Klinke:Publications

The Klinke Lab @ West Virginia University

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Publications

• Note: Search "klinke dj" via PubGet for a third-party automatically generated set of PubMed-listed publications from the lab.

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 a rule-based 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; 240:323-35. PMID 16448670

1. Klinke DJ 2nd, An age-structured model of dendritic cell trafficking in the lung, Am J Physiol Lung Cell Mol Physiol 2006; 291:L1038-49. PMID 17030902
2. 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; 35:937-55. PMID 17457675
3. Klinke DJ 2nd, Integrating epidemiological data into a mechanistic model of type 2 diabetes: validating the prevalence of virtual patients, Ann Biomed Eng 2008; 36:321-34. PMID 18046647
   

Provides a glimpse of the size and complexity of the proprietary PhysioLab models developed by Entelos, Inc.

1. WVU-5 pmid 18167535

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

1. WVU-6 pmid 18281385

// 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.

1. WVU-7 pmid 19513847

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

1. WVU-8 pmid 19582872

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

1. WVU-9 pmid 19767469

// 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.

1. WVU-10 pmid 19900289

// This is a highly accessed publication in BMC Bioinformatics

1. WVU-11 pmid 20179207

// This publication was highlighted as Research News on the Physical Sciences in Oncology website hosted by the National Cancer Institute.

1. WVU-12 pmid 20479776

// This publication uses an empirical Bayesian approach to infer the contributions of different mechanisms that regulate IL-12 signaling in naïve CD4+ T cells derived from Balb/c mice.

1. WVU-13 pmid 20550684

// This publication uses a proteomics workflow that includes 2D-gel electrophoresis and MALDI-TOF MS peptide mass fingerprinting to identify predominant pathways in two breast cancer cell models.

1. WVU-14 Klinke DJ 2nd, A multiscale systems perspective on cancer, immunotherapy, and Interleukin-12, Molecular Cancer 2010 Sept 15; 9:242.
2. WVU-15 Klinke DJ 2nd, Inferring the dynamic role of beta cell function in the natural history of diabetes using mathematical prototypes, 2010 submitted.

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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.