Molecular Genetics & Microbiology

Jeremy Edwards

Jeremy S. Edwards, Ph.D.

Molecular Genetics and Microbiology
MSC08 4660
1 University of New Mexico
Albuquerque, NM 87131-0001
Office: CRTC 332
Tel: (505) 272-5465
Fax: (505) 272-6029

Keywords: Spatial temporal modeling, epidermal growth factor receptor, functional genomics technologies, polony sequencing.

Research Interests

The research interests of my group fall into two categories:
(1) Spatial-Temporal Modeling of Signaling Networks
(2) Functional Genomics Tool Development

Spatial-Temporal Modeling of Signaling Networks. Amplification of genes in the ErbB family (i.e. EGFR, ErbB2, etc) is associated with poor outcome in women's cancers, including breast, ovarian and endometrial cancer.  While it is clear that overexpression is a factor leading to ligand-independent signaling via these receptors, the mechanism by which functional dimerization and activation occurs is unknown.  It is my hypothesis that the spatial organization and the heterogeneity of the receptors in the plasma membrane and the downstream signaling components is essential for the control of signaling pathways. The focus of my work is on the development of spatially realistic simulations with the goal of understanding the importance of spatial regulation in signal transduction. The results of my future work will provide an unprecedented level of detail regarding the changing topography of membrane organization. Results of these analyses will contribute new insight into the nature and assembly of membrane microdomains controlling signal transduction and membrane trafficking in eucaryotic cells.

Functional Genomics Tool Development. The resounding success of the Human Genome Project clearly illustrates how early investments in developing cost-effective methods of data acquisition can have tremendous payoffs for the biomedical community. We maintain that the completion of the human genome marks the end-of-the-beginning, rather than the beginning-of-the-end, of the era of nucleic-acid (NA) technologies.  For a wide range of biomedical and bioagricultural goals, a strong need is evolving for low-cost NA technology.  The list of realized and potential applications is rich and growing.  NA technology has the potential to significantly and substantially impact cancer related health care (and health care in general), both directly by providing diagnostic and prognostic markers for the clinical setting, and indirectly by accelerating the pace of basic and clinical biomedical research.

Selected Publications

Link to PubMed

1.            Chatterjee, A., Mayawala, K., Edwards, J. S. & Vlachos, D. G. Time accelerated Monte Carlo simulations of biological networks using the binomial {tau}-leap method. Bioinformatics (2005).

2.            Gadkar, K. G., Doyle III, F. J., Edwards, J. S. & Mahadevan, R. Estimating optimal profiles of genetic alterations using constraint-based models. Biotechnol Bioeng 89, 243-51 (2005).

3.            Mayawala, K., Vlachos, D. G. & Edwards, J. S. Heterogeneities in EGF receptor density at the cell surface can lead to concave up scatchard plot of EGF binding. FEBS Lett 579, 3043-7 (2005).

4.            Merritt, J., Butz, J. A., Ogunnaike, B. A. & Edwards, J. S. Parallel analysis of human glucose-6-phosphate dehydrogenase single-nucleotide mutants via functional complementation in S. cerevisiae using polymerase colonies. Biotech Bioeng In press (2005).

5.            Butz, J., Goodwin, K. & Edwards, J. S. Detecting changes in the relative expression of K-ras2 splice variants using polymerase colonies. Biotechnol Prog 20, 1836-1839 (2004).

6.            Butz, J., Yan, H., Mikkilineni, V. & Edwards, J. S. Detection of allelic variations of human gene expression by polymerase colonies. BMC Genetics 5 (2004).

7.            Goodkind, J. R. & Edwards, J. S. Gene Expression Measurement Technologies: Innovations and Ethical Considerations. Computers & Chemical Engineering In Press (2004).

8.            Mayawala, K., Gelmi, C. A. & Edwards, J. S. MAPK cascade possesses decoupled controllability of signal amplification and duration. Biophys J 87, L01-2 (2004).

9.            Merritt, J. & Edwards, J. S. Assaying gene function by growth competition experiment. Metab Eng 6, 212-219 (2004).

10.            Mikkilineni, V., Mitra, R. D., DiTonno, J. R., Merritt, J., Church, G. M., Ogunnaike, B. A. & Edwards, J. S. Digital Quantitative Measurements of Gene Expression. Biotech Bioeng 86, 117-124 (2004).

11.            Mutalik, V. K., Singh, A. P., Edwards, J. S. & Venkatesh, K. V. Robust global sensitivity in multiple enzyme cascade system explains how the downstream cascade structure may remain unaffected by cross-talk. FEBS Letters 558, 79-84 (2004).

12.            Mutalik, V. K., Singh, A. P., Edwards, J. S. & Venkatesh, K. V. Equilibrium analysis of allosteric interactions shows zero-order effects. Cell Biochemistry and Biophysics 41, 179-192 (2004).

13.            Patel, S. & Edwards, J. S. RecA mediated initial alignment of homologous DNA molecules displays apparent first order kinetics with little effect of heterology. DNA Repair 3, 61-65 (2004).

14.            Patel, S., Venkatesh, K. V. & Edwards, J. S. An integrated mechanistic model for transcription-coupled nucleotide excision repair. DNA Repair 3, 343-348 (2004).

15.            Ruhela, A., Verma, M., Edwards, J. S., Bhat, P. J., Bhartiya, S. & Venkatesh, K. V. Autoregulation of Regulatory Proteins is Key for Dynamic Operation of GAL Switch in Saccharomyces cerevisiae. FEBS Lett 576, 119-126 (2004).

