Integrative & Quantitative Biology Group
Xujing Wang, PhD
With the progress of the Human Genome Project, the technology and bioinformatics advancements in genetic studies provide many new approaches for the investigation of human diseases. However, for polygenic complex disorders like type 1 diabetes where the exact disease etiology and pathogenesis is still not known, identification of all disease genes has not been easy. We think that understanding the dynamics of biological processes is crucial in a disease study, as a biological system is not just an assembly of genes and proteins, and the complexity of the biological processes underlying a disease cannot be fully understood by merely cataloging the genes and proteins involved. We need to understand the underlying principles and design. A mathematical formulation will allow a comprehensive investigation of all factors involved, and is able to reveal the non-intuitive characteristics of the system.
We currently have several projects along this general direction. (1) Genetic regulatory network modeling and inference from microarray data, including the transcription regulation using Bayesian network models and binding potential approaches. (2) Mathematical modeling in type 1 diabetes, which includes the dynamic analysis of disease processes, identification of disease-relevant gene regulation pathways, and the glucose-insulin response and dynamics. (3) Integrating the microarray studies and dynamic modeling to identify disease genes in diabetes, and applying such approaches to our genetic linkage and association studies of diabetes. The overall goal is to develop new systems biology approaches for human genetic disease research.
For more information, please visit my Integrative and Quantitative Biology Homepage.
Journal publications/Original Papers:
Geoffrey, R., Jia, S., Kwitek, A.E., Woodliff, J., Ghosh, S., Lernmark, A., Wang X., Hessner M.J.,: Evidence of a Functional Role for Mast Cells in the Development of Type 1 Diabetes Mellitus in the BioBreeding Rat. J. Immunol., Nov.; 177:7275-7286, 2006.
Wang, X., He, Z., Ghosh, S.,: Investigation of the age-at-onset heterogeneity in type 1 diabetes through mathematical modeling. Mathematical Biosciences, 203(1):79-99, 2006.
Smith, E.M., Wang, X., Littrell, J., Eckert, J., Cole, R., Kissebah, A.H., Olivier, M., Comparison of linkage disequilibrium patterns between the HapMap CEPH samples and a family-based cohort of Northern-European descent. Genomics, 88(4):407-14, 2006.
Nittala, A., Ghosh, S., Stefanovski, D., Bergman, R., Wang, X.,: Dimensional analysis of MINMOD leads to definition of the disposition index and improved simulation algorithm. Biomedical Engineering Online. 5(44): doi:10.1186/1475-925X-5-44, 2006.
Guo, S.-W., Magnuson, V.L., Schiller, J.J., Wang, X., Wu, Y., Ghosh, S. Meta-Analysis of Vitamin D Receptor Polymorphisms and Type 1 Diabetes: A HuGE Review of Genetic Association Studies. Am J Epidemiol., Oct. 15; 164(8):711-24, 2006.
Wang, X., Jia, S., Xiang, B., Jiang, N., Meyer, L., Chen, Li.-Y., Moreno-Quinn, C. Ghosh, S. Jacob, H.J., Hessner. M.J. Accurate gene expression measurements by cDNA microarrays utilizing TDAV. BMC bioinformatics. 7(1):378, 2006.
Hessner, M.J., Xiang, B., Jia, S., Geoffrey, R., Holmes, S., Meyer, L., Muheisen, S., Wang, X. Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms. Physiol Genomics. 25(1): 166-78, 2006.
Wu, Y., Kajdacsy-Balla, A., Strawn, E., Basir, Gloria Halverson Z., Jailwala, P., Wang, Y., Wang, X., Ghosh, S., Guo, S.-W. Transcriptional characterizations of differences between eutopic and ectopic endometrium. Endocrinology, 147:232-246, 2006.
Yang, J., Wang, X., Greene, S., Hessner M.J., Wolf, B.A., Gao, Z. Leucine increases pancreatic beta cell sensitivity to glucose via up-regulation of ATP synthase. Journal of Biological Chemistry, 279:53915-53923, 2004.
Hessner, M.J., Wang, X., Meyer, L. Geoffrey, R., Jia, S., Fuller, J., Lernmark, A., Ghosh, S. Microarray analysis reveals involvement of eosinophils, eotaxin, and underlying pancreatic stress in the prediabetic BioBreeding (BB) rat. Journal of Immunology, 173: 6993-7002, 2004.
