Publications

Reprints for most publications are available electronically. If you cannot obtain a particular offprint and would like to receive it, please contact Dr. Schnell the reference and we will send you a copy. You can also visit our Cover Featured Publications page.

(2021). Explaining inter-lab variance in C. elegans N2 lifespan: Making a case for standardized reporting to enhance reproducibility. Exp Gerontol, under review.

(2021). Phosphotyrosine-mediated regulation of ACLY controls lipid metabolism and oncogenesis. bioRxiv, 2020.01.20.910752.

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(2021). Concentration sensing in crowded environments. Biophys J 120, 1718-1731.

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(2021). On the quasi-steady-state approximation in an open Michaelis-Menten reaction mechanism. AIMS Math 6, 6781-6814.

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(2021). Mapping protein-protein interactions in homodimeric CYP102A1 by crosslinking and mass spectrometry. Biophys Chem 274, 106590.

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(2021). On the validity of the stochastic quasi-steady-state approximation in open enzyme catalyzed reactions: Timescale separation or singular perturbation?. arXiv, 2103.10566 [math.DS].

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(2021). Assumptions of biological measurements: important considerations when evaluating western blot data. Authorea, DOI: 10.22541/au.161144035.53972444/v1.

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(2021). Interpreting SARS-CoV-2 seroprevalence, deaths, and fatality rate: Making a case for standardized reporting to improve communication. Math Biosci 333, 108545.

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(2021). Stochastic enzyme kinetics and the quasi-steady-state reductions: Application of the slow scale linear noise approximation a la Fenichel. arXiv, 2101.04814 [physics.chem-ph].

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(2020). The embryonic trunk neural crest microenvironment regulates the plasticity and invasion of human neuroblastoma via TrkB signaling. bioRxiv, in progress.

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(2020). Beta-arrestin mediates communication between plasma membrane and intracellular GPCRs to regulate signaling. Commun Biol 3, 789.

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(2020). Trends in NIH-supported career development funding: Implications for institutions, trainees, and the future research workforce. JCI Insight 5, e142817.

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(2020). Firing patterns of gonadotropin-releasing hormone neurons are sculpted by their biologic state. R Soc Open Sci 7, 201040.

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(2020). Applying the quasi-steady-state approximation to the autocatalytic zymogen activation: A novel general methodology for scaling analysis. ChemRxiv DOI 10.26434/chemrxiv.8847596.

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(2020). Knitting Proteins. In: The Art of Theoretical Biology, pp 54-55.

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(2020). The quasi-steady-state approximations revisited: Timescales, small parameters, singularities, and normal forms in enzyme kinetics. Math Biosci 325, 108339.

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(2020). Are the biomedical sciences ready for synthetic biology?. Biomol Concepts 11, 23-31.

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(2019). Have we come to the end of theoretical and mathematical biology?. J Theor Biol 481, 1-2.

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(2019). Characteristic, completion or matching timescales? An analysis of temporary boundaries in enzyme kinetics. J Theor Biol 481, 28-43.

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(2019). Information processing by endoplasmic reticulum stress sensors. J Royal Soc Interface 16, 20190288.

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(2019). Autoantibodies directed towards a novel IA-2 variant protein enhance prediction of type 1 diabetes. Diabetes 68, 1819-1829.

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(2019). Disorder Atlas: A web software for the proteome-based interpretation of intrinsic disorder predictions. Comput Biol Chem 83, 107090.

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(2019). Clathrin heavy chain knockdown impacts CXCR4 signaling and post-translational modification. Front Cell Dev Biol 7, 77.

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(2019). Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality. Mol Cell 74, 521-533.

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(2019). Enhancing career development of postdoctoral trainees: Act locally and beyond. J Physiol 597, 2317-2322.

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(2019). On the need to develop guidelines for characterizing and reporting intrinsic disorder in proteins. Proteomics 19, 1800415.

