Klinke:Publications

The Klinke Lab @ West Virginia University

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Publications

1. Klinke, D. J. and Broadbelt, L. J., "Mechanism Reduction during Computer Generation of Compact Reaction Models", AIChE J. 43:1828-1837 (1997).

2. Klinke, D. J.; Wilke, S.; and Broadbelt, L. J.; "A Theoretical Study of Carbon Chemisorption on Ni(111) and Co(0001) Surfaces", J. Catal. 178:540-554 (1998).

3. Klinke, D. J. and Broadbelt, L. J., "Construction of a Mechanistic Model of Fischer-Tropsch Synthesis on Ni(111) and Co(0001) Surfaces", Chem. Eng. Sci. 54:3379-3389 (1999).

   The first application of an automatic reaction network generation algorithm to catalytic chemistry.

4. Klinke, D. J.; Dooling, D. J.; and Broadbelt, L. J.; "A Theoretical Study of Methylidyne Chemisorption on Ni(111) and Co(0001) Surfaces"; Surf. Sci. 425:334-342 (1999).

5. Klinke, D. J. and Broadbelt, L. J., "A Theoretical Study of Hydrogen Chemisorption on Ni(111) and Co(0001) Surfaces", Surf. Sci. 429:169-177 (1999).

6. Broadbelt, L. J. and Klinke, D. J., "Kinetics of Catalyzed Reactions – D (Heterogeneous)" in Encyclopedia of Catalysis, Istvan T. Horvath (Editor-in-Chief), ISBN 0-471-24183-0, pp. 4772, December 2002.

7. Klinke DJ 2nd. The ratio of P40 monomer to dimer is an important determinant of IL-12 bioactivity. J Theor Biol. 2006 May 21;240(2):323-35. DOI:10.1016/j.jtbi.2005.09.022 |
8. Klinke DJ 2nd. An age-structured model of dendritic cell trafficking in the lung. Am J Physiol Lung Cell Mol Physiol. 2006 Nov;291(5):L1038-49. DOI:10.1152/ajplung.00048.2006 |
9. Klinke DJ 2nd. A multi-scale model of dendritic cell education and trafficking in the lung: implications for T cell polarization. Ann Biomed Eng. 2007 Jun;35(6):937-55. DOI:10.1007/s10439-007-9318-6 |
10. Klinke DJ 2nd. Integrating epidemiological data into a mechanistic model of type 2 diabetes: validating the prevalence of virtual patients. Ann Biomed Eng. 2008 Feb;36(2):321-34. DOI:10.1007/s10439-007-9410-y |

    Provides a glimpse of the kind of models developed by Entelos, Inc.

11. Klinke DJ 2nd, Ustyugova IV, Brundage KM, and Barnett JB. Modulating temporal control of NF-kappaB activation: implications for therapeutic and assay selection. Biophys J. 2008 Jun;94(11):4249-59. DOI:10.1529/biophysj.107.120451 |

    Finds that our ability to observe significant biological events is limited by the signal-to-noise characteristics of the assays that we use to observe cellular responses.

12. Klinke DJ 2nd. Extent of beta cell destruction is important but insufficient to predict the onset of type 1 diabetes mellitus. PLoS One. 2008 Jan 2;3(1):e1374. DOI:10.1371/journal.pone.0001374 |

    Evaluates the conventional wisdom regarding the extent of beta cell destruction required before presenting with symptoms of type 1 diabetes.

13. Klinke DJ 2nd and Brundage KM. Scalable analysis of flow cytometry data using R/Bioconductor. Cytometry A. 2009 Aug;75(8):699-706. DOI:10.1002/cyto.a.20746 |

    Provides a tutorial for using R/Bioconductor to process flow cytometry data.

14. Klinke DJ 2nd. Validating a dimensionless number for glucose homeostasis in humans. Ann Biomed Eng. 2009 Sep;37(9):1886-96. DOI:10.1007/s10439-009-9733-y |

    Develops and validates a dimensionless number for the ratio of insulin production and insulin-dependent glucose metabolism in humans.

15. Klinke, D. J.; "An Empirical Bayesian Approach for Model-based Inference of Cellular Signaling Networks", BMC Bioinformatics 2009 accepted in principle.

16. Leski, T. A.; Caswell, C. C.; Pawlowski, M.; Klinke, D. J.; Bujnicki, M.; Hart, S. J.; Lukomski, S.; "bcl- Genes of Bacillus cereus Group Organisms: Identification, Classification and Application in Anthrax Detection and Fingerprinting", Appl Environ Microbiol 2009 in press.

17. Klinke, D. J.; ``Signal Transduction Networks in Cancer: Quantitative Parameters Influence Network Topology", 2009 submitted.

18. Finley, S.D.; Gupta, D.; Cheng, N; Klinke, D. J.; ``Inferring Relevant Control Mechanisms for Interleukin-12 Signaling in Naïve CD4+ T Cells", 2009 submitted.

Patents and Patent Applications

1. Defranoux, N.A.; Dubnicoff, T.B.; Klinke, D.J.; Lewis, A.K.; Paterson, T.S.; Ramanujan, S.; Shoda, L.K.M.; Soderstrom, K.P.; Struemper, H.K.; "Method and apparatus for computer modeling a joint", US Patent #6,862,561.
2. Kelly, S.D.; Klinke, D.J.; Leong, C.; Lewis, A.K.; Okino, M.S.; Paterson, T.S.; Shoda, L.K.M.; Stokes, C.; Struemper, H.K.; "Method and apparatus for computer modeling of an adaptive immune response", US Patent Application #10/154,123.
3. Friedrich, C.M.; Kansal, A.; Klinke, D.J.; Michelson, S.G.; Paterson, T.S.; Polidori, D.; Trimmer, J.; Wennerberg, L.G.; "Defining Virtual Patient Populations", US Patent Application #11/346,990.
4. Defranoux, N.A.; Dubnicoff, T.B.; Klinke, D.J.; Lewis, A.K.; Paterson, T.S.; Ramanujan, S.; Shoda, L.K.M.; Soderstrom, K.P.; Struemper, H.K.; "Method and apparatus for computer modeling a joint", US Patent #7,472,050.