas chromatography mass spectrometry. J. Chromatogr. A 2013, 1298, 132-138.
  8. Phillips, M.; Byrnes, R.; Cataneo, R.N.; Chaturvedi, A.; Kaplan, P.; Libardoni, M.; Mehta, V.; Mundada, M.; Patel, U.; Ramakrishna, N.; Schiff, P.; Zhang, X. Detection of volatile biomarkers of therapeutic radiation in breath. J. Breath Res. 2013, 7:036002.
  9. Song, M.; Schuschke, D.A.; Zhou, Z.; Chen, T.; Shi, X.; Zhang, J.; Zhang, X.; Pierce, W.M.; Johnson, T.W.; Vos, M.B.; McClain, C. Modest fructose beverage intake causes liver injury and fat accumulation in marginal copper deficient rats. Obesity 2013, 21(8), 1669-1675.
  10. Wei, X.; Shi, X.; Tang, Y.; Sun, W.; Yin, X.; Sun, X.; Bogdanov, B.; Kim, S.; McClain, C.; Zhou, Z.; Zhang, X. Chronic alcohol exposure disturbs lipid homeostasis at the adipose-liver axis: analysis of triacylglycerols using high-resolution mass spectrometry in combination with in vivo metabolite deuterium labeling. Plos One 2013, 8(2):e55382.
  11. Jeong, J.; Zhang, X.; Shi, X.; Kim, S.; Shen, C. An efficient post-hoc integration method improving peak alignment of metabolomics data from GC×GC/TOF-MS. BMC Bioinformatics 2013, 14:123.
  12. Shi, X.; Yin, X.; Zhang, X. Analysis of mouse liver metabolites on GC×GC-TOF MS. Mass Spectrometry Methods in Metabolomics 2013. [Book Chapter]
  13. Wei, X.; Shi, X.; Kim, S. H.; Zhang, L.; Patrick, J. S.; Binkley, J.; McClain, C.; Zhang, X. A data pre-processing method for liquid chromatography mass spectrometry-based metabolomics. Anal. Chem. 2012, 84, 7963–7971.
  14. Kim, S.; Koo, I.; Jeong, J.; Wu, S.; Shi, X.; Zhang, X. Compound identification using partial and semi-partial correlations for gas chromatography mass spectrometry data. Anal. Chem. 2012, 84, 6477–6487.
  15. Kim, S.; Koo, I.; Wei, X.; Zhang, X. A method of finding optimal weight factors for compound identification in gas chromatography–mass spectrometry. Bioinformatics 2012, 28(8), 1158–1163.
  16. Shi, X.; Wahlang, B.; Wei, X.; Yin, X.; Falkner, K.; Prough, R.; Kim, S.; McClain, C.; Cave, M.; Zhang, X. Metabolomic analysis of the effects of polychlorinated biphenyls in non-alcoholic fatty liver disease. J. Proteome Res. 2012, 11, 3805–3815.
  17. Zhong, W.; Zhao, Y.; Sun, X.; Wei, X.; Shi, X.; Sun, W.; Yin, X.; Sun, X.; Kim, S.; McClain, C. J.; Zhang, X.; Zhou, Z. Chronic alcohol exposure stimulates adipose tissue lipolysis in mice: Role of reverse triglyceride transport in the pathogenesis of alcoholic steatosis. Am. J. Pathol. 2012, 180, 998–1007.
  18. Zhang, C.; Lu, X.; Tan, Y.; Li, B.;  Miao, X.; Jin, L.; Shi, X.; Zhang, X.; Miao, L.; Li, X.; Cai, L. Diabetes-induced hepatic pathogenic damage, inflammation, oxidative stress, and insulin resistance was exacerbated in zinc deficient mouse model. Plos One 2012, 7(12):e49257.
  19. Koo, I.; Zhao, Y.; Zhang, J.; Kim, S.; Zhang, X. A method of calculating the second dimension hold-up time for comprehensive two-dimensional gas chromatography. J. Chromatogr. A 2012, 1260, 193–199.
