Ingalls, Brian

Affiliations

Faculty of Health Sciences , McMaster University
Lecturer (Adjunct), Medicine , Faculty of Health Sciences

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academic article
- Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design. Processes. 7:52-52. 2019
- Effective implicit finite-difference method for sensitivity analysis of stiff stochastic discrete biochemical systems. Systems Biology IEE Proceedings Systems Biology IET Systems Biology. 12:123-130. 2018
- New opportunities for optimal design of dynamic experiments in systems and synthetic biology. Current Opinion in Systems Biology. 9:42-48. 2018
- Parametric Sensitivity Analysis of Oscillatory Delay Systems with an Application to Gene Regulation. Bulletin of Mathematical Biology. 79:1539-1563. 2017
- An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems. BioSystems. 151:43-52. 2017
- Predictive Modeling of a Batch Filter Mating Process. Frontiers in Microbiology. 8:461. 2017
- Microbial Herd Protection Mediated by Antagonistic Interaction in Polymicrobial Communities. Applied and Environmental Microbiology. 82:6881-6888. 2016
- Exploiting stoichiometric redundancies for computational efficiency and network reduction. In Silico Biology. 12:55-67. 2015
- Amplified Ras-MAPK signal states correlate with accelerated EGFR internalization, cytostasis and delayed HER2 tumor onset in Fer-deficient model systems. Oncogene. 34:4109-4117. 2015
- Displacement of Bacterial Plasmids by Engineered Unilateral Incompatibility. IEEE Life Sciences Letters. 1:19-21. 2015
- Modeling of cell culture damage and recovery leads to increased antibody and biomass productivity in CHO cell cultures. Biotechnology Journal. 9:1152-1163. 2014
- Mathematical modeling in systems biology: an introduction. Choice Reviews Online. 51. 2014
- Modeling the coupled extracellular and intracellular environments in mammalian cell culture. Metabolic Engineering. 19:57-68. 2013
- Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in Rhodobacter sphaeroides chemotaxis. Journal of the Royal Society Interface. 10:20120935-20120935. 2013
- Effects of multimerization on the temporal variability of protein complex abundance. BMC Systems Biology. 7:S3-S3. 2013
- Population-based modeling of the progression of apoptosis in mammalian cell culture. Biotechnology and Bioengineering. 109:1193-1204. 2012
- A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. BMC Systems Biology. 6:78-78. 2012
- Proteomics analysis of chinese hamster ovary cells undergoing apoptosis during prolonged cultivation. Cytotechnology Methods in Cell Science Journal of Tissue Culture Methods. 63:663-677. 2011
- Development of a mathematical model for evaluating the dynamics of normal and apoptotic Chinese hamster ovary cells. Biotechnology Progress. 27:1197-1205. 2011
- Robust L-type calcium current expression following heterozygous knockout of the Cav1.2 gene in adult mouse heart. Journal of Physiology. 589:3275-3288. 2011
- Differential chromatin proteomics of the MMS-induced DNA damage response in yeast. Proteome Science. 9:62-62. 2011
- Dynamic Modeling of Apoptosis and its Interaction with Cell Growth in Mammalian Cell Culture. IFAC Proceedings Volumes (IFAC-PapersOnline). 44:9691-9696. 2011
- Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network. Journal of Theoretical Biology. 266:723-738. 2010
- Estimating the Stochastic Bifurcation Structure of Cellular Networks. PLoS Computational Biology. 6:e1000699-e1000699. 2010
- Metabolic flux and nutrient uptake modeling of normal and apoptotic CHO cells. IFAC Proceedings Volumes (IFAC-PapersOnline). 43:395-400. 2010
- Modeling the progression of apoptosis in Chinese Hamster Ovary cells. IFAC Proceedings Volumes (IFAC-PapersOnline). 43:467-472. 2010
