Publications of David Klinke, PhD

Identifying causal networks linking cancer processes and anti-tumor immunity using Bayesian network inference and metagene constructs.
Kaiser JL, Bland CL, Klinke DJ.
Biotechnol Prog. 2016; [Epub ahead of print]


Enhancing the discovery and development of immunotherapies for cancer using quantitative and systems pharmacology: Interleukin-12 as a case study.
Klinke DJ.
J Immunother Cancer. 2015;3:27

PMC4468964.

In silico model-based inference: an emerging approach for inverse problems in engineering better medicines.
Klinke DJ, Birtwistle MR.
Curr Opin Chem Eng. 2015;10:14-24.

PMC4545575.

Interlocked positive and negative feedback network motifs regulate beta-catenin activity in the adherens junction pathway.
Klinke DJ, Horvath N, Cuppett V, Wu Y, Deng W, Kanj R.
Mol Biol Cell. 2015;26(22):4135-4148.

PMC Journal - In Process.

CD8 (+) T cell response to adenovirusvaccination and subsequent suppression of tumor growth: modeling, simulation and analysis.
Wang Q, Klinke DJ, Wang Z.
BMC Syst Biol. 2015;9:27

PMC4458046.

Exosomes: improved methods to characterize their morphology, RNA content, and surface protein biomarkers.
Wu Y, Deng W, Klinke DJ.
Analyst. 2015;140(19):6631-6642.


Exosomes: improved methods to characterize their morphology, RNA content, and surface protein biomarkers.
Wu YT, Deng W, Klinke DJ.
Analyst. 2015;140(19):6631-6642.


In silico model-based inference: A contemporary approach for hypothesis testing in network biology.
Klinke DJ.
Biotechnol Prog. 2014;30(6):1247-1261.

PMC4261023.

Inferring alterations in cell-to-cell communication in HER2+ breast cancer using secretome profiling of three cell models.
Klinke DJ, Kulkarni YM, Wu Y, Byrne-Hoffman C.
Biotechnol Bioeng. 2014;111(9):1853-1863.

PMC4423606.

Induction of Wnt-inducible signaling protein-1 correlates with invasive breast cancer oncogenesis and reduced type 1 cell-mediated cytotoxic immunity: a retrospective study.
Klinke DJ.
PLoS Comput Biol. 2014;10(1):e1003409

PMC3890420.

Differential proteomic analysis of caveolin-1 KO cells reveals Sh2b3 and Clec12b as novel interaction partners of caveolin-1 and Capns1 as a potential mediator of caveolin-1-induced apoptosis.
Kulkarni YM, Liu C, Qi Q, Zhu Y, Klinke DJ, Liu J.
Analyst. 2013;138(22):6986-6996.

PMC4165583.

Quantifying crosstalk among Interferon-gamma, Interleukin-12, and tumor necrosis factor signaling pathways within a TH1 cell model.
Klinke DJ, Cheng N, Chambers E.
Sci Signal. 2012;5(220):ra32

PMC3373264.

An evolutionary perspective on anti-tumor immunity.
Klinke DJ.
Front Oncol. 2012;2:202

PMC3541690.

Understanding immunology via engineering design: the role of mathematical prototyping.
Klinke DJ, Wang Q.
Comput Math Methods Med. 2012;2012:676015

PMC3438878.

Timescale analysis of rule-based biochemical reaction networks.
Klinke DJ, Finley SD.
Biotechnol Prog. 2012;28(1):33-44.

PMC3381993.

A quantitative systems approach to identify paracrine mechanisms that locally suppress immune response to Interleukin-12 in the B16 melanoma model.
Kulkarni YM, Chambers E, McGray AJ, Ware JS, Bramson JL, Klinke DJ.
Integr Biol (Camb). 2012;4(8):925-936.

PMC3428131.

Protein-based identification of quantitative trait loci associated with malignant transformation in two HER2+ cellular models of breast cancer.
Kulkarni YM, Klinke DJ.
Proteome Sci. 2012;10(1):11

PMC3305585.

