Publications

Preprints

• S. Schnell (2026). Who wrote this? Turing, total variation, and the mathematics of AI-text detection. The Mathematical Intelligencer, submitted. (viewpoint) [Preprint arXiv:2609.13660]

• J. Eilertsen, V. G. Romanovski, S. Schnell, S. Walcher (2026). Lumping of reaction networks: Generic and critical parameters. Nonlinearity, submitted [Preprint arXiv, 606.28895, math.DS]. code

• S. Gilbert, S. Schmid, S. Schnell, J. Svoboda, M. X. Yeo (2026). Liquid democracy under vote correlation: on the fallacies of averaging and the excluded middle. arXiv, 2608.16738 [cs.GT].

• S. Schnell (2026). Decision-grade evidence in rare diseases: A validity-first framework for design, small-sample analysis, and evidence borrowing. Orphanet Journal of Rare Diseases, submitted. (review) code

• J. R. Rohr, M. E. Pfrender, S. Schnell (2026). When editors outnumber articles: Editorial board scaling in special issue and author pays publishing. Quantitative Science Studies, submitted.

• J. Eilertsen, M. A. Tyczynska, S. Schnell (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.v4.

• J. Basappa, M. ElAzzouny, D. Rolland, A. Sahasrabuddhe, K. Ma, G. Bazilevsky, S. Hwang, V. Mendoza-Reinoso, V. Basrur, K. Conlon, N. Bailey, J. Frederiksen, S. Schnell, Y. Zhou, D. Cookmeyer, J. Pawlicki, J. Riley, R. Faryabi, A. D. Amin, J. Schatz, K. Wellen, R. Marmorstein, C. Burant, K.S.J. Elenitoba-Johnson, M. Lim (2020). Phosphotyrosine-mediated regulation of ACLY controls lipid metabolism and oncogenesis. bioRxiv 2020.01.20.910752, DOI: 10.1101/2020.01.20.910752.

2026

• J. D. Calhoun, C. Wang, C. Biar, J. R. Gunti, J. Lee, A. M. Geller, J. H. Hong, S. Schnell, L. T. Dang, Y. Wang, J. Parent, L. L. Isom, M. D. Uhler, H. C. Mefford, M. E. Ross, V. Pulido, G. Carvill (2026). EpiPred: A gene-specific machine learning model for classifying missense variants in the epilepsy-related gene STXBP1. Journal of Clinical Investigation, in press.

• S. Schnell (2026). The stairs of reconciliation: A mathematical tourist in Graz. The Mathematical Intelligencer, in press.

• S. Schnell (2026). From Signals to measurands: A measurement-science roadmap for reproducible analytical biochemistry. ACS Measurement Science Au, ASAP articles. (perspective) code

• I. V. Gimón, C. Sandefur, S. Schnell (2026). Reproducible agent-based simulations of protein aggreation: A FAIR implementation. Bulletin of Mathematical Biology 88, art. 181. code

• S. Schnell (2026). Reaction acceleration: Reviving the second derivative in chemical kinetics. ChemSystemsChem 8, e70047. code

• J. Eilertsen, S. Schnell, S. Walcher (2026). Ehrlich occupancy time: Beyond \(k_{\rm off}\) to a complete residence time framework. Journal of Pharmacokinetics and Pharmacodynamics 53, art. 46. code

• S. Pal, A. Mallela, L. Pracher, C. Wei, F. Fu, S. Schnell, M. A. Nowak (2026). Large language models instantiate evolutionarily robust strategies of cooperation. PNAS Nexus 5, pgag210. data code

• H. V. Westerhoff, B. M. Bakker, A. S. Bommarius, M. L. Cárdenas, A. Cornish-Bowden, P. Fitzpatrick, P. Halling, V. Hatzimanikatis, C. Kettner, Y. Liu, A. G. McDonald, E. Noor, J. Pleiss, F. Raushel, J. Rohwer, S. Schnell, K. F. Tipton, M.-D. Tsai, U. von Stockar, U. Wittig, R. Wohlgemuth, J. M. Woodley (2026). Metabolic thermodynamics: Pertinent reference state and energy potentials FEBS Journal 293, 3111-3126.

• S. Marques, J. Planas-Iglesias, J. Velecký, M. Musil, Y. Asano, T. Borowski, V. Brissos, M. Cespugli, K. Chorozian, M. Dadashipour, E. Erdem, E. Ferrandi, K. Grigorakis, A. Kluza, J. Lawniczek, K. Makryniotis, D. Monti, B. Nestl, A. Ngo, E. Nikolaivits, S. Patti, C. Pentari, C. Ferro Rodrigues, T. Schopper, K. Seweryn-Ożóg, M. Szaleniec, A. Taborda, M. Tataruch, D. Tischler, E. Topakas, J. Wang, P. Wójcik, A. Wojtkiewicz, J. Woodley, O. Zastawny, L. Martins, M. Fraaije, J. Pleiss, S. Schnell, J. Damborský, S. Mazurenko, D. Bednar (2026). Mobilizing the biocatalysis community for reproducible and reusable data collection. ACS Catalysis 16, 8858–8868.

