Xiang Zhang, Ph.D.

Associate Professor
Department of Chemistry

Belknap Research Building, rm 349

2210 S. Brook Street
University of Louisville
xiang.zhang@louisville.edu

Areas of Research Interest:

We are interested in multidisciplinary life sciences research. The ultimate goal of our research is to integrate experimental and computational approaches for better understanding of living systems. Our bioanalytical research exploits practical and efficient high-throughput technologies for the analyses of complex mixtures derived from living systems. This will facilitate the development of preventive, predictive and personalized 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, inductively coupled plasma - mass spectrometry (ICP-MS) for analyses of physiologically relevant elements, and for metabolomics; liquid chromatography - mass spectrometry (LC-MS), two dimensional gas chromatography - mass spectrometry (GCxGC/TOF-MS) and  nuclear  magnetic resonance (NMR). Each type of analysis affords limited analyte coverage of molecules present in a patient sample and therefore provides only a partial molecular profile for an individual patient. These diverse analytical data must be integrated with advanced bioinformatics methods for accurate evaluation of health and detection of disease susceptibility.

Our long term goal for bioinformatics research is to develop a complete system that enables mining of high throughput data for identification of molecular networks and ‘systems level’ knowledge assembly. An integrated data mining pipeline for metabolomics is one of our projects that provides metabolite identification, quantification, pattern recognition, and description of metabolite networks. We are also developing innovative bioinformatics tools for protein identification, quantification, and verification. Diverse data integration and knowledge assembly is another of our bioinformatics research areas. We are developing informatics tools to integrate scientific information extracted from biological databases by achieving a virtual integration of those databases.

Student training is a core goal in our group. Our philosophy is for everyone in the group to contribute to our overall knowledge and understanding of the biological systems under study. Due to the multidisciplinary nature of our research, we accept that the goals, backgrounds, and interests of students will differ. Depending on the student's interest, s/he can choose to focus on either bioanalytical method development or bioinformatics. However, students are always highly encouraged to interact and collaborate with others within or outside of the group.

Recent Publications.

Zhang, X.; Orcun S.; Ouzzani, M.; Oh, C. Mass informatics in differential proteomics. Encyclopedia of Data Warehousing and Mining - 2^nd Edition. 

Culbertson, A. W.; Williams, W. B.; Mckee, A. G.; Zhang, X.; March, K. L.; Naylor, S.; Stephen J.;  Valentine, S. J. Inside the personalized medicine toolbox: GC×GC-mass spectrometry for high throughput profiling of the human plasma metabolome. LC/GC in press.

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.

Zhang, M.; Ouyang, Q.; Stephenson, A.; Kane, M. D.; Salt, D. E.; Prabhakar, S.; Buck, C.;  Zhang, X. Interactive analysis of ‘omics molecular expression data. BMC Systems Biology accepted.

Ralston-Hooper, K.; Baker, S.; Hopf, A.; Oh, C.; Zhang, X.; Adamec, J.; Sepúlveda, M. S. Development of GC-GC-MS metabolomics for biomarker identification in vertebrate and invertebrate species exposed to environmental stressors. Environmental Toxicology and Chemistry, submitted.

Riley, C. B.; Adamec, J.; Zhang, X.; Walls, E. K.; Lloyd, F.; Buck, C. R.; Mohammed, S. I. Proteomic profile of lymph in metastatic breast cancer. Biomarker Insight in press.

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.

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.

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.

Zhang, M.; Zhang, X.; Zhang, X.; Prabhakar, S. Tracing lineage beyond relational operators. 33^rd International Conference on Very Large Data Bases University of Vienna, Austria. Sept. 23-28, 2007.

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.

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.

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.

Pevtsov, S.; Fedulova, I.; Mirzaei, H.; Buck, C.; Zhang, X. Performance evaluation of existing de novo sequencing algorithms. J. Proteome Res. 2006, 5, 3018-3028.

Asara, J. M.; Zhang, X.; Zheng, B.; Christofk, H. H.; Wu, N.; Cantley, L. C. In­-gel stable isotope labeling for relative quantification using mass spectrometry. Nature Protocols 2006, 1, 46-51.

Asara, J. M.; Zhang, X.; Zheng, B.; Christofk, H. H.; Wu, N.; Cantley, L. C. In-­gel stable isotope labeling: a strategy for mass spectrometry based relative quantification. J. Proteome Res. 2006, 5, 155-163.

Zhang, X.; Asara, J. M.; Adamec, J.; Ouzzani, M.;  Elmagarmid, A. K. Data pre­processing in liquid chromatography­ mass spectrometry based proteomics. Bioinformatics 2005, 21, 4054­-4059.

Ouzzani, M.; Aref, W. G.; Bertino, E.; Christine, A. C.; Clifton, C. W.; Hon, W.; Elmagarmid, A. K.; Ghafoor, A.; HambruschS. E.; Prabhakar, S.; Vitter, J.; Zhang, X. The Indiana Center for Database Systems at Purdue University. SIGMOD Record 2005, 34, 53­-58.

