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:

Xue Shi
Juju Xiao
Hai Haba
Xinmin Yin
Yuan Zhang

Recent Publications:

2012

1. 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, in press (DOI: 10.1021/ac301350n).
2. 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.
3. 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.
4. 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.
5. 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.
6. 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]
7. 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]
8. 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.
9. 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.

 
2011

1. 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.
2. 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.
3. 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.
4. 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]
5. 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.
6. 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.
7. 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.
8. 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.
9. 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, China. [Conference paper]
10. 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, China. [Conference paper]
11. 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.
12. Zhang, X. Review on the book “Proteome Bioinformatics” (ISBN 978-1-60761-443-2). Briefings in Bioinformatics 2011, 12, 80-81.
13. 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.