• A. Mallela, S. Schnell (2026). Structural hormesis in protein aggregation: A minimal mechanistic model Journal of the Royal Society Interface 23, 20251037. code

• I. V. Gimón, C. Sandefur, S. Schnell (2026). Macromolecular crowding and protein aggregation: Friend, foe or contextual force?. Progress in Biophysics and Molecular Biology 199, 79-98. (review)

2025

• I. V. Gimón, C. Sandefur, S. Schnell (2025). The hidden influences of macromolecular crowding: A new frontier in cellular biology and medicine. In: Uversky, V.N. (eds) (Macro)Molecular Crowding. Subcellular Biochemistry, vol 109. Springer, Cham. (review)

• S. Schnell, D. L. Gumucio (2025). Medicine and The Arts: Commentary on Thistle. Academic Medicine 100, 1153. (see the image, Thistle by Maria Morrell, PhD)

• K. Srivastava, J. Eilertsen, V. Booth, S. Schnell (2025). Accuracy versus Predominance: Reassessing the validity of the quasi-steady-state approximation. Bulletin of Mathematical Biology 87, 73.

2024

• S. Schnell, P. K. Maini (2024). In Memory of Edmund John Crampin: Multi-scale and multi-physics phenomena in biology. Mathematical Biosciences 376, 109283. (editorial)

• J. Eilertsen, S. Schnell, S. Walcher (2024). The Michaelis-Menten reaction at low substrate concentrations: Pseudo-first-order kinetics and conditions for timescale separation. Bulletin of Mathematical Biology 86, 68.

• M. S. DeNies, Allen P. Liu, S. Schnell (2024). Seeing beyond the blot: A critical look at assumptions and raw data interpretation in Western blotting. Biomolecular Concepts 15, 20220047.

• J. Eilertsen, S. Schnell, S. Walcher (2024). The unreasonable effectiveness of the total quasi-steady state approximation, and its limitations. Journal of Theoretical Biology 583, 111770.

• J. Eilertsen, S. Schnell, S. Walcher (2024). Rigorous estimates for the quasi-steady state approximation of the Michaelis-Menten reaction mechanism at low enzyme concentrations. Nonlinear Analysis: Real World Applications 120, e2219683120.

2023

• K. Ikami, S. Shoffner-Beck, M. Tyczynska Weh, S. Schnell, S. Yoshida, E. A. Diaz Miranda, S. Ko, L. Lei (2023). Branched germline cysts and female-specific cyst fragmentation facilitate oocyte determination in mice. Proceedings of the National Academy of Sciences of the United States of America 120, e2219683120.

• J. Eilertsen, S. Schnell, S. Walcher (2023). Natural parameter conditions for singular perturbations of chemical and biochemical reaction networks. Bulletin of Mathematical Biology 85, 48.

• M. A. Gingerich, J. Zhu, B. Chai, M. P. Vincent, N. Xie, V. Sidarala, N. A. Kotov, D. Sahu. D. J. Klionsky, S. Schnell, S. A. Soleimanpour (2023). Reciprocal regulatory balance within the CLEC16A-RNF41 mitophagy complex depends on an intrinsically disordered protein region. Journal of Biological Chemistry 299, 103057.

• S. Lauterbach, H. Dienhart, J. Range, S. Malzacher, J.-D. Spöring, D Rother, M. Filipa Pinto, P. Martins, C. E. Lagerman, A. S. Bommarius, A. V. Høst, J. M. Woodley, S. Ngubane, T. Kudanga, F. T. Bergmann, J. M. Rohwer, D. Iglezakis, A. Weidemann, U. Wittig, C. Kettner, N. Swainston, S. Schnell, J. Pleiss (2023). EnzymeML at work: seamless data flow and modelling of enzymatic data. Nature Methods 20, 400–402. github

• M. A. Gingerich, X. Liu, B. Chai, G. L. Pearson, M. P. Vincent, T. Stromer, J. Zhu, V. Sidarala, A. Renberg, D. Sahu, D. J. Klionsky, S. Schnell, S. A. Soleimanpour (2023). An intrinsically disordered protein region encoded by the human disease gene CLEC16A regulates mitophagy. Autophagy 19, 525-543.

2022

• J. Range, C. Halupczok, J. Lohmann, N. Swainston, C. Kettner, F. T. Bergmann, A. Weidemann, U. Wittig, S. Schnell, J. Pleiss (2022). EnzymeML - an exchange format for biocatalysis and enzymology. FEBS Journal 289, 5864-5874. github

• J. Eilertsen, S. Schnell, S. Walcher (2022). On the anti-quasi-steady-state conditions of enzyme kinetics. Mathematical Biosciences 350, 108870.

• J. Eilertsen, K. Srivastava, S. Schnell (2022). Stochastic enzyme kinetics and the quasi-steady-state reductions: Application of the slow scale linear noise approximation à la Fenichel. Journal of Mathematical Biology 85, 3. code

• J. Eilertsen, S. Schnell (2022). On the validity of the stochastic quasi-steady-state approximation in open enzyme catalyzed reactions: Timescale separation or singular perturbation?. Bulletin of Mathematical Biology 84, 7.

2021

• J. Eilertsen, M. A. Tyczynska, S. Schnell (2021). Hunting \(\epsilon\): The origin and validity of quasi-steady-state reductions in enzyme kinetics. SIAM Journal on Applied Dynamical Systems 20, 2450-2481.