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(2019). Changes in both neuron intrinsic properties and neurotransmission are needed to drive the increase in GnRH neuron firing rate during estradiol positive feedback. J Neurosci 39, 2091-2101.

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(2018). Phase-plane geometries in coupled enzyme assays. Math Biosci 306, 126-135.

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(2018). How to design an optimal sensor network for the unfolded protein response. Mol Biol Cell 29, 3052-3062.

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(2018). A kinetic analysis of coupled (or auxiliary) enzyme reactions. Bull Math Biol 80, 3154-3183.

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(2018). 'Reproducible' research in mathematical sciences requires changes in our peer review culture and modernization of our current publication approach. Bull Math Biol 80, 3095-3105.

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(2018). An empirical analysis of enzyme function reporting for experimental reproducibility: Missing/incomplete information in published papers. Biophys Chem 242, 22-27.

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(2018). A theory of reactant-stationary kinetics for a mechanism of zymogen activation. Biophys Chem 242, 34-44.

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(2018). Radial WNT5A-guided post-mitotic filopodial pathfinding is critical for midgut tube elongation. Dev Cell 46, 173-188.

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(2018). Do cellular condensates accelerate biochemical reactions? Lessons from microdroplet chemistry. Biophys J 115, 3-8.

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(2018). Predicting neuroblastoma using developmental signals and a logic-based model. Biophys Chem 238, 30-38.

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(2018). STRENDA DB: enabling the validation and sharing of enzyme kinetics data. FEBS J 285, 2193-2204.

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(2018). Inferring intracellular signal transduction circuitry from molecular perturbation experiments. Bull Math Biol 80, 1310-1344.

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(2018). Gonadotropin-Releasing Hormone (GnRH) neuron excitability is regulated by estradiol feedback and kisspeptin. J Neurosci 38, 1249-1263.

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(2017). On the origin of non-membrane-bound organelles, and their physiological function. J Theor Biol 434, 42-49.

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(2017). Globalization and changing trends of biomedical research output. JCI Insight 2, e95206.

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(2017). On the validity and errors of the pseudo-first-order kinetics in ligand-receptor binding. Math Biosci 287, 3-11.

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(2017). Approaches for the estimation of timescales in nonlinear dynamical systems: Timescale separation in enzyme kinetics as a case study. Math Biosci 287, 122-129.

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(2017). The importance of accurately correcting for the natural abundance of stable isotopes. Anal Biochem 520, 27-43.

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(2017). Novel hybrid phenotype revealed in small cell lung cancer by a transcription factor network model that can explain tumor heterogeneity. Cancer Res 77, 1063-1074.

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(2016). On the estimation errors of $K_M$ and $V$ from time-course experiments using the Michaelis-Menten equation. Biophys Chem 219, 17-27.

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(2016). Coordination of signaling and tissue mechanics during morphogenesis of murine intestinal villi: A role for mitotic cell rounding. Integr Biol 8, 918-928.

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(2016). Estimation of the lag time in a subsequent monomer addition model for fibril elongation. Phys Chem Chem Phys 18, 21259-21268.

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(2016). RhoC GTPase is a potent regulator of glutamine metabolism and N-acetylaspartate production in inflammatory breast cancer cells. J Biol Chem 291, 13715-13729.

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(2016). A collection of intrinsic disorder characterizations from eukaryotic proteomes. Sci Data 3, 160045.

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(2016). Quantitative proteome-based guidelines for intrinsic disorder characterization. Biophys Chem 213, 6-16.

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(2016). A computational approach to studying ageing at the individual level. Proc R Soc B-Biol Sci 283, 20152346.

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(2016). Loss of the ubiquitin-conjugating enzyme UBE2W results in susceptibility to early postnatal lethality and defects in skin, immune, and male reproductive systems. J Biol Chem 291, 3030-3042.

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(2016). Villification in the mouse: BMP signals control intestinal villus patterning. Development 143, 427-436.