Zhang, X.; Hines, W.; Adamec, J.; Asara, J.; Naylor, S.; Regnier, F. E. An automated method for the analysis of stable isotope labeling data for proteomics. J. Am. Soc. Mass Spectrom. 2005, 16, 1181-­1191.

Davidov, E.; Clish, C. B.; Oresic, M.; Meys, M.; Stochaj, W.; Snell, P.; Lavine, G.; Londo, T. R.; Adourian, A.; Zhang, X.; Johnston, M.; Morel, N.; Marple, E. W.; Plasterer, T. N.; Neumann, E.; Verheij, E.; Vogels, J, T.W.E.; Havekes, L. M.; Greef, J.; Naylor, S. Methods for the differential integrative omics analysis of plasma from a transgenic disease animal model. Omics: A Journal of Integrative Biology  2004, 8, 267-­288.

Clish, C. B.; Davidov, E.; Oresic, M.; Plasterer, T.; Lavine, G.; Londo, T. R.; Meys, M.; Snell, P.; Stochaj, W.; Adourian, A.; Zhang, X.; Morel, N.; Neumann, E.; Verheij, E.; Vogels, J, T.W.E.; Havekes, L. M.; Afeyan, N.; Regnier, F. E.; Greef, J.; Naylor, S. Integrative biological analysis of the APOE*3­ Leiden transgenic mouse. Omics: A Journal of Integrative Biology  2004, 8, 3­-13.

Wang, S.; Zhang, X.; Regnier, F. E. Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates. J. Chromatogr. A.  2002, 949, 153­-162.

Regnier, F. E.; Zhang, X.; Chakraborty, A. Affinity selected signature peptides for protein identification and quantification. World Intellectual Property Orgnization, WO0186306, Nov. 15, 2001.

Regnier, F. E.; Amini, A.; Chakraborty, A.; Geng, M.; Ji, J.; Riggs, L.; Sioma, C.; Wang, S.; Zhang, X. Multidimensional chromatography and the signature peptide approach to proteomics. LC/GC 2001, 19, 200-­213.

Geng, M.; Zhang, X.; Bina, M.; Regnier, F. E. Proteomics of glycoproteins based on affinity selection of glycopeptides from tryptic digests. J. Chromatogr. B. 2001, 752, 293-­306.

He, B.; Burke, J.; B.; Zhang, X.; Zhang, R.; Regnier, F. E. A picoliter volume mixer for microfluidic analytical systems. Anal. Chem. 2001, 73, 1942-­1947.

Wang, X.; Tian, J.; Yin, X.; Zhang, X.; Qin, Z.; Li, Z.; Wang, Q.; Li, S. Distribution of trace elements in normal and tumor-bearing mice using the multitracer technique. Biological Trace Element Research 2001, 81, 177-183.

Ji, J.; Chakraborty, A.; Geng M.; Zhang, X.; Amini, A.; Bina, M.; Regnier, F. E. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J. Chromatogr. A 2000, 745, 197­-210.

Zhang, X.; Regnier, F. E. Analysis of channel effects on separation efficiency in rectangular­capillary electrochromatography columns. J. Chromatogr. A. 2000, 869, 319-­328.

Wang, X.; Tian, J.; Yin, X.; Zhang, X.; Wang, Q. The excretion of biotrace elements using the multitracer technique in tumor-bearing mice. Applied Radiation and Isotopes 2000, 53, 969-974.

Li, W.; Yin, X.; Zhang, X.; Sun, T.; Qin, Z.; Ambe, S.; Ohkubo, Y.; Ambe, F. Projectile-mass dependence of the linear momentum transfer in central collisions. J. Radioanal. Nucl. Chem. 2000, 243, 797-801.

Wang, X.; Yin, X.; Zhang, X.; Li, Z.; Tian J.; Wu, M.; Sheng, X. Excretion of biotrace elements using the multitracer technique in mice. J. Radioanal. Nucl. Chem. 1999, 240, 963-­967.

Yin, X.; Wang, X.; Zhang, X.; Li, W.; Tao, Z.; Du, J. Preparation of a radioactive multitracer solution from the reaction of selenium with 25 Mev/nucleon ⁴⁰Ar ions. J. Radioanal. Nucl. Chem. 1997, 221, 225­-226.

Yin, X.; Zhang, X.; Sun, T.; Qin, Z.; Zhao, L. Preparation of multi­tracer from the interaction of selenium with 25 MeV/A ⁴⁰Ar ions. J. Nucl. Tech. 1997, 20, 382-­384.

Du, J.; Yin, X.; Wang, X.; Dai, X.; Zhang, X.; Sun, T.; Tao, Z. Adsorption study of 47 elements on alumine and bentonite using a multitracer technique. Adsorption Science and Technology 1997, 15, 341­-347.