• N. D. Urban, J. P. Cavataio, Y. Berry, B. Vang, A. Maddali, R. J. Sukpraphrute, S. Schnell, M. Truttmann (2021). Explaining inter-lab variance in C. elegans N2 lifespan: Making a case for standardized reporting to enhance reproducibility. Experimental Gerontology 156, 111622.

• J. C. Kasemeier-Kulesa, J. A. Spengler, C. E. Muolo, J. A. Morrison, T. E. Woolley, S. Schnell, P. M. Kulesa (2021). The embryonic trunk neural crest microenvironment regulates the plasticity and invasion of human neuroblastoma via TrkB signaling. Developmental Biology 480, 78-90.

• J. Eilertsen, M. R. Roussel, S. Schnell, S. Walcher (2021). On the quasi-steady-state approximation in an open Michaelis-Menten reaction mechanism. AIMS Mathematics 6, 6781-6814.

• D. Felker, H. Zhang, Z. Bo, M. Lau, Y. Morishima, S. Schnell, Y. Osawa (2021). Mapping protein-protein interactions in homodimeric CYP102A1 by crosslinking and mass spectrometry. Biophysical Chemistry 274, 106590. (cover article)

• W. Stroberg and S. Schnell (2021). Concentration sensing in crowded environments. Biophysical Journal 120, 1718-1731. code

• J. Cavataio and S. Schnell (2021). Interpreting SARS-CoV-2 fatality rate estimates: A case for introducing standardized reporting to improve communication. Mathematical Biosciences 333, 108545. (review)

2020

• M. S. DeNies, A. Smrcka, S. Schnell, A. P. Liu (2020). \(\beta\)-arrestin mediates communication between plasma membrane and intracellular GPCRs to regulate signaling. Communications Biology 3, 789.

• J. Penix, R. A. DeFazio, E. A. Dulka, S. Schnell, and S. M. Moenter (2020). Firing patterns of gonadotropin-releasing hormone neurons are sculpted by their biologic state. Royal Society Open Science 7, 201040. code

• M. L. Conte, S. Schnell, A. S. Ettinger, M. B. Omary (2020). Trends in NIH-supported career development funding: implications for institutions, trainees, and the future research workforce. JCI Insight 5, e142817. (perspective)

• J. Eilertsen, S. Schnell (2020). The quasi-steady-state approximations revisited: Timescales, small parameters, singularities, and normal forms in enzyme kinetics. Mathematical Biosciences 325, 108339.

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

• M. S. DeNies, Allen P. Liu, S. Schnell (2020). Are the biomedical sciences ready for synthetic biology?. Biomolecular Concepts 11, 23-31. (review)

2019

• J. Eilertsen, W. Stroberg and S. Schnell (2019). Characteristic, completion or matching timescales? An analysis of temporary boundaries in enzyme kinetics. Journal of Theoretical Biology 481, 28-43.

• S. Schnell (2019). Have we come to the end of theoretical and mathematical biology? Journal of Theoretical Biology 481, 1-2. (editorial)

• W. Stroberg, J. Eilertsen and S. Schnell (2019). Information processing by endoplasmic reticulum stress sensors. Journal of the Royal Society Interface 16, 20190288. code

• M. Vincent and S. Schnell (2019). Disorder Atlas: A web-based tool to characterize protein disorder at the proteome level. Computational Biology & Chemistry 83, 107090. website

• M. J. Acevedo-Calado, S. L. Pietropaolo, M. P. Morran, S. Schnell, A. D. Vonberg, C. F. Verge, R. Gianani, D. J. Becker, S. Huang, C. J. Greenbaum, L. Yu, H. W. Davidson, A. W. Michels, S. S. Rich and M. Pietropaolo (2019). Autoantibodies directed toward a novel IA-2 variant protein enhance prediction of type 1 diabetes. Diabetes 68, 1819-1829. (cover article)

• M. S. DeNies, L. Kauer-Rosselli, S. Schnell and A. P. Liu (2019). Clathrin heavy chain knockdown impacts CXCR4 signaling and post-translational modification. Frontiers in Cell and Developmental Biology 7, 77.

• S. Pitchiaya, M. D.A. Mourao, A. Jalihal, L. Xiao, X. Jiang, A. M. Chinnaiyan, S. Schnell and N. G. Walter (2019). Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality. Molecular Cell 74, 521-533.

• M. B. Omary, Y. M. Shah, S. Schnell, S. Subramanian, M. S. Swanson and M X. O'Riordan (2019). Enhancing career development of postdoctoral trainees: Act locally and beyond. Journal of Physiology 597, 2317-2322. (cover article)

• M. Vincent, V. N. Uversky and S. Schnell (2019). On the need to develop guidelines for characterizing and reporting intrinsic disorder in proteins. Proteomics 19, 1800415. (perspective, cover article)

• C. E. Adams, R. A. DeFazio, C. A. Christian, L. Milescu, S. Schnell, and S. M. Moenter (2019). Changes in both neuron intrinsic properties and neurotransmission are needed to drive the increase in GnRH neuron firing rate during estradiol positive feedback. Journal of Neuroscience 39, 2091-2101. (cover article)

2018

• J. Eilertsen and S. Schnell (2018). A kinetic analysis of coupled (or auxiliary) enzyme reactions. Bulletin of Mathematical Biology 80, 3154-3183.

• J. Eilertsen, W. Stroberg and S. Schnell (2018). Phase-plane geometries in coupled enzyme assays. Mathematical Biosciences 306, 126-135.