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(2015). Rethinking models of pattern formation in somitogenesis. Cell Syst 1, 248-249.

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(2015). Ten simple rules for a computational biologist's laboratory notebook. PLoS Comput Biol 11, e1004385.

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(2015). Evidence for residual and partly reparable insulin secretory function and maintained beta-cell gene expression in islets from patients with type 1 diabetes. Diabetes 64, 2335-2337.

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(2015). Unraveling the contribution of pancreatic beta-cell suicide in autoimmune type 1 diabetes. J Theor Biol 375, 77-87.

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(2015). Molecular aspects of pancreatic beta cell failure and diabetes. Mol Aspects Med 42, 1-2.

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(2015). Development, growth and maintenance of beta-cell mass: Models are also part of the story. Mol Aspects Med 42, 78-90.

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(2014). Connecting the dots: The effects of macromolecular crowding on cell physiology. Biophys J 107, 2761-2766.

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(2014). Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. Comput Biol Chem 53, 242-250.

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(2014). Surveying the floodgates: Estimating protein flux into the endoplasmic reticulum lumen in Saccharomyces cerevisiae. Front Physiol 5, 444.

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(2014). Inferring the effects of Honokiol on the Notch signaling pathway in SW480 colon cancer cells. Cancer Inform 13s5, 1-12.

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(2014). Competitive inhibition reaction mechanisms for the two-step model of protein aggregation. Biophys Chem 193-194, 9-19.

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(2014). Optimal experimental design to estimate statistically significant periods of oscillations in time course data. PLoS ONE 9, e93826.

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(2014). Unravelling the impact of obstacles in diffusion and kinetics of an enzyme catalysed reaction. Phys Chem Chem Phys 16, 4492-4503.

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(2014). Unraveling intestinal stem cell behavior with models of crypt dynamics. Integr Biol 6, 243-257.

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(2014). Single-molecule enzymology a la Michaelis-Menten. FEBS J 281, 518-530.

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(2014). Validity of the Michaelis-Menten equation-steady-state or reactant stationary assumption: that is the question. FEBS J 281, 464-472.

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(2014). The circadian clock in oral health and diseases. J Dent Res 93, 27-35.

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(2014). A two-step kinetic model of insulin aggregation with a competitive inhibitor. In: BIOMAT 2013 Int S Math Comput Biol, 107-120.

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(2013). Network representations and methods for the analysis of chemical and biochemical pathways. Mol BioSyst 9, 2189-2200.

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(2013). Integration of steady-state and temporal gene expression data for the inference of gene regulatory networks. PLoS ONE 8, e72103.

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(2013). Circadian rhythms regulate amelogenesis. Bone 55, 158-165.

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(2013). Follow-the-leader cell migration requires biased cell-cell contact and local microenvironmental signals. Phys Biol 10, 035003.

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(2013). Designing nanoparticle treatment of autoimmunity with quantitative biology. Immunol Cell Biol 91, 333-334.

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(2013). Network motifs provide signatures that characterize metabolism. Mol BioSyst 9, 352-360.

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(2013). More than skew: asymmetric wave propagation in a reaction-diffusion-convection systems. Biomath 2, 201303027.

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(2012). Logic-based models in systems biology: network analysis method. Integr Biol 4, 1323-1337.

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(2012). The art of mathematical biology: A foreword for the launch of BIOMATH. Biomath 1, 1210115.

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(2012). Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi. Proc Natl Acad Sci USA 109, 15817-15822.

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(2012). Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour. J R Soc Interface 9, 1576-1588.

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(2012). Unraveling the complex regulatory relationships between metabolism and signal transduction in cancer. Adv Exp Med Biol 736, 179-189.

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(2011). Molecular and circadian controls of ameloblasts. Eur J Oral Sci 119, 35-40.

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(2011). A graphical user interface for a method to infer kinetics and network architecture (MIKANA). PLoS ONE 23, 233-244.