Inferring relevant control mechanisms for interleukin-12 signaling in naive CD4+ T cells.
Finley SD, Gupta D, Cheng N, Klinke DJ.
Immunol Cell Biol. 2011;89(1):100-110.

PMC3004982.

Age-corrected Beta cell mass following onset of type 1 diabetes mellitus correlates with plasma C-Peptide in humans.
Klinke DJ.
PLoS One. 2011;6(11):e26873

PMC3206867.

A multiscale systems perspective on cancer, immunotherapy, and Interleukin-12.
Klinke DJ.
Mol Cancer. 2010;9:242

PMC3243044.

Signal transduction networks in cancer: quantitative parameters influence network topology.
Klinke DJ.
Cancer Res. 2010;70(5):1773-1782.

PMC2831142.

Inferring predominant pathways in cellular models of breast cancer using limited sample proteomic profiling.
Kulkarni YM, Suarez V, Klinke DJ.
BMC Cancer. 2010;10:291

PMC2896362.

Scalable analysis of flow cytometry data using R/Bioconductor.
Klinke DJ, Brundage KM.
Cytometry A. 2009;75(8):699-706.

PMC2941976.

Validating a dimensionless number for glucose homeostasis in humans.
Klinke DJ.
Ann Biomed Eng. 2009;37(9):1886-1896.


An empirical Bayesian approach for model-based inference of cellular signaling networks.
Klinke DJ.
BMC Bioinformatics. 2009;10:371

PMC2781012.

Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting.
Leski TA, Caswell CC, Pawlowski M, Klinke DJ, Bujnicki JM, Hart SJ, Lukomski S.
Appl Environ Microbiol. 2009;75(22):7163-7172.

PMC2786505.

Modulating temporal control of NF-kappaB activation: implications for therapeutic and assay selection.
Klinke DJ, Ustyugova IV, Brundage KM, Barnett JB.
Biophys J. 2008;94(11):4249-4259.

PMC2480691.

Extent of beta cell destruction is important but insufficient to predict the onset of type 1 diabetes mellitus.
Klinke DJ.
PLoS One. 2008;3(1):e1374

PMC2147725.

Integrating epidemiological data into a mechanistic model of type 2 diabetes: validating the prevalence of virtual patients.
Klinke DJ.
Ann Biomed Eng. 2008;36(2):321-334.


A multi-scale model of dendritic cell education and trafficking in the lung: implications for T cell polarization.
Klinke DJ.
Ann Biomed Eng. 2007;35(6):937-955.


An age-structured model of dendritic cell trafficking in the lung.
Klinke DJ.
Am J Physiol Lung Cell Mol Physiol. 2006;291(5):L1038-L1049.


The ratio of P40 monomer to dimer is an important determinant of IL-12 bioactivity.
Klinke DJ.
J Theor Biol. 2006;240(2):323-335.


Construction of a mechanistic model of Fischer-Tropsch synthesis on Ni(111) and Co(0001) surfaces.
Klinke DJ, Broadbelt LJ.
Chem Eng Sci. 1999;54(15-16):3379-3389.


A theoretical study of methylidyne chemisorption on Ni(111)and Co(0001)surfaces.
Klinke DJ, Dooling DJ, Broadbelt LJ.
Surface Science. 1999;425(2-3):334-342.


A theoretical study of hydrogen chemisorption on Ni(111) and Co(0001) surfaces.
Klinke DJ, Broadbelt LJ.
Surface Science. 1999;429(1-3):169-177.


A theoretical study of carbon chemisorption on Ni(111) and Co(0001) surfaces.
Klinke DJ, Wilke S, Broadbelt LJ.
J Catal. 1998;178(2):540-554.


Mechanism reduction during computer generation of compact reaction models.
Klinke DJ, Broadbelt LJ.
Aiche Journal. 1997;43(7):1828-1837.