• W. Stroberg, H. Atkin, Y. Savir and S. Schnell (2018) How to design an optimal sensor network for the unfolded protein response. Molecular Biology of the Cell 29, 3052-3062. (cover article) code

• S. Schnell (2018). 'Reproducible' research in mathematical sciences requires changes in our peer review culture and modernization of our current publication approach. Bulletin of Mathematical Biology 80, 3095-3105.

• J. Eilertsen, W. Stroberg and S. Schnell (2018). A theory of reactant-stationary kinetics for a mechanism of zymogen activation. Biophysical Chemistry 242, 34-44.

• P. Halling, P. Fitzpatrick, F. M. Raushel, J. Rohwer, S. Schnell, U. Wittig, R. Wohlgemuth and C. Kettner (2018). An empirical analysis of enzyme function reporting for experimental reproducibility: missing/incomplete information in published papers. Biophysical Chemistry 242, 22-27.

• S. Wang, C. Cebrian, S. Schnell and D. L. Gumucio (2018). Radial WNT5A-guided post-mitotic filopodial pathfinding is critical for midgut tube elongation. Developmental Cell 46, 173-188.

• W. Stroberg and S. Schnell (2018) Do cellular condensates accelerate biochemical reactions? Lessons from microdroplet chemistry. Biophysical Journal 115, 3-8. (review)

• N. Swainston, and C. Kettner on behalf of STREDA Commission [A. Baici, B. M. Bakker, A. Cornish-Bowden, P. F. Fitzpatrick, P. Halling, T. S. Leyh, C. O'Donovan, F. M. Raushel, J. M. Rohwer, S. Schnell, D. Schomburg, K. F. Tipton, M.-D. Tsai, U. Wittig, R. Wohlgemuth] (2018) A repository for quality-assured data on enzyme activity. Nature 556, 309. (correspondence)

• N. Swainston, A. Baici, B. M. Bakker, A. Cornish-Bowden, P. F. Fitzpatrick, P. Halling, T. S. Leyh, C. O'Donovan, F. M. Raushel, U. Reschel, J. M. Rohwer, S. Schnell, D. Schomburg, K. F. Tipton, M.‐D. Tsai, H. V. Westerhoff, U. Wittig, R. Wohlgemuth, and C. Kettner (2018). STRENDA DB: enabling the validation and sharing of enzyme kinetics data. FEBS Journal 285, 2193-2204. website

• J. C. Kasemeier-Kulesa, S. Schnell, T. Woolley, J. A. Spengler, J. A. Morrison, M. C. McKinney, L. A. Wolfe, and P. M. Kulesa (2018). Predicting Neuroblastoma using developmental signals and a logic-based model. Biophysical Chemistry 238, 30-38. code

• M. L. Wynn, M. Egbert, N. Consul, J. Chang, Z.-F. Wu, S. D. Meravjer, S. Schnell (2018). Inferring intracellular signal transduction circuitry from molecular perturbation experiments. Bulletin of Mathematical Biology 80,1310-1344.

• C. Adams, W. Stroberg, R. A. DeFazio, S. Schnell and S. M. Moenter (2018). Gonadotropin-releasing hormone (GnRH) neuron excitability is regulated by estradiol feedback and kisspeptin. Journal of Neuroscience 38, 1249-1263.

2017

• W. Stroberg and S. Schnell (2017) On the origin of non-membrane-bound organelles, and their physiological function. Journal of Theoretical Biology 434, 42-49.

• M. L. Conte, J. Liu, S. Schnell and M. B. Omary (2017). Globalization and changing trends of biomedical research output. JCI Insight 2, e95206. (perspective)

• F. S. Midani, M. L. Wynn and Santiago Schnell (2017). The importance of accurately correcting for the natural abundance of stable isotopes. Analytical Biochemistry 520, 27-43. (review)

• A R. Udyavar, D. J. Wooten, M. Hoeksema, M. Bansal, A. Califano, L. Estrada, S. Schnell, J. Irish, P. P. Massion and V. Quaranta (2017). A systems-level approach to gene expression profiling reveals a hybrid phenotype in Small-Cell Lung Cancer. Cancer Research 77, 1063-1074.

• S. K. Shoffner and S. Schnell (2017). Approaches for the estimation of timescales in nonlinear dynamical systems: Timescale separation in enzyme kinetics as a case study. Mathematical Biosciences 287, 122-129. (review)

• W. Stroberg and S. Schnell (2017). On the validity and errors of the pseudo-first-order kinetics in ligand-receptor binding. Mathematical Biosciences 287, 3-11.

2016

• W. Stroberg and S. Schnell (2016) On the estimation errors of \(K_M\) and \(V\) from time-course experiments using the Michaelis-Menten equation. Biophysical Chemistry 219, 17-27. code

• A. M. Freddo, S. K. Shoffner, Y. Shao, K. Taniguchi, A. S. Grosse, M. N. Guysinger, S. Wang, S. Rudraraju, B. Margolis, K. Garikipati, S. Schnell and D. L. Gumucio (2016). Coordination of signaling and tissue mechanics during morphogenesis of murine intestinal villi: a role for mitotic cell rounding. Integrative Biology 8, 918-928. (cover article)

• S. K. Shoffner and S. Schnell (2016). Estimation of the lag time in a subsequent monomer addition model for fibril elongation. Physical Chemistry Chemical Physics 18, 21259-21268. (cover article) code

• M L. Wynn, J. Yates, C. Evans, L. Van Wassenhove, Z. F. Wu, S. Bridges, L. Bao, C. Fournier, S. Ashrafzadeh, M. J. Merrins, L. S. Satin, S. Schnell, C. F. Burant , and S. D. Merajver (2016). RhoC is a potent regulator of glutamine metabolism and N-acetylaspartate production in inflammatory breast cancer cells. Journal of Biological Chemistry 291, 13715-13729.