Olivier, M., Wang, X., Pennacchio, L.A., Cole, R., Gau, B., Kim J., Rubin, E.M. Hyplotype analysis of the apolipoprotein gene cluster on human chromosome 11. Genomics, 83:912-923, 2004.
Hessner, M. J., Meyer, L., Tackes, J., Muheisen, S., Wang, X. Immobilized support-bound probe and glass surface chemistry as variables in microarray fabrication. BMC genomics, 5:53, 2004.
Hessner, M.J., Singh, V.K., Wang, X., Khan, S., Tschannen, M.R., Zahrt, T.C.,Utilization of Labeled Tracking Oligonucleotide for Visualization and Quality Control of Spotted 70-mer Arrays. BMC genomics, 5:12, 2004.
Wang, X., Jiang, N., Feng, X., Xie, Y., Tonellato, P.J., Ghosh, S., Hessner, M.J. A novel approach for high quality microarray processing using third-dye array visualization technology. IEEE trans. Nanobioscience, 4(2):193, 2003.
Tatay, J.W., Feng, X., Sobczak, H., Jiang, N., Chen, C.F., Kirova, R., Struble, C., Jiang, N., Wang, X., Tonellato, P.J. Multiple approach to data mining of proteomic data based on statistical and pattern classification methods. Proteomics, 3(9):1704-1709, 2003.
Waukau, J., Jailwala, P., Wang, Y., Khoo, H., Ghosh, S., Wang, X., Hessner, M.J. The design of a gene chip for functional immunological studies on a high-quality control platform. Annals of the New York Academy of Sciences. 1005:284, 2003.
Pati, N., Ghosh, S., Hessner, M.J., Khoo H., and Wang, X. Difference in Gene Expression Profiles Between Fresh Human CD4+CD25+ and CD4+CD25- T Cells. Annals of the New York Academy of Sciences. 1005:279, 2003.
Hessner, M.J., Wang, X., Khan, S., Meyer, L., Schlicht, M., Tackes, J., Datta, M., Jacob, H.J., Ghosh, S. Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. Nucl. Acids. Res. 31: e60, 2003.
Wang, X., Hessner, M.J., Wu, Y., Pati, N., Ghosh, S. Quantitative quality control in microarray experiment and the application in data filtering, normalization and false positive rate prediction. Bioinformatics, 19:1341-1347, 2003.
Hessner, M.J., Wang, X., Hulse K., Meyer L., Wu, Y., Nye S., Guo S.-W., Ghosh S. Three color cDNA microarrays: quantitative assessment through the use of Fluorescein-Labeled Probes. Nucl. Acids. Res., 31(4): e14, 2003.
Wang, X., Becker, F.F., Gascoyne, P.R.C. Alterations in membrane dielectric responses precede surface expression of PS or DNA-fragmentation in apoptotic HL-60 cells. Biphys. Biochem. Acta. 1564(2):412-420, 2002.
Wang, Y., Wang, X., Ghosh, S., Guo, S.-W. Is hybridization truly competitive in two-color cDNA microarray experiments? A theoretical modeling and its implications. BioTechniques 32:1342-1346, 2002.
Wang, X., Ghosh, S., Guo, S.-W. Quantitative quality control in microarray image processing and data acquisition. Nucl. Acids. Res. 29(15):e75, 2001.
Yang, J., Huang, Y., Wang, X., Becker, F.F., Gascoyne, P.R.C. Dielectric Properties of Human Leukocyte Subpopulations determined by Electrorotation as a Cell Separation Criterion. Biophys. J. 76: 3307-3314, 1999.
Wang, X., Yang, J., Gascoyne, P.R.C. Role of peroxide in AC electrical field exposure effects on Friend murine erythroleukemia cells during dielectrophoretic manipulations. Biochim. Biophys. Acta 1426(1): 53-68, 1999.
Wang, X., Wang, X.-B., Gascoyne, P.R.C. General expressions for dielectrophoretic force and electrorotational torque derived using the Maxwell Stress Tensor method. J. Electrosta. 39:277-295, 1997.
Wang, X.-B., Huang, Y., Wang, X., Becker, F.F., Gascoyne, P.R.C. Dielectrophoretic manipulation of cells with spiral electrodes. Biophys. J. 72:1887-1899, 1997.