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(2011). Macroscopic simulations of microtubule dynamics predict two steady-state processes governing array morphology. Comput Biol Chem 35, 269-281.

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(2011). A model of threshold behavior reveals rescue mechanisms of bystander proteins in conformational diseases. Biophys J 100, 1864-1873.

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(2011). Expression of clock proteins in developing tooth. Gene Expr Patterns 11, 202-206.

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(2011). Effects of protein quality control machinery on protein homeostasis. In: Understanding the Dynamics of Biological Systems, 11-37.

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(2010). Stability of open pathways. Math Biosci 228, 147-152.

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(2010). Enzyme catalyzed reactions: From experiment to computational mechanism reconstruction. Comput Biol Chem 34, 11-18.

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(2010). Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res 70, 12-13.

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(2009). Waves and patterning in developmental biology: vertebrate segmentation and feather bud formation as case studies. Int J Dev Biol 53, 783-794.

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(2009). A model of the unfolded protein response: Pancreatic beta-cell as a case study. Cell Physiol Biochem 23, 233-244.

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(2009). How can mathematics help us explore vertebrate segmentation?. HFSP J 3, 1-5.

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(2009). Should digestion assays be used to estimate persistence of potential allergens in tests for safety of novel food proteins?. Clin Mol Allergy 7, 1.

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(2008). Modelling reaction kinetics inside cells. Essays Biochem 45, 41-56.

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(2008). Reactant stationary approximation in enzyme kinetics. J Phys Chem A 112, 8654-8658.

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(2008). Formation of monocarboxylic acids and polyols on a graphite surface. J Phys Chem A 602, 1053-1060.

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(2008). The intranuclear environment. Methods Mol Biol 463, 3-19.

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(2008). Multiscale Modeling of Developmental Systems. Curr Top Dev Biol 81.

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(2008). Mathematical models for somite formation. Curr Top Dev Biol 81, 183-203.

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(2008). Limit cycles in the presence of convection: a first-order analysis. J Math Chem 43, 101-110.

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(2008). Coordinated action of N-CAM, N-cadherin, EphA4, and ephrinB2 translates genetic prepatterns into structure during somitogenesis in chick. Curr Top Dev Biol 81, 205-247.

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(2007). Limit cycles in the presence of convection: A traveling wave analysis. Phys Rev E 76, 036216.

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(2007). Turing pattern outside of the Turing domain. Appl Math Lett 20, 959-963.

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(2007). Can tissue surface tension drive somite formation?. Dev Biol 307, 248-257.

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(2007). A mesoscopic simulation approach for modeling intracellular reactions. J Stat Phys 128, 139–164.

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(2007). From segment to somite: Segmentation to epithelialization analyzed within quantitative frameworks. Dev Dyn 236, 1392-1402.

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(2007). Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein-protein interaction networks?. Proteomics 7, 961-964.

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(2007). Reconstructing biochemical pathways from time course data. Proteomics 7, 828-838.

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(2007). Multiscale modeling in biology. Am Sci 95, 134–142.

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(2007). The effects of time delays in a phosphorylation-dephosphorylation pathway. Biophys Chem 125, 286-297.

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(2007). A test for measuring the effects of enzyme inactivation. Biophys Chem 125, 269-274.

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(2006). A systematic investigation of the rate laws valid in intracellular environments. Biophys Chem 124, 1-10.

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(2006). Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. Comput Biol Chem 30, 241-248.

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(2006). How reaction kinetics with time-dependent rate coefficients differs from generalized mass action. ChemPhysChem 7, 1422-1424.

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(2006). Use and abuse of the quasi-steady-state approximation. IEE Proc Syst Biol 153, 187-191.

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(2006). Unravelling the function and kinetics of biochemical networks. IEE Proc Syst Biol 153, 139.

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(2006). Why substrate depletion has apparent first-order kinetics in enzymatic digestion. Comput Biol Chem 30, 209-214.