• M. Vincent and S. Schnell (2016). A collection of intrinsic disorder characterizations from eukaryotic proteome. Scientific Data 3, 160045. dataset

• M. Vincent, M. Whidden and S. Schnell (2016). Quantitative proteome-based guidelines for protein disorder characterization. Biophysical Chemistry 213, 6-16.

• Z. M. Harvanek, M. A. Mourão, S. Schnell and S. D. Pletcher (2016). A computational approach to studying ageing at the individual level. Proceedings of the Royal Society B 283, 20152346.

• B. Wang, S. A. Merillat, M. Vincent, A. K. Huber, V. Basrur, D. Mangelberger, L Zeng, K. Elenitoba-Johnson, R. A. Miller, D. N. Irani, A. A. Dlugosz, S. Schnell, K. M. Scaglione and H. L. Paulson (2016). Loss of the Ubiquitin-conjugating Enzyme Ube2W results in susceptibility to early postnatal lethality and defects in skin, immune and male reproductive systems. Journal of Biological Chemistry 291, 3030-3042.

• K. D. Walton, M. Whidden, Å. Kolterud, S. K. Shoffner, M. J. Czerwinski, J. Kushwaha, N. Parmar, D. Chandhrasekhar, A. M. Freddo, S. Schnell and D. L. Gumucio (2016). Villification in the mouse: Bmp signals control intestinal villus patterning. Development 143, 427-436.

2015

• P. K. Maini, R. E. Baker and S. Schnell (2015). Rethinking models of pattern formation in somitogenesis. Cell Systems 1, 248-249. (commentary)

• S. Schnell (2015). Ten simple rules for a computational biologist's laboratory notebook. PLoS Computational Biology 11, e1004385. (pedagogical article)

• L. Satin and S. Schnell (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. (commentary)

• M. Jaberi-Douraki, S. Schnell, M. Pietropaolo and A. Khadra (2015). Unraveling the contribution of pancreatic beta-cell suicide in autoimmune type 1 diabetes. Journal of Theoretical Biology 375, 77-87.

• A. Khadra and S. Schnell (2015). Development, growth and maintenance of \(\beta\)-cell mass: Models are also part of the story. Molecular Aspects of Medicine 42, 78-90. (review)

• P. Arvan, E. Bernal-Mizrachi, M. Liu, M. Pietropaolo, L. S. Satin, S. Schnell and S. A. Soleimanpour (2015). Molecular aspects of pancreatic beta cell failure and diabetes. Molecular Aspects of Medicine 42, 427-436. (editorial, cover article)

2014

• M. A. Mourao, J. B. Hakim and S. Schnell (2014). Connecting the dots: The effects of macromolecular crowding on cell physiology. Biophysical Journal 107, 2761-2766. (review)

• E. R. Shellman, Y. Chen, X. Lin, C. F. Burant and S. Schnell (2014). Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. Computational Biology and Chemistry 53, 242-250.

• M. Vincent, M. Whidden and S. Schnell (2014) Surveying the floodgates: Estimating protein flux into the endoplasmic reticulum lumen in Saccharomyces cerevisiae. Frontiers in Physiology 5, 444.

• M. L. Wynn, N. Consul, S. D. Merajver and S. Schnell (2014). Inferring the effects of Honokiol on the Notch signaling pathway in SW480 colon cancer cells. Cancer Informatics 13s5, 1-12.

• M. Whidden, A. Ho, M. I. Ivanova and S. Schnell (2014). Competitive inhibition reaction mechanisms for the two-step model of protein aggregation. Biophysical Chemistry 193-194, 9-19.

• M. A. Mourao, L. Satin and S. Schnell (2014). Optimal experimental design to estimate statistically significant periods of oscillations in time course data. PLoS ONE 242, 22-27. code

• M. A. Mourao, D. Kreitman and S. Schnell (2014). Unravelling the impact of obstacles in diffusion and kinetics of an enzyme catalysed reaction. Physical Chemistry Chemical Physics 16, 4492-4503. (cover article) code

• A. J. Carulli, L. C. Samuelson and S. Schnell (2014) Unraveling intestinal stem cell behavior with models of crypt dynamics. Integrative Biology 6, 243-257. (review, cover article)

• R. Grima, N. G Walter and S. Schnell (2014). Single-molecule enzymology à la Michaelis–Menten. FEBS Journal 281, 518-530. (review)

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

• S. Papagerakis, L. Zheng, S. Schnell, M. A. Sartor, E. Somers, W. Marder, B. McAlpin, D. Kim, J. McHugh and P. Papagerakis (2014). The circadian clock in oral health and diseases. Journal of Dental Research 93, 27-35. (review)

• M. Whidden, A. Ho and S. Schnell (2014). A two-step kinetic model of insulin aggregation with a competitive inhibitor. In: BIOMATH 2013, 107-120. (book chapter)

2013

• C. I. Sandefur, M. Mincheva and S. Schnell (2013). Network representations and methods for the analysis of chemical and biochemical pathways. Molecular BioSystems 9, 2189-2200. (review)

• Y. K. Wang, D. G. Hurley, S. Schnell, C. G. Print and E. J. Crampin (2013). Integration of steady-state and temporal gene expression data for the inference of gene regulatory networks. PLoS ONE 8, e72103.