  20. Zhang, J.; Koo, I.; Wang, B.; Gao, Q.; Zheng, C.; Zhang, X. A large scale test dataset to determine optimal retention index threshold based on three mass spectral similarity measures. J. Chromatogr. A 2012, 1251, 188–193.
  21. Laulhe,S.; Bogdanov, B.; Johannes, L. M.; Gutierrez, O.; Harrison, J. G.; Tantillo, D. J.; Zhang, X.; Nantz, M. H. Fragmentation of oxime and silyl oxime ether odd-electron positive ions by the McLafferty rearrangement: new insights on structural factors that promote α,β-fragmentation. J. Mass Spectrom. 2012, 47(6), 676–686.
  22. Jeong, J.; Shi, X.; Zhang, X.; Kim, S.; Shen, C. Model-based peak alignment of metabolomics profiling from comprehensive two-dimensional gas chromatography mass spectrometry. BMC Bioinformatics 2012, 13:27.
  23. Feutz, M. M.; Riley, P. C.; Zhang, X.; Adamec, J.; Thompson, C.; Couetil, L. L. Proteomic analysis of bronchoalveolar lavage fluid in an equine model of asthma during a natural antigen exposure trial. J. Integrated Omics 2012, 2, 123-131.
  24. Kim, S.; Ouyang, M.; Zhang, X. Compute Spearman correlation coefficient with Matlab/CUDA. IEEE International Symposium on Signal Processing and Information Technology, Dec. 12-15, 2012. Ho Chi Minh City, Vietnam. [Conference paper]
  25. Koo, I.; Zhang, X.; Kim, S. H. Reconstruction of metabolic association networks using high-throughput mass spectrometry data. 2012 International Conference on Intelligent Computing, July 25-29, 2012. Huangsan, Hunan, China. [Conference paper]
  26. Wei, X.; Shi, X.; Kim, S. H.; McClain, C.; Zhang, X. A novel two-stage alignment method for liquid chromatography mass spectrometry-based metabolomics. 2012 International Conference on Intelligent Computing, July 25-29, 2012. Huangsan, Hunan, China. [Conference paper]
  27. Wei, X.; Sun, W.; Shi, X.; Koo, I.; Wang, B.; Yin, X.; Tang, Y.; Bogdanov, B.; Kim, S. H.; Zhou, Z., McClain, C. J.; Zhang, X. MetSign: A computational platform for high-resolution mass spectrometry-based metabolomics. Anal. Chem. 2011, 83, 7668–7675.
  28. Koo, I.; Zhang, X.; Kim, S. Wavelet- and Fourier-Transforms-based spectrum similarity approaches to compound identification in gas chromatography/mass spectrometry. Anal. Chem. 2011, 83, 5631–5638.
  29. Kim, S.; Fang, A.; Wang, B.; Jeong, J.; Zhang, X. An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure. Bioinformatics 2011, 27, 1660–1666.
  30. Zhang, J.; Fang, A.; Wang, B.; Bogdanov, B.; Kim, S. H.; Zhou, Z.; McClain, C.; Zhang, X. iMatch, A retention index tool for analysis of gas chromatography mass spectrometry data. J. Chromatogr. A 2011, 1218, 6522–6530.
  31. Zhao, Y.; Zhang, J.; Wang, B.; Kim, S.; Fang, A.; Bogdanov, B.; Zhou, Z.; McClain, C.; Zhang, X. A method of calculating the second dimension retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. J. Chromatogr. A 2011, 1218, 2577–2583.
  32. Jeong, J.; Shi, X.; Zhang, X; Kim, S.; Shen, C. An empirical Bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry. BMC Bioinformatics 2011, 12:392.
  33. Kim, S.; Koo, I.; Fang, A.; Zhang, X. Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry. BMC Bioinformatics 2011, 12:235.
  34. Riley, C. P.; Zhang, X.; Nakshatri, H.; Schneider, B.; Regnier, F. E.; Adamec, J.; Buck, C.  A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples. J. Transl. Med. 2011, 9:80.