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(2006). Book Review: Computational Modeling of Genetic and Biochemical Networks. Brief Bioinform 7, 204-206.

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(2006). A clock and wavefront mechanism for somite formation. Dev Biol 293, 116-126.

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(2006). A mathematical investigation of a Clock and Wavefront model for somitogenesis. J Math Biol 52, 458-482.

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(2006). A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies. Theor Biol Med Model 3, 7.

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(2006). The mechanism distinguishability problem in biochemical kinetics: The single-enzyme, single-substrate reaction as a case study. C R Biol 329, 51-61.

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(2004). Extracting biochemical reaction kinetics from time series data. Lect Notes Comput Sc 3214, 329-336.

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(2004). New approaches to modelling and analysis of biochemical reactions, pathways and networks. Prog Biophys Mol Biol 86, 1-4.

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(2004). Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog Biophys Mol Biol 86, 77-112.

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(2004). Stochastic approaches for modelling in vivo reactions. Comput Biol Chem 28, 165-178.

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(2004). Bulletin of mathematical biology - Facts, figures and comparisons. Bull Math Biol 66, 595-603.

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(2004). Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws. Prog Biophys Mol Biol 85, 236-260.

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(2004). A mathematical formulation for the cell-cycle model in somitogenesis: Analysis, parameter constraints and numerical solutions. Math Med Biol 5, 23-35.

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(2004). Mechanism equivalence in enzyme-substrate reactions: Distributed differential delay in enzyme kinetics. J Math Chem 35, 253-264.

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(2004). Book Review: Parametric Sensitivity in Chemical Systems. Bull Math Biol 66, 393-395.

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(2004). The condition for pseudo-first-order kinetics in enzymatic reactions is independent of the initial enzyme concentration. Biophys Chem 107, 165-174.

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(2003). Formation of vertebral precursors: Past models and future predictions. J Theor Med 5, 23-35.

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(2003). Book Review: Computational Cell Biology. Brief Bioinform 4, 87-89.

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(2003). A century of enzyme kinetics: Reliability of the $K_M$ and $v_{max}$ estimates. Comment Theor Biol 8, 169-187.

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(2002). Models for pattern formation in somitogenesis: a marriage of cellular and molecular biology. C R Biol 325, 179-189.

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(2002). Enzyme kinetics far from the standard quasi-steady-state and equilibrium approximations. Math Comput Model 35, 137-144.

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(2001). A fast method to estimate kinetic constants for enzyme inhibitors. Acta Biotheor 49, 109-113.

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(2000). A cell cycle model for somitogenesis: Mathematical formulation and numerical simulation. J Theor Biol 207, 305-316.

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(2000). Enzyme kinetics at high enzyme concentration. Bull Math Biol 62, 483-499.

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(2000). Clock and induction model for somitogenesis. Dev Dyn 217, 415-420.

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(2000). Time-dependent closed form solutions for fully competitive enzyme reactions. Bull Math Biol 62, 321-336.

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(2000). A formula for integrating inverse functions. Math Gaz 62, 103-104 (Note 84.20).

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(2000). Spatiotemporal pattern formation in early development: A review of primitive streak formation and somitogenesis. IMA Vol Math Appl 121, 11-37.

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(2000). Enzyme kinetics of multiple alternative substrates. J Math Chem 27, 155-170.

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(1997). Theoretical description of the polymerase chain reaction. J Theor Biol 188, 313-318.

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(1997). Closed form solution for time-dependent enzyme kinetics. J Theor Biol 187, 207-212.

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(1997). Enzymological considerations for a theoretical description of the quantitative competitive polymerase chain reaction (QC-PCR). J Theor Biol 184, 433-440.

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(1996). A quantitative description of the competitive polymerase chain reaction. WIT Trans Biomed Health 3, 13-22.

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(1994). Expression of sodium-channels with different affinity during rat forebrain development. Dev Brain Res 81, 26-40.

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