Klinke:Publications
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Publications
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Klinke, D. J. and Broadbelt, L. J., "Mechanism Reduction during Computer Generation of Compact Reaction Models", AIChE J. 43:1828-1837 (1997).
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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).
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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.
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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).
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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).
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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.
- 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 |
- 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 |
- 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 |
- 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.
- 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.
- 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.
- 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.
- 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.
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Klinke, D. J.; "An Empirical Bayesian Approach for Model-based Inference of Cellular Signaling Networks", BMC Bioinformatics 2009 in press.
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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.
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Klinke, D. J.; ``Signal Transduction Networks in Cancer: Quantitative Parameters Influence Network Topology", 2009 submitted.
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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
- 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.
- 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.
- 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.