• L. Zheng, Y. J. Seon, M. A. Mourao, S. Schnell, D. Kim, H. Harada, S. Papagerakis and P. Papagerakis (2013). Circadian rhythms regulate amelogenesis. Bone 55, 158-165.

• M. L. Wynn, P. Rupp, P. A. Trainor, S. Schnell* and P. M. Kulesa* (2013). Follow-the-leader cell migration requires biased cell–cell contact and local microenvironmental signals. Physical Biology 10, 035003.

• S. Schnell and M. Pietropaolo (2013). Designing nanoparticle treatment of autoimmunity with quantitative biology. Immunology & Cell Biology 91, 333-334. (commentary)

• E. R. Shellman, C. F. Burant and S. Schnell (2013). Network motifs provide signatures that characterize metabolism. Molecular BioSystems 9, 352-360. (cover article)

• E. H. Flach, J. Norbury and S. Schnell (2013). More than skew: asymmetric wave propagation in a reaction-diffusion-convection systems. Biomath 2, 201303027.

2012

• M. L. Wynn, N. Consul, S. D. Merajver and S. Schnell (2012). Logic-based models in systems biology: network analysis method. Integrative Biology 4, 1323-1337. (review, cover article)

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

• K. D. Walton, A. Kolterud, M. J. Czerwinski, M. J. Bell, A. Prakash, J. Kushwaha, A. S. Grosse, S. Schnell and D. L. Gumucio (2012). Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi. Proceedings of the National Academy of Sciences of the United States of America 109, 15817-15822.

• M. L. Wynn, P. M. Kulesa and S. Schnell (2012). Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour. Journal of the Royal Society Interface 9, 1576-1588.

• M. L. Wynn, S. D. Merajver and S. Schnell (2012). Unraveling the Complex Regulatory Relationships Between Metabolism and Signal Transduction in Cancer. In: Advances in Systems Biology. Advances in Experimental Medicine and Biology 736, 179-189. (perspective)

2011

• M. Athanassiou-Papaefthymiou, D. Kim, L. Harbron, S. Papagerakis, S. Schnell, H. Harada and P. Papagerakis (2011). Molecular and circadian controls of ameloblasts. European Journal of Oral Sciences 119 (Suppl. 1), 35-40. (review)

• M. A. Mourao, J. Srividhya, P. E. McSharry, E. J. Crampin and S. Schnell (2011). A graphical user interface for a method to infer kinetics and network architecture (MIKANA). PLoS ONE 3, 233-244. code

• M. Mourao, S. Schnell, S. L. Shaw (2011) Macroscopic simulations of microtubule dynamics predict two steady-state processes governing array morphology. Computational Biology and Chemistry 35, 269-281. code

• C. I. Sandefur and S. Schnell (2011). A model of threshold behavior reveals rescue mechanisms of bystander proteins in conformational diseases. Biophysical Journal 100, 1864-1873. (cover article)

• L. Zheng, S. Papagerakis, S. Schnell, M. A. Hoogerwerf, P. Papagerakis (2011). Expression of clock proteins in developing tooth. Gene Expression Patterns 11, 202-206.

• C. I. Sandefur, S. Schnell (2011). Effects of protein quality control machinery on protein homeostasis. In: Dubitzky, W., Southgate, J., Fuß, H. (eds) Understanding the Dynamics of Biological Systems. Springer, New York, NY.

2010

• E. H. Flach, S. Schnell (2010). Stability of open pathways. Mathematical Biosciences 228, 147-152.

• J. Srividhya, M. A. Mourao, E. J. Crampin, S. Schnell (2010). Enzyme catalyzed reactions: From experiment to computational mechanism reconstruction. Computational Biology and Chemistry 34, 11-18.

• O. Wolkenhauer, C. Auffray, S. Baltrusch, N. Bluthgen, H. Byrne, M. Cascante, A. Ciliberto, T. Dale, D. Drasdo, D. Fell, J. E. Ferrell Jr, D. Gallahan, R. Gatenby, U. Gunther, B. D. Harms, H. Herzel, C. Junghanss, M. Kunz, I. van Leeuwen, P. Lenormand, F. Levi, M. Linnebacher, J. Lowengrub, P. K. Maini, A. Malik, K. Rateitschak, O. Sansom, R. Schafer, K. Schurrle, C. Sers, S. Schnell, D. Shibata, J. Tyson, J. Vera, M. White, B. Zhivotovsky and R. Jaster (2010). Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Research 70, 12-13. (meeting report)

2009

• R. E. Baker, S. Schnell and P. K. Maini (2009). Waves and patterning in developmental biology: vertebrate segmentation and feather bud formation as case studies. The International Journal of Developmental Biology 53, 783-794. (review)

• S. Schnell (2009). A model of the unfolded protein response: Pancreatic beta-cell as a case study. Cellular Physiology and Biochemistry 23, 233–244.

