Article/Book Listings
Allen W. Heinemann, Dominique Kinnett-Hopkins, Chaithanya K. Mummidisetty, Rachel A. Bond, Linda Ehrlich-Jones, Catherine Furbish, Edelle Field-Fote & Arun Jayaraman (2020) Appraisals of robotic locomotor exoskeletons for gait: focus group insights from potential users with spinal cord injuries, Disability and Rehabilitation: Assistive Technology, 15:7, 762-772, DOI: 10.1080/17483107.2020.1745910
Abstract: Purpose: To describe appraisals of robotic exoskeletons for locomotion by potential users with spinal cord injuries, their perceptions of device benefits and limitations, and recommendations for manufacturers and therapists regarding device use. Read More
Contact: dkh@northwestern.edu
Finley, S.D., Broadbelt, L.J., and Hatzimanikatis, V. (2009) ''Thermodynamic analysis of biodegradation pathways''. Biotechnology and Bioengineering. 103(3), 532-541.
Abstract: Microorganisms provide a wealth of biodegradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental data for the thermodynamic properties of xenobiotics is scarce.... Read More
Keywords: complex systems, metabolic engineering, network analysis, synthetic biology, systems biology
Contact: sfinley@usc.edu
Finley, S.D., Broadbelt, L.J., and Hatzimanikatis, V. (2010) ''In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene''. BMC Systems Biology. 4:7.
Abstract: Background: Bioremediation offers a promising pollution treatment method in the reduction and elimination of man-made compounds in the environment. Computational tools to predict novel biodegradation pathways for pollutants allow one to explore the capabilities of microorganisms in cleaning up the environment.... Read More
Keywords: Shadow Price, Enzyme Commission, Metabolic Flux Analysis, Glyoxylate Shunt, Biodegradation Pathway
Contact: sfinley@usc.edu
Finley, S.D., Gupta, D., Cheng, N., and Klinke, D.J. (2011) ''Inferring relevant control mechanisms for Interleukin-12 signaling in naive CD4+ T cells''. Immunology and Cell Biology. 89(1), 100-110.
Abstract: Interleukin-12 (IL-12) is a key cytokine involved in shaping the cell-mediated immunity to intracellular pathogens. IL-12 initiates a cellular response through the IL-12 signaling pathway, a member of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) family of signaling... Read More
Keywords: interleukin‐12, Bayesian inference, CD4+ T cells, signal transduction, ordinary differential equations
Contact: sfinley@usc.edu
Yen, P., Finley, S.D., Stefanini, M.O., and Popel, A.S. (2011) ''A two-compartment model of VEGF distribution in the mouse''. PLoS ONE. 6:e27514.
Abstract: Vascular endothelial growth factor (VEGF) is a key regulator of angiogenesis–the growth of new microvessels from existing microvasculature. Angiogenesis is a complex process involving numerous molecular species, and to better understand it, a systems biology approach is necessary. In vivo... Read More
Keywords: Systems biology, Mathematical modeling, Mathematical oncology, Mechanistic modeling, Immune cell signaling, Multi-cellular models, Angiogenesis, Cellular metabolism, Kinetic modeling
Contact: sfinley@usc.edu
Finley, S.D., Engel-Stefanini, M.O., Imoukhuede, P.I., and Popel, A.S. (2011) ''Pharmacokinetics and pharmacodynamics of VEGF-neutralizing agents''. BMC Systems Biology. 5:193.
Abstract: Background: Vascular endothelial growth factor (VEGF) is a potent regulator of angiogenesis, and its role in cancer biology has been widely studied. Many cancer therapies target angiogenesis, with a focus being on VEGF-mediated signaling such as antibodies to VEGF. However, it... Read More
Keywords: Vascular Endothelial Growth Factor, Vascular Endothelial Growth Factor Receptor, Vascular Endothelial Growth Factor Concentration, Vascular Endothelial Growth Factor Secretion, Tumor Compartment
Contact: sfinley@usc.edu
Klinke, D.J. and Finley, S.D. (2012) ''Timescale analysis of rule-based biochemical reaction networks''. Biotechnology Progress. 28(1), 33-44. [pubmed] [journal]
Abstract: The flow of information within a cell is governed by a series of protein–protein interactions that can be described as a reaction network. Mathematical models of biochemical reaction networks can be constructed by repetitively applying specific rules that define how... Read More
Keywords: Bayesian statistics, JAK‐STAT signaling, model‐based inference, cellular signal transduction
Contact: sfinley@usc.edu
Finley, S.D. and Popel, A.S. (2012) ''Predicting the effects of anti-angiogenic agents targeting specific VEGF isoforms''. The AAPS Journal. 14(3), 500-509.
Abstract: Vascular endothelial growth factor (VEGF) is a key mediator of angiogenesis, whose effect on cancer growth and development is well characterized. Alternative splicing of VEGF leads to several different isoforms, which are differentially expressed in various tumor types and have... Read More
Keywords: angiogenesis, cancer drug target, computational model, pharmacokinetic model, systems biology
Contact: sfinley@usc.edu
Finley, S.D. and Popel, A.S. (2013) ''Effect of tumor microenvironment on tumor VEGF during anti- VEGF treatment: systems biology predictions''. Journal of the National Cancer Institute. 105(11), 802-11.
Abstract: Background: Vascular endothelial growth factor (VEGF) is known to be a potent promoter of angiogenesis under both physiological and pathological conditions. Given its role in regulating tumor vascularization, VEGF has been targeted in various cancer treatments, and anti-VEGF therapy has been... Read More
Keywords: vascular endothelial growth factor a, protein isoforms, neoplasms, systems biology, anti-vascular endothelial growth factor therapy, tumor microenvironment
Contact: sfinley@usc.edu