Klinke:Publications

The Klinke Lab @ West Virginia University

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Publications

1. Klinke DJ 2nd and Broadbelt LJ, Mechanism Reduction during Computer Generation of Compact Reaction Models, AIChE J. 1997; 43:1828-1837.

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

3. Klinke DJ 2nd and Broadbelt LJ, Construction of a Mechanistic Model of Fischer-Tropsch Synthesis on Ni(111) and Co(0001) Surfaces, Chem. Eng. Sci. 1999; 54:3379-3389.

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

4. Klinke DJ 2nd, Dooling DJ, and Broadbelt LJ, A Theoretical Study of Methylidyne Chemisorption on Ni(111) and Co(0001) Surfaces; Surf. Sci. 1999; 425:334-342.

5. Klinke DJ 2nd and Broadbelt LJ, A Theoretical Study of Hydrogen Chemisorption on Ni(111) and Co(0001) Surfaces, Surf. Sci. 1999; 429:169-177.

6. Broadbelt LJ and Klinke DJ 2nd, 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. 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.

12. 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.

13. 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.

14. 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.

15. Leski TA, Caswell CC, Pawlowski M, Klinke DJ, Bujnicki JM, Hart SJ, and Lukomski S. Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting. Appl Environ Microbiol. 2009 Nov;75(22):7163-72. DOI:10.1128/AEM.01069-09 |

    Describes an approach to distinguish with confidence among B. anthracis strains using variability in collagen-like proteins. This addresses one of the problems with finding the perpetrators of the B. anthracis attacks on the U.S. Capital in 2001.

16. Klinke DJ 2nd. An empirical Bayesian approach for model-based inference of cellular signaling networks. BMC Bioinformatics. 2009 Nov 9;10:371. DOI:10.1186/1471-2105-10-371 |

    This is a highly accessed publication in BMC Bioinformatics

17. Klinke DJ 2nd. Signal transduction networks in cancer: quantitative parameters influence network topology. Cancer Res. 2010 Mar 1;70(5):1773-82. DOI:10.1158/0008-5472.CAN-09-3234 |

    This publication was highlighted as Research News on the Physical Sciences in Oncology website hosted by the National Cancer Institute http://physics.cancer.gov/news/2010/march/po_news_f.asp

18. Finley SD, Gupta D, Cheng N, and Klinke DJ 2nd, Inferring Relevant Control Mechanisms for Interleukin-12 Signaling in Naïve CD4+ T Cells, 2010 submitted.

19. Klinke DJ 2nd, Understanding human physiology via engineering design: The role of mathematical prototyping, 2010 submitted.

20. Kulkarni Y, Suarez V, and Klinke DJ 2nd, Inferring Predominant Pathways in Cellular Models of Breast Cancer Using Limited Sample Proteomic Profiling, 2010 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.