• R. E. Baker and S. Schnell (2009). How can mathematics help us explore vertebrate segmentation?. HFSP Journal 3, 1-5. (commentary)

• S. Schnell and Rod A. Herman(2009). Should digestion assays be used to estimate persistence of potential allergens in tests for safety of novel food proteins?. Clinical and Molecular Allergy 7, 1. (perspective)

2008

• R. Grima and S. Schnell (2008). Modelling reaction kinetics inside cells. Essays in Biochemistry 45, 41-56. (review)

• S. M. Hanson and S. Schnell (2008). Reactant stationary approximation in enzyme kinetics. The Journal of Physical Chemistry A 112, 8654–8658.

• C. Mendoza, L. S. Rodriguez, F. Ruette and S. Schnell (2008). Formation of monocarboxylic acids and polyols on a graphitic surface. Surface Science 602, 1053-1060.

• S. Schnell and R. Hancock (2008). The intranuclear environment. In: The Nucleus. Methods in Molecular Biology 463, 3-19. (review)

• E. H. Flach, J. Norbury and S. Schnell (2008). Limit cycles in the presence of convection: a first-order analysis. Journal of Mathematical Chemistry 43, 101-110.

• J. A. Glazier, Y. Zhang, M. Swat, B. Zaitlen and S. Schnell (2008). Coordinated action of N-CAM, N-cadherin, EphA4, and ephrinB2 translates genetic prepatterns into structure during somitogenesis in chick. Current Topics in Developmental Biology 81, 205-247.

• R. E. Baker, S. Schnell and P. K. Maini (2008). Mathematical models for somite formation. Current Topics in Developmental Biology 81, 183-203. (review)

• S. Schnell, P. K. Maini, S. A. Newman and T. J. Newman (2008). Multiscale Modeling of Developmental Systems. Current Topics in Developmental Biology 81 (book)

2007

• E. H. Flach, S. Schnell and J. Norbury (2007). Limit cycles in the presence of convection: A traveling wave analysis. Physical Review E 76, 036216.

• E. H. Flach, S. Schnell and J. Norbury (2007). Turing pattern outside of the Turing domain. Applied Mathematics Letters 20, 959-963.

• R. Grima and S. Schnell (2007). Can tissue surface tension drive somite formation?. Developmental Biology 307, 248-257.

• R. Grima and S. Schnell (2007). A mesoscopic simulation approach for modeling intracellular reactions. Journal of Statistical Physics 128, 139–164.

• P. M. Kulesa, S. Schnell, S. Rudloff, R. E. Baker and P. K. Maini (2007). From segment to somite: Segmentation to epithelialization analyzed within quantitative frameworks. Developmental Dynamics 236, 1392-1402.

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

• J. Srividhya, E. J. Crampin, P. E. McSharry and S. Schnell (2007). Reconstructing biochemical pathways from time course data. Proteomics 7, 828-838.

• S. Schnell, R. Grima and P. K. Maini (2007). Multiscale modeling in biology. American Scientist 95, 134–142. (review, cover article)

• J. Srividhya, A. S. Gopinathan and S. Schnell (2007). The effects of time delays in a phosphorylation-dephosphorylation pathway. Biophysical Chemistry 125, 286-297.

• S Schnell and S. M. Hanson (2007). A test for measuring the effects of enzyme inactivation. Biophysical Chemistry 125, 269-274.

2006

• R. Grima and S. Schnell (2006). A systematic investigation of the rate laws valid in intracellular environments. Biophysical Chemistry 124, 1-10. code

• S. Roy, S. Schnell and P. Radivojac (2006). Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. Computational Biology and Chemistry 30, 241-248.

• R. Grima and S. Schnell (2006). How reaction kinetics with time-dependent rate coefficients differs from generalized mass action. ChemPhysChem 7, 1422-1424. (communication)

• E. H. Flach and S. Schnell (2006). Use and abuse of the quasi-steady-state approximation. IEE Proceedings - Systems Biology 153, 187-191.

• S. Schnell (2006). Unravelling the function and kinetics of biochemical networks. IEE Proceedings - Systems Biology 153, 139. (editorial)

• J. Srividhya and S. Schnell (2006). Why substrate depletion has apparent first-order kinetics in enzymatic digestion. Computational Biology and Chemistry 30, 209-214.

• S. Schnell (2006). Computational Modeling of Genetic and Biochemical Networks. Briefings in Bioinformatics 7, 204-206. (book review)

• R. E. Baker, S. Schnell and P. K. Maini (2006). A clock and wavefront mechanism for somite formation. Developmental Biology 293, 116-126.

• R. E. Baker, S. Schnell and P. K. Maini (2006). A mathematical investigation of a clock and wavefront model for somitogenesis. Journal of Mathematical Biology 52, 458-482.

• B. Ribba, T. Colin, S. Schnell (2006). A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies. Theoretical Biology and Medical Modelling 3, 7.

• S. Schnell, M. J. Chappell, N. D. Evans and M. R. Roussel (2006). The mechanism distinguishability problem in biochemical kinetics: The single-enzyme, single-substrate reaction as a case study. Comptes Rendus Biologies 329, 51-61.