  35. Zhao, Y.; Tan, Y.; Dai, J.; Li,  B.; Guo, L.; Cui, J.; Wang, G.; Shi, X.; Zhang, X.; Mellen, N.; Li, W.; Cai, L. Exacerbation of diabetes-induced testicular apoptosis by zinc deficiency is most likely associated with oxidative stress; p38 MAPK activation; and p53 activation in mice. Toxicol. Lett. 2011, 200, 100–106.
  36. Wang, B.; Fang, A.; Shi, X.; Kim, S.; Zhang, X. A comprehensive peak alignment algorithm for two-dimensional gas chromatography time-of-flight mass spectrometry. 2011 International Conference on Intelligent Computing, Aug 11-14, 2011. Zhengzhou, Henan, China. [Conference paper]
  37. Koo, I.; Zhang, X.; Kim, S. Comparison of spectral similarity measures for compound identification. The 5th International Conference on Bioinformatics and Biomedical Engineering, May 10-12, 2011. Wuhan, Hubei, China. [Conference paper]
  38. Chen, Y.T.; Zhang, J.; Zhang, X.; Kim, S. Statistical analysis of gas chromatography retention index database. The 5th International Conference Bioinformatics and Biomedical Engineering, May 10-12, 2011. Wuhan, Hubei, China. [Conference paper]
  39. Zhang, X. Review on the book “Proteome Bioinformatics” (ISBN 978-1-60761-443-2). Briefings in Bioinformatics 2011, 12, 80-81.
  40. Wang, B.; Fang, A.; Heim, J.; Bogdanov, B.; Pugh, S.; Libardoni, M.; Zhang, X. DISCO: distance and spectrum correlation optimization alignment for two dimensional gas chromatography time-of-flight mass spectrometry - based metabolomics. Anal. Chem. 2010, 82, 5069–5081.
  41. Wang, B.; Valentine, S.; Plasencia, M.; Raghuraman, S.; Zhang, X. Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. BMC Bioinformatics 2010, 11:182.
  42. Zhang, X.; Fang, A.; Riley, C. P.; Wang, M.; Regnier, F. E. Buck, C. Multi-dimensional liquid chromatography in quantitative proteomics. Anal. Chimica Acta 2010, 664, 101–113.
  43. Riley, P. C.; Gough, S. E.; He, J.; Jandhyala, S. S.; Kennedy, B.; Orcun, S.; Ouzzani, M.; Buck, C.; Roumani, A.M.; Zhang, X.  The Proteome Discovery Pipeline – A data analysis pipeline for mass spectrometry-based differential proteomics discovery. The Open Proteomics Journal 2010, 3, 8–19.
  44. Wang, B.; Valentine, S.; Plasencia, M.; Zhang, X. Prediction of drift time in ion mobility-mass spectrometry based on peptide molecular weight. Protein & Peptide Letters 2010, 17(9), 1143–1147.
  45. Wang, B.; Chen, P.; Zhang, J.; Zhao G.; Zhang, X. Inferring protein-protein interactions using a hybrid GA/SVM method. Protein & Peptide Letters 2010, 17(9), 1079 –1084.
  46. Wang, B.; Chen, P.; Wang, P.; Zhao, G.; Zhang, X. Construction of radial basis function neural networks optimized by expectation maximization algorithm for predicting protein-protein interaction sites. Protein & Peptide Letters 2010, 17(9), 1111–1116.
  47. Wang, B.; Zhang, X. Evolutionary computation applications in current bioinformatics. New Achievement in Evolutionary Computation 2010, 173–180. [Book Chapter]
  48. Zhang, J.; Wang, B.; Zhang, X. Optimal selection of support vector regression parameters and molecular descriptors for retention indices prediction. Advanced Intelligent Computing Theories and Applications with Aspects of Artificial Intelligence. Aug. 18–21, 2010, Changsha, Hunan, China. [Conference paper]

 

 

Document Actions
Personal tools