- Sequential Activation of Metabolic Pathways: a Dynamic Optimization Approach. Bulletin of Mathematical Biology. 71:1851-1872. 2009
- Exponential stability of singularly perturbed switched systems with time delay. Nonlinear Analysis: Hybrid Systems. 2:913-921. 2008
- Optimal Metabolic Pathway Activation. IFAC Proceedings Volumes (IFAC-PapersOnline). 41:12587-12592. 2008
- Systems level modeling of the cell cycle using budding yeast.. Cancer Informatics. 3:357-370. 2007
- The ‘Cell-See-Us’ cellular thermometer. IET Synthetic Biology. 1:79-82. 2007
- Deterministic characterization of stochastic genetic circuits. Proceedings of the National Academy of Sciences of the United States of America. 104:7402-7407. 2007
- Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks. Chaos. 16:026107-026107. 2006
- Uniform Global Asymptotic Stability of Differential Inclusions. Journal of Dynamical and Control Systems Dynamics and Control. 10:391-412. 2004
- Autonomously oscillating biochemical systems: parametric sensitivity of extrema and period. Systems Biology IEE Proceedings Systems Biology IET Systems Biology. 1:62-70. 2004
- Conservation analysis in biochemical networks: computational issues for software writers. Biophysical Chemistry. 109:1-15. 2004
- A Frequency Domain Approach to Sensitivity Analysis of Biochemical Networks. Journal of Physical Chemistry B Journal of Physical Chemistry B Materials. 108:1143-1152. 2004
- Discussion on: “The Non-Uniform in Time Small-Gain Theorem for a Wide Class of Control Systems with Outputs”. European Journal of Control. 10:324-325. 2004
- Separation Principles for Input-Output and Integral-Input-to-State Stability. SIAM Journal on Control and Optimization SIAM J Control. 43:256-276. 2004
- Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. Journal of Theoretical Biology. 222:23-36. 2003
- A small-gain theorem with applications to input/output systems, incremental stability, detectability, and interconnections. Journal of the Franklin Institute. 339:211-229. 2002
- An extended model for pairwise conflict resolution in air traffic management. Optimal Control Applications and Methods. 20:183-197. 1999
article
chapter
- Probing the Input–Output Behavior of Biochemical and Genetic Systems: System Identification Methods from Control Theory - ScienceDirect. Methods in Enzymology. 279-317. 2011
- Sensitivity analysis: from model parameters to system behaviour. Essays in Biochemistry. 177-194. 2008
conference paper
- ATPase binding and consequent disassembly of the type VI secretion system in Vibrio cholerae: a dynamic model. IFAC-PapersOnLine. 82-83. 2018
- Comparator-based gene regulatory network designs for control of expression. IFAC-PapersOnLine. 38-41. 2018
- Numerical Modelling of C. elegans L1 Aggregation. IFAC-PapersOnLine. 12-15. 2018
- Optimal experimental design for characterizing gene expression: sample scheduling. IFAC-PapersOnLine. 48-51. 2018
- Response time re-scaling and Weber's law in adapting biological systems. Proceedings of the American Control Conference. 4557-4562. 2013
- Designing synchronization protocols in networks of coupled nodes under uncertainty. Proceedings of the American Control Conference. 4945-4950. 2012
- Fold-change detection as a chemotaxis model discrimination tool. Proceedings of the IEEE Conference on Decision and Control. 5523-5527. 2012
- Feedback Control Architecture of the R. sphaeroides Chemotaxis Network. Proceedings of the IEEE Conference on Decision and Control. 3014-3019. 2011
- "Metabolic Control Analysis" from a Control Theoretic Perspective. Proceedings of the IEEE Conference on Decision and Control. 2116-2121. 2006
- Detectability of nonlinear systems under singular perturbations. Dynamics of Continuous, Discrete and Impulsive Systems Series A: Mathematical Analysis Dynamics of Continuous, Discrete and Impulsive Systems Series B: Applications and Algorithms. 318-323. 2005