Before 2005

• E. J. Crampin, P. E. McSharry, S. Schnell (2004). Extracting biochemical reaction kinetics from time series data. In: Negoita, M.G., Howlett, R.J., Jain, L.C. (eds) Knowledge-Based Intelligent Information and Engineering Systems. KES 2004. Lecture Notes in Computer Science, vol 3214. Springer, Berlin, Heidelberg.

• E. J. Crampin, S. Schnell and P. E. McShary (2004). Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Progress in Biophysics and Molecular Biology 86, 77-112. (review)

• E. J. Crampin and S. Schnell (2004). New approaches to modelling and analysis of biochemical reactions, pathways and networks. Progress in Biophysics and Molecular Biology 86, 1-4. (editorial)

• T. E. Turner, S. Schnell and K. Burrage (2004). Stochastic approaches for modelling in vivo reactions. Computational Biology and Chemistry 28, 165-178. (review)

• P. K. Maini, S. Schnell and S. Jolliffe (2004). Bulletin of mathematical biology—facts, figures and comparisons. Bulletin of Mathematical Biology 66, 595–603. (editorial)

• S. Schnell and T. E. Turner (2004). Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws. Progress in Biophysics and Molecular Biology 85, 235-260. code

• D. McInerney, S. Schnell, R. E. Baker, P. K. Maini (2004). A mathematical formulation for the cell-cycle model in somitogenesis: Analysis, parameter constraints and numerical solutions. Mathematical Medicine and Biology: A Journal of the IMA 21, 85-113.

• R. Hinch, S. Schnell (2004). Mechanism Equivalence in Enzyme–Substrate Reactions: Distributed Differential Delay in Enzyme Kinetics. Journal of Mathematical Chemistry 35, 253–264.

• S. Schnell (2004). Parametric Sensitivity in Chemical Systems. Bulletin of Mathematical Biology 66, 393–395. (book review)

• S. Schnell and C. Mendoza (2004). The condition for pseudo-first-order kinetics in enzymatic reactions is independent of the initial enzyme concentration. Biophysical Chemistry 107, 165-174.

• R. E. Baker, S. Schnell and P. K. Maini (2003). Formation of Vertebral Precursors: Past Models and Future Predictions. Journal of Theoretical Medicine 5, 23-35. (review)

• S. Schnell and J. Hein (2003) Computational Cell Biology. Briefings in Bioinformatics 4, 87–89. (book review)

• S. Schnell and P. K. Maini (2003) A century of enzyme kinetics: Reliability of the K\(*M\) and v\(*{max}\) estimates. Comments on Theoretical Biology 8, 169-187. (review)

• S. Schnell, P. K. Maini, D. McInerney, D. J. Gavaghan and P. Houston (2002). Models for pattern formation in somitogenesis: a marriage of cellular and molecular biology. Comptes Rendus Biologies 325, 179-189.

• S. Schnell and P. K. Maini (2002) Enzyme kinetics far from the standard quasi-steady-state and equilibrium approximations. Mathematical and Computer Modelling 35, 137-144.

• S. Schnell and C. Mendoza (2001). A fast method to estimate kinetic constants for enzyme inhibitors. Acta Biotheoretica 49, 109-113.

• J. R. Collier, D. McInerney, S. Schnell, P. K. Maini, D. J. Gavaghan, P. Houston, C. D. Stern (2000). A cell cycle model for somitogenesis: Mathematical formulation and numerical simulation. Journal of Theoretical Biology 207, 305-316.

• S. Schnell and C. Mendoza (2000). Enzyme kinetics of multiple alternative substrates. Journal of Mathematical Chemistry 27, 155-170.

• S. Schnell and P. K. Maini (2000). Enzyme kinetics at high enzyme concentration. Bulletin of Mathematical Biology 62, 483-499.

• S. Schnell and P. K. Maini (2000). Clock and induction model for somitogenesis. Developmental Dynamics 217, 415-420.

• S. Schnell and C. Mendoza (2000). Time-dependent closed form solutions for fully competitive enzyme reactions. Bulletin of Mathematical Biology 62, 321-336.

• S. Schnell and C. Mendoza (2000). A formula for integrating inverse functions. Mathematical Gazette 62, 103-104. (Note: 84.20)

• S. Schnell, K. J. Painter, P. K. Maini, H. G. Othmer (2001). Spatiotemporal pattern formation in early development: A review of primitive streak formation and somitogenesis. In: Maini, P.K., Othmer, H.G. (eds) Mathematical Models for Biological Pattern Formation. The IMA Volumes in Mathematics and its Applications, vol 121. Springer, New York, NY.

• S. Schnell and C. Mendoza (1997). Theoretical description of the polymerase chain reaction. Journal of Theoretical Biology 188, 313-318.

• S. Schnell and C. Mendoza (1997). Closed form solution for time-dependent enzyme kinetics. Journal of Theoretical Biology 187, 207-212.

• S. Schnell and C. Mendoza (1997). Enzymological considerations for a theoretical description of the quantitative competitive polymerase chain reaction (QC-PCR). Journal of Theoretical Biology 184, 433-440.

• S. Schnell and C. Mendoza (1996). A quantitative description of the competitive polymerase chain reaction. WIT Transactions on Biomedicine and Health 3, 13-22. (book chapter)

• R. Villegas, C. Castillo, M. E. Poo, S. Schnell, C. Piernavieja, D. Balbi, G. M. Villegas (1994). Expression of sodium-channels with different affinity during rat forebrain development. Developmental Brain Research 81, 26-40.

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