Sun, T.; Li, W.; Wu, D.; Yin, X.; Zhao, L.; Zhang, X.; Qin, Z.; Zheng, J.; Liu, G.; Jing, G. Target residues from interaction of ¹⁹⁷Au with 8­~24 MeV/nucleon ⁴⁰Ar ions. J. Nucl. Radiochem. 1997, 19, 49­-54.

Zhang, X.; Yin, X.; Li, W.; Sun T.; Qin, Z.; Zhao L.; Wu D. Production of hafnium nuclides in the rections of 6.3­~24.5 MeV/nucleon ⁴⁰Ar ions with nature tungsten. Radiochem. Acta 1996, 75, 7-­10.

Yin, X.; Du, J.; Zhang, X.; Wang, X.; Dai, X.; Sun, T.; Tao, Z. Preparation of multitracer nuclides from UO₂(NO₃)₂ irradiated by ⁴⁰Ar ion beam. J. Radioanal. Nucl. Chem. 1996, 214, 89-­94.

Qin, Z.; Li, W.; Yin, X.; Zhang, X. , Sun, T.; Zhao, L.; Wang, X. Multitracer technique and prospects of its application. TREND in Nucl. Phys. 1996, 13, 31-34.

Zhang, X.; Li, W.; Sun, T.; Yin, X.; Qin, Z.; Zhao, L.; Wu, D.; Zheng, J.; Liu, G. Production of hafnium isotopes from interaction of ^natW with 6.3~­24.6 MeV/u ⁴⁰Ar ions. J. High­ Energy Phys. Nucl. Phys. 1996, 20, 21-­25.

Qin, Z.; Li, W.; Sun, T.; Zhao, L.; Zhang, X.; Yin, X.; Wu, D.; Zhen, J.; Liu, G.; Zhao, Z. Target residues from the interaction of natural uranium target with 20 MeV/nucleon ⁴⁰Ar ions. J. Nucl. Radiochem, 1996, 18, 229-­233.

Li, W.; Sun, T.; Wu, D.; Sun, R.; Zhao, L.; Yin, X.; Zhang, X.; Luo, Q.; Zhang, F.; Jin, G. Target residues from the interaction of copper with 20~­46 MeV/nucleon ¹²C ions. Radiochim. Acta 1996, 72, 109-­119.

Liu, G.; Cheng, K.; Yu, X.; Zheng, J.; Jin, W.; Sun T.; Wu, D.; Zhao, L.; Zhang, X.; Yin, X.;  Qin, Z. Fragment angular distributions for ⁴⁰Ar + ¹⁹⁷Au reaction. Chin. J. Nucl. Phys. 1995, 17, 21-­23.

Zhang, X.; Li, W.; Yin, X.; Wen, W.; Sun, T.; Jin, G.;  Luo, Q. Mass yield distribution in intermediate energy heavy ion reactions. Chinese J. Nucl. Phys. 1995, 17, 247­-249.

Zhang, X.; Li, W.; Yin, X.; Sun, T.; Ambe, S.; Ohkubo, Y.; Iwamoto, M.; Kobyashi, Y.; Maeda, H.;  Ambe, F. Isotopic distributions of Hf from the interaction of heavy ions with W. J. Nucl. Radiochem. 1995, 17, 193-­197.

Yang, W.; Yuan, S.; Mou, W.; Zhang, X.; Li, Z.; Yu, X.; Gan, Z.; Liu, H.; Guo, Y.; Zhang, J.; Lei, X.; Guo, J.; Du, Y.; Zhao, L.;  Zhang, X. A new heavy neutron-rich isotope ²³⁹Pa. J. High­ Energy Phys. Nucl. Phys. 1995, 19, 479-480.

Zhang, X.; Yin, X.; Li, W.; Qin, Z.; Zhao, L.; Wu, D.; Sun, T. Study on the adsorption behavior of fission products on mud and sand in Yellow River using multitracer. J. Nucl. Radiochem. 1995, 17, 60­-64.

Yin, X.; Li, W.; Zhang, X.; Sun, T.; Ambe, S.; Ohkubo, Y.; Iwamoto, M.; Kobyashi, Y.; Maeda, H.;  Ambe, F. Target residues from the interaction of copper with 40 MeV/u ⁴⁰Ar ions. J. High ­Energy Phys. Nucl. Phys. 1995, 19, 991­-997.

Liu, G.; Cheng, K.; Yu, X.; Zheng, J.; Jin, W.; Sun T.; Wu, D.; Zhao, L.; Zhang, X.; Yin, X.; Qin, Z.  Fragment angular distributions of the 600 Mev ⁴⁰Ar + ¹⁹⁷Au reaction. J. High ­Energy Phys. Nucl. Phys. 1995, 19, 305-­309.