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Thomas Jefferson University - Gregory E. Gonye, Ph.D.
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Gregory E. Gonye, Ph.D.
Pathology, Anatomy and Cell Biology
Thomas Jefferson University
Jefferson Medical College and the
College of Graduate Studies
Research Assistant Professor
Daniel Baugh Institute for Functional Genomics/Computational Biology
Farber Institute for Neurosciences
Cell and Developmental Biology Graduate Program
Neuroscience Graduate Program
Genetics Graduate Program
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Mailing Address
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Rm 381 JAH 1020 Locust St
Philadelphia, Pennsylvania 19107
United States
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Qualifications
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B.S., University of Massachusetts Amherst, Biochemistry, 1985
B.S., University of Massachusetts Amherst, Microbiology, 1985
Ph.D., University of Connecticut, Molecular Biology and Biochemistry, 1993
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Expertise and Research Interests
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My research uses the study of neuropeptide receptor-dependent transcription regulation networks in an attempt to understand how neuropeptides modulate neuronal function and how neurons distinguish one neuropeptide from another with such very high fidelity. Neuropeptides are involved in nearly all medically important physiological processes and are best known for their role in blood pressure regulation, sleep, pain, appetite, stress, libido, drug addiction, and depression.
We use a system level approach that incorporates highly parallel gene expression measurements (using microarrays), transcription factor studies (chromatin immunoprecipitation) and computational approaches including bioinformatics and modeling and simulation. This has lead to a number of collaborations in cancer and neuroscience.
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Keywords
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Angiotensin II; Central Nervous System; Functional Genomics: Systems Biology; Health And Medicine; Hypertension; Neuroanatomy; Neurological Disorders; Neuropeptides; Neuropharmacology; Neurotransmitters; Receptors; Transcription Regulation
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Publications
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- Brown L.J., Gonye G.E., and Schwaber J.S., 1999. Non-Linear PI Control Inspired by Biological Control Systems. Proceedings of the 37th IEEE Conference on Decision and Control: 1040-1045.
- Brown L.J., Gonye G.E., and Schwaber J.S., 1999. Non-Linear PI Control Inspired by Biological Control Systems. Advances in Neural Information Processing Systems 11: 975-981.
- Jia, M.H., LaRossa, R.A., Lee, J-M., Rafalski, A., DeRose, E.J., Gonye, G.E., and Xue, Z. 2000. Global Expression Profiling of Yeast Treated with Sulfometuron Methyl, an Inhibitor of Amino Acid Biosynthesis. Physiological Genomics, 3: 83-92.
- Van Dyk, T.K., DeRose, E.J., and Gonye, G.E. 2001. LuxArray, a high-density, genome-wide transcription analysis of Escherichia coli using bioluminescent reporter strains. J. Bacteriology, 183(19):5496-5505.
- Zak, D.E., Doyle, F.J. 3rd, Gonye, G.E., and Schwaber, J.S. 2001. Simulation studies for the identification of genetic networks from cDNA array and regulatory activity data. Proceedings of the Second International Conference on Systems Biology: pp 231-238.
- Pearson, R.K., Gonye, G.E., and Schwaber, J.S., 2003. Outliers in microarray data analysis. In: Johnson, K. and Lin, S. (eds) Methods of Microarray Data Analysis , 41-55. .Kluwer Academic Publishers, Boston.
- Zak D.E., Gonye G.E., Schwaber J.S., and Doyle F.J. III. 2003. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from the identifiability analysis of an in silico network. Genome Research, 13(11):2396-405.
- Zak D.E., Pearson R.K., Vadigepalli R., Gonye G.E., and Schwaber J.S., Doyle F.J. 3rd., 2003. Continuous-time identification of gene expression models. Omics. 7(4):373-86.
- Vadigepalli R., Chakravarthula P., Zak D.E., Schwaber J.S., and Gonye G.E. 2003. PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification. Omics. 7(3):235-52.
- Gonye, G.E., Hanafey, M.K., LaRossa, R.A., Rafalski; J.A. and Van Dyk, T.K. 2004. Cellular arrays for the identification of altered gene expression. U.S. Patent 6,716,582.