Wang, X., Wang, X.-B., Gascoyne, P.R.C., Becker, F.F. A theoretical method of electrical field analysis for dielectrophoretic electrode arrays using Green's theorem. J. Phys. D. 29:1649-1660, 1996.
Jacques, S.L., Wang, X. Path integral description of light transport in tissue. In Proceedings of the Society for Photon-Optical Instrumentation Engineers. 2979:488-499, 1997.
Publications below were in the field of theoretical physics, which has a tradition of listing authors in alphabetical orders based on last names. In terms of contribution, X. Wang deserves first authorship in all highlighted in blue.
Khviengia, Z., Lu, H., Pope, C.N., Sezgin, E. Wang, X., Xu. K. N=1 superstring theory in 2+2 dimensions. Nucl. Phys. B444:468, 1995.
Lu, H., Pope, C.N., Thielemans, K., Wang, X., Xu. K. Quantising higher-spin string theories. Int. J. Mod. Phys. A10:2123-2142, 1995.
Lu, H., Pope, C.N., Wang, X., Zhao, S. A note on W2,s strings. Phys. Lett. 327B:241, 1994.
Lu, H., Pope, C.N., Wang, X., Zhao, S. Critical and non-critical W2,4 strings. Class. Quantum Grav. 11:939, 1994.
Lu, H., Pope, C.N., Wang, X., Xu. K. The complete cohomology of the W3 string. Class. Quantum Grav. 11:967, 1994.
Lu, H., Pope, C.N., Thielemans, K., Wang, X. Higher-spin strings and W minimal models. Class. Quantum Grav. 11:119, 1994.
Lu, H., Pope, C.N., Wang, X. On higher-spin generalisations of string theory. Int. J. Mod. Phys. A9: 527, 1994.
Lu, H., Pope, C.N., Schrans. S., Wang, X. On the spectrum and scattering of W3 strings. Nucl. Phys. B403:351, 1993.
Lu, H., Pope, C.N., Schrans. S., Wang, X. The interacting W3 string. Nucl. Phys. B403:351, 1993.
Pope, C.N., Sezgin, E., Stelle, K.S., Wang, X. Discrete states in the W3 string. Phys. Lett. 299B:247, 1993.
Lu, H., Pope, C.N., Wang, X., Xu. K. Aspects of N=2 super-Wn strings. Int. J. Mod. Phys. A8:351, 1993.
Lu, H., Pope, C.N., Schrans. S., Wang, X. New realisations of W algebras and W strings. Mod. Phys. Lett. A7:1835, 1992.
Lu, H., Pope, C.N., Schrans. S., Wang, X. On sibling and exceptional W strings. Nucl. Phys. B379:47, 1992.
Lu, H., Pope, C.N., Wang, X., Xu. K. N=2 superstrings with (1,2m) spacetime signature. Phys. Lett. 284B:268, 1992.
Lu, H., Pope, C.N., Wang, X., Xu. K. Anomaly freedom and realisations for super-W3 strings. Nucl. Phys. B379:24, 1992.
Shen, X., Wang, X . Bosonisation of the complex-boson realisations of Winf. Phys. Lett. 278B:63, 1992.
Lu, H., Pope, C.N., Shen, X., Wang, X. The complete structure of WNfrom Winf. Phys. Lett. 267B:356, 1991.
Lu, H., Pope, C.N., Romans, L.J., Shen, X., Wang, X. Polyakov construction of the N=2 super-W3 algebra. Phys. Lett. 264B:91, 1991.
BOOK CHAPTER & REVIEWS
Jia, S., Gao, S., Hessner, M.J., Wang, X. Acquisition of accurate gene expression information from microarray measurements. In Current Trends in Genetic Research, World Scientific Publishing. 2006.
Wang, X., Hessner, M.J. Quantitative quality control of microarray experiments: toward accurate gene expression measurements. In Gene expression profiling by microarrays – clinical implications. Cambridge Press, 2006.
Hessner, M.J., Wang, X., Ghosh S. Genetics of Type 1 Diabetes, A chapter for: Diabetes Mellitus: A Fundamental and Clinical Text. Editors: LeRoith D., Taylor S.I. and Olefsky J.M. Lippincott Williams & Wilkins Publishers, 2004.