16.            Altenbaugh, R. E., Kauffman, K. J. & Edwards, J. S. Suitability and utility of computational analysis tools: characterization of erythrocyte parameter variation. Pac Symp Biocomput, 104-15 (2003).

17.            Butz, J., Wickstrom, E. & Edwards, J. S. Characterization of Mutations and LOH of p53 and K-ras2 in Pancreatic Cancer Cell Lines by Immobilized PCR. BMC Biotechnol 3, 11 (2003).

18.            Edwards, J. S. & Battista, J. R. Using DNA microarray data to understand the ionizing radiation resistance of Deinococcus radiodurans. Trends Biotechnol 21, 381-382 (2003).

19.            Edwards, J. S. & Kauffman, K. J. Biochemical Engineering in the 21st Century. Curr Opin Biotechnol 14, 451-453 (2003).

20.            Ibarra, R. U., Fu, P., Palsson, B. O., DiTonno, J. R. & Edwards, J. S. Quantitative Analysis of E. coli Metabolic Phenotypes within the Context of Phenotypic Phase Planes. J Mol Microbiol Biotechnol 6, 101-108 (2003).

21.            Kauffman, K. J., Prakash, P. & Edwards, J. S. Advances in Flux Balance Analysis. Current Opinion in Biotechnology 14, 491-496 (2003).

22.            Lall, R., Gao, G., Dhurjati, P. & Edwards, J. S. MRAD:  Metabolic Reaction Analysis Database – An Entity-Relationship Approach. J Mol Microbiol Biotechnol 6, 12-18 (2003).

23.            Merritt, J., DiTonno, J. R., Mitra, R. D., Church, G. M. & Edwards, J. S. Functional characterization of mutant yeast PGK1 within the context of the whole cell. Nucleic Acids Res 31, e84 (2003).

24.            Edwards, J. S., Covert, M. W. & Palsson, B. O. Metabolic Modeling of Microbes: the Flux-Balance Approach. Environ Microbiol 4, 133-140 (2002).

25.            Edwards, J. S., Ramakrishna, R. & Palsson, B. O. Characterizing the metabolic phenotype: A phenotype phase plane analysis. Biotechnol Bioeng 77, 27-36 (2002).

26.            Ibarra, R. U., Edwards, J. S. & Palsson, B. O. Evolution towards predicted optimal growth in Escherichia coli K-12. Nature 420, 186-189 (2002).

27.            Kauffman, K. J., Pajerowski, J. D., Jamshidi, N., Palsson, B. O. & Edwards, J. S. Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys J 83, 646-62 (2002).

28.            Mahadevan, R., Edwards, J. S. & Doyle, F. J., III. Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli. Biophys J 83, 1331-1340 (2002).

29.            Papin, J. A., Price, N. D., Edwards, J. S. & Palsson, B. O. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. Journal of Theoretical Biology 215, 67-82 (2002).

30.            Schilling, C. H., Covert, M. W., Famili, I., Church, G. M., Edwards, J. S. & Palsson, B. O. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriology 184, 4582-4593 (2002).

31.            Badarinarayana, V., Estep, P. W., 3rd, Shendure, J., Edwards, J., Tavazoie, S., Lam, F. & Church, G. M. Selection analyses of insertional mutants using subgenic-resolution arrays. Nat Biotechnol 19, 1060-1065 (2001).

32.            Covert, M. W., Schilling, C. H., Famili, I., Edwards, J. S., Goryanin, I. I., Selkov, E. & Palsson, B. O. Metabolic Modeling of Microbial Strains in silico. Trends Biochem Sci 26, 179-86 (2001).

33.            Edwards, J. S., Ibarra, R. U. & Palsson, B. O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19, 125-130 (2001).

34.            Jamshidi, N., Edwards, J. S., Fahland, T., Church, G. M. & Palsson, B. O. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17, 286-7. (2001).

35.            Ramakrishna, R., Edwards, J. S., McCulloch, A. & Palsson, B. O. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am J Physiol Regul Integr Comp Physiol 280, R695-R704 (2001).

36.            Tchieu, J. H., Norris, V., Edwards, J. S. & Saier, M. H., Jr. The complete phosphotranferase system in Escherichia coli. J Mol Microbiol Biotechnol 3, 329-46. (2001).

37.            Edwards, J. S. & Palsson, B. O. Multiple steady states in kinetic models of red cell metabolism. J Theor Biol 207, 125-127 (2000).

38.            Edwards, J. S. & Palsson, B. O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A 97, 5528-33 (2000).

39.            Edwards, J. S. & Palsson, B. O. Robustness Analysis of the Escherichia coli metabolic network. Biotechnol Prog 16, 927-939 (2000).

40.            Edwards, J. S. & Palsson, B. O. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1, 1 (2000).

41.            Schilling, C. H., Edwards, J. S., Letscher, D. & Palsson, B. O. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnology and Bioengineering 71, 286-306 (2000).

42.            Edwards, J. S. & Palsson, B. O. Systems Properties of the Haemophilus influenzae Rd Metabolic Genotype. Journal of Biological Chemistry 274, 17410-17416 (1999).

43.            Edwards, J. S., Ramakrishna, R., Schilling, C. H. & Palsson, B. O. in Metabolic Engineering (eds. Lee, S. Y. & Papoutsakis, E. T.) 13-57 (Marcel Deker, New York, 1999).

44.            Schilling, C. H., Edwards, J. S. & Palsson, B. O. Towards metabolic phenomics: Analysis of genomic data using flux balances. Biotechnology Progress 15, 288-95 (1999).

45.            Edwards, J. S. & Palsson, B. O. How will bioinformatics influence metabolic engineering? Biotechnology and Bioengineering 58, 162-169 (1998).