- Addya S., Keller M.A., Delgrasso, K., Ponte, C.M., Vadigepalli, R., Gonye, G.E. and Surrey, S. 2004. Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements. Physiological Genomics 19:117-130.
- Zak, D.E., Vadigepalli, R., Gonye, G.E., Doyle, F.J. 3rd, Schwaber, J.S., and Ogunnaike, B.A. 2004. Unconventional systems analysis problems in molecular biology: a case study in gene regulatory network modeling. Computers and Chemical Engineering 29: 547-563.
- Pearson, R.K., Zylkin T., Schwaber, J.S., and Gonye G.E. 2004. Quantitative evaluation of clustering results using computational negative controls. Proceedings of the Fourth Society for Industrial and Applied Mathematics International Conference on Data Mining.
- Vadigepalli, R., Chakravarthula, P., Zak, D.E., Schwaber, J.S. and Gonye, G.E. 2004. Transcription Regulatory Network Analysis using PAINT: Promoter Analysis and Interaction Network Tool. Proceedings of the Fourth Society for Industrial and Applied Mathematics International Conference on Data Mining.
- Vadigepalli R., Chakravarthula P., Zak D.E., Schwaber J.S., and Gonye G.E. 2004. Transcription regulatory network analysis using PAINT: Promoter Analysis and Interaction Network Tool. Proceedings of Fourth Society for Industrial and Applied Mathematics International Conference on Data Mining.
- Addya S., Keller M.A., Delgrasso, K., Ponte, C.M., Vadigepalli, R., Gonye, G.E. and Surrey, S. 2004. Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements. Physiological Genomics, 19: 117-130.
- Zak, D.E., Vadigepalli, R., Gonye, G.E., Doyle, F.J. 3rd, Schwaber, J.S., and Ogunnaike, B.A. 2005. Unconventional systems analysis problems in molecular biology: a case study in gene regulatory network modeling. Computers and Chemical Engineering, 29: 547-563.
- Xaun, G., Kolodzey, J., Kapoor, V., and Gonye, G. 2005. Characteristics of field-effect devices with gate oxide modification by DNA. Applied Physics Letters, 87: [103903-1]-[103903-3].
- Bell, M.G., Lankford, E.B., Gonye, G.E., Ellis-Davies, G.C.R., Regnier, M., Martyn, D.A., and Barsotti, R.J. 2005. Kinetics of cardiac thin-filament activation probed by fluorescence polarization of rhodamine-labeled troponin C in skinned guinea pig trabeculae. Biophys J. 2006 Jan 15; 90(2):531-43.
- Khan, R.L., Gonye, G.E., Gao, G. and Schwaber, J.S. 2006. A universal reference sample derived from clone vector for improved detection of differential gene expression. BMC Genomics, May 5; 7(1):109.
- Gonye, G.E., Chakravarthula, P., Schwaber, J.S. and Vadigepalli, R. 2007. From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT . In: M. Ochs (ed.), Methods in Molecular Biology: Gene Function Analysis, Humana Press Inc., 408: 49-68.
- Pratt, C., Vadigepalli R., Chakravarthula, P., Gonye, G. E., Philp, N. and Gerald Grunwald. 2008. Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium. Molecular Vision 14:1414-1428.
- Hao, H., Liu, H., Gonye, G.E. and Schwaber, J.S. 2008. A Fast carrier chromatin immunoprecipitation method applicable to microdissected tissue samples. Journal of Neuroscience Methods, 172(1):38-42.
- Gupta OP, Maguire JI, Eagle RC Jr, Garg SJ, Gonye G.E. 2009. The competency of pars plana vitrectomy incisions: a comparative histologic and spectrophotometric analysis. Am J Ophthalmol. 147(2): 243-250.
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Individual Expertise profile of
Gregory E. Gonye, Ph.D., Copyright © Gregory E. Gonye, Ph.D..
Last Updated
by Gregory Gonye, Ph.D. : Friday, September 18, 2009 12:35:31 PM
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