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:

Xiaoli Wei - Postdoc
Imhoi Koo - Postdoc
Jun Zhang - Postdoc
Bing Wang - Postdoc

Xue Shi - PhD student
Aiqin Fang - PhD student
Shiwen Wu - PhD, visiting student
Yaping Zhao - PhD, visiting student
Wenlong Sun - MS, visiting student

Selected Publications:

1. Zhao, Y.; Zhang, J.; Wang, B.; Kim, S.; Zhang, X. Investigation of metabolite retention indices in two dimensional gas chromatography mass spectrometry. In preparation for Analytical Chemistry.
   
2. Wei, X.; Sun, W.; Wang, B.; Yin, X.; Bogdanov, B.; Zhou, Z., McClain, C.; Zhang, X. LipidSign: a computational platform for high resolution mass spectrometry based lipidomics. In preparation for Analytical Chemistry.
   
3. Kong, L.; Yin, X.; Bogdanov, B.; Zhang, J.; Wang, B.; Nelson, W.; Zhang, X. Identification of three hundred thirty six proteins from the wheat (Triticum Aestivum) proteome using one-dimensional Gel Electrophoresis and reversed phase chromatography coupled with hybrid linear ion trap - Fourier transform mass spectrometry. Submitted.
   
4. Zhang, J.; Wang, B.; Kim, S. H.; Zhang, X.  Optimization enhanced genetic algorithm-support vector regression for the prediction of molecular retention indices in gas chromatography. Submitted.
   
5. 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.
   
6. Wang, B.; Valentine, S.; Plasencia, M.; Raghuraman, S.; Zhang, X. Use of artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. BMC Bioinformatics 2010, 11:182.
   
7. 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.
   
8. 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.
9. Wang, B.; Zhang, X. Evolutionary computation applications in current bioinformatics. New Achievement in Evolutionary Computation 2010, 173-180. [Book Chapter]
10. Wang, B.; Valentine, S.; Plasencia, M.; Zhang, X. Prediction of drift time in ion mobility-mass spectrometry based on peptide molecular weight. Peptide & Protein Letters 2010, 17(9), 1143-1147.
    
11. Wang, B.; Chen, P.; Zhang, J.; Zhao G.; Zhang, X. Inferring protein-protein interactions using a hybrid GA/SVM method. Peptide & Protein Letters 2010, 17(9), 1079-1084.
    
12. 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. Peptide & Protein Letters 2010, 17(9), 1111-1116.
    
13. Zhang, X.; Oh, C.; Riley, C. P.; Buck, C.; Cho, H. Computational approaches to peptide retention time prediction for proteomics. Biological Data Mining 2009, 337-349. [Book Chapter]
14. Culbertson, A. W.; Williams, W. B.; Mckee, A. G.; Zhang, X.; March, K. L.; Naylor, S.; Valentine, S. J. Inside the personalized medicine toolbox: GC×GC-mass spectrometry for high throughput profiling of the human plasma metabolome. LC/GC 2008, 26(6), 560-569.
15. Ralston-Hooper, K.; Baker, S.; Hopf, A.; Oh, C.; Zhang, X.; Adamec, J.; Sepúlveda, M. S. Development of GC-GC/TOF-MS metabolomics for use in ecotoxicological studies with invertebrates. Aquatic Toxicology 2008, 88, 48-52.
    
16. Saha, S.; Harrison, S. H.; Shen, C.; Tang, H.; Radivojac, P.; Arnold, R. J.; Zhang, X.; Chen, J. Y. HIP2: an online database of human plasma proteins from healthy individuals. BMC Medical Genomics 2008, 1:12.
    
17. Zhang, X.; Orcun S.; Ouzzani, M.; Oh, C. Mass informatics in differential proteomics. Encyclopedia of Data Warehousing and Mining - 2nd Edition, 2008, 1176-1181. [Book Chapter]
18. Oh, C.; Huang, X.; Buck, C.; Regnier, E. F.; Zhang, X. Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm. J. Chromatogr. A 2008, 1179, 205-215.
    
19. Zhang, M.; Ouyang, Q.; Stephenson, A.; Kane, M. D.; Salt, D. E.; Prabhakar, S.; Burger, J.; Buck, C.;  Zhang, X. Interactive analysis of ‘omics molecular expression data. BMC Systems Biology 2008, 2:23.
    
20. Shen, C.; Wang, Z.; Shankar, G.; Zhang, X.; Li, L. A hierarchical statistical model to assess the confidence of peptide and protein identifications made by tandem mass spectrometry. Bioinformatics 2008, 24, 202-208.
    
21. Zhang, X.; Oh, C.; Riley, C. P.; Buck, C. Current status of computational approaches for protein identification using tandem mass spectra. Current Proteomics 2007, 4, 121-130.
    
22. Fedulova, I.; Ouyang, Z.; Buck, C.; Zhang, X. PepTiger: search engine for error-tolerant protein identification from de novo sequence tags. The Open Spectroscopy Journal 2007, 1, 1-8.
    
23. Zhang, M.; Zhang, X.; Zhang, X.; Prabhakar, S. Tracing lineage beyond relational operators. 33rd International Conference on Very Large Data Bases University of Vienna, Austria. Sept. 23-28, 2007.
24. Zhao, Y.; Fleet, C. J, Adamec, J.; Terry, D, E, Zhang, X.; Kemeh, S.; Davisson, J. V.; Weaver, M. C. Effects of hindlimb unloading and bisphosphonates on the serum proteome of rats. Bone 2007, 41, 646-658.
    
25. Oh, C.; Zak, S. H.; Mirzaei, H.; Regnier, F. E.; Zhang, X. Neural network prediction of peptide behavior in strong anion exchange chromatography. Bioinformatics 2007, 23, 114-118.
    
26. Qiu, R.; Zhang, X.; Regnier, F. E. A method for the identification of glycoproteins from human serum by a combination of lectin affinity chromatography along with anion exchange and Cu-IMAC selection of tryptic peptides. J. Chromatogr. B.  2007, 845, 143-150. 

Patents:

1. Regnier, F. E.; Ademec, J.; Zhang, X. Digital chromatography. World Intellectual Property Orgnization, WO/2005/011576, Oct. 02, 2005.
2. Regnier, F. E.; Zhang, X.; Chakraborty, A. Affinity selected signature peptides for protein identification and quantification. World Intellectual Property Orgnization, WO/2001/086306, Nov. 15, 2001.