Peer-reviewed journal publications


Reprints for most publications are available electronically. If you cannot obtain a particular offprint and would like to receive it, please email Dr. Schnell the reference and we will send you a copy. A list of commentaries and editorials, chapters in books, special issues and books are also available.


Our research has also been featured on journal covers. A list of our cover articles is also available.




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 DOI: 10.1074/jbc.M115.676601


K. D. Walton, M. Whidden, Å. Kolterud, S. Shoffer, 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 DOI: 10.1242/dev.130112


Z. M. Harvanek, M. A. Mourão, S. Schnell and S. D. Pletcher (2016). Disentangling individual and population mortality dynamics in aging Drosophila. Proceedings of the Royal Society B DOI: 10.1098/rspb.2015.2346.


M. Vincent, M. Whidden and S. Schnell (2016). Quantitative proteome-based guidelines for protein disorder characterization. Biochimica et Biophysica Acta - Proteins and Proteomics, in review.

Preprint available at bioRxiv DOI: 10.1101/032847


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, in review.

Preprint available at bioRxiv DOI: 10.1101/034900


M. Vincent and S. Schnell (2016). A collection of intrinsic disorder characterizations from eukaryotic proteomes. Scientific Data, in review.

Data available at Dryad DOI: 10.5061/dryad.sm107




A. Khadra and S. Schnell (2015). Development, growth and maintenance of β-cell mass: Models are also part of the story. Molecular Aspects of Medicine 42, 78-90. (review, cover article) DOI: 10.1016/j.mam.2015.01.005


M. Jaberi-Douraki, S. Schnell, M. Pietropaolo and A. Khadra (2015). Unraveling the contributions of pancreatic beta-cell suicide in autoimmune type 1 diabetes.  Journal of theoretical Biology 375, 77-87. DOI: 10.1016/j.jtbi.2014.05.003


S. Schnell (2015). Ten simple rules for a computational biologist's laboratory notebook. PLoS Computational Biology 11, e1004385. DOI:  10.1371/journal.pcbi.1004385




S. Papagerakis, L. Zheng, S. Schnell, M. A. Sartor, W. Marder, E. Somers, L. Ehardt, B. McAlpin, D. Kim, A. Imad, P. Papagerakis (2014). The circadian clock in oral health and diseases. Journal of Dental Research 93, 27-35. (review) DOI: 10.1177/0022034513505768


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) DOI: 10.1111/febs.12564


R. Grima, N. G. Walter and S. Schnell (2014). Single molecule enzymology à la Michaelis-Menten. FEBS Journal 281, 518-530. (review) DOI: 10.1111/febs.12663


M. Mourão, 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. DOI: 10.1039/C3CP52417E (cover article)


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) DOI: 10.1039/C3IB40163D


M. Mourão, L. Satin and S. Schnell (2014). Optimal experimental design to estimate statistically significant periods of  oscillations in time course data. PLoS ONE 9, e93826. DOI: 10.1371/journal.pone.0093826


M. Whidden, A. Ho, M. I. Ivanova and S. Schnell (2014). Competitive reaction mechanisms for the two-step model of protein aggregation.  Biophysical Chemistry 193-194, 9-19. DOI: 10.1016/j.bpc.2014.06.006


M. L. Wynn, N. Consul, S. D. Meravjer and S. Schnell (2014). Inferring the effects of Honokiol on the Notch signaling pathway in SW480 colon cancer cells. Cancer Informatics Suppl. 5, 1-12. DOI: 10.4137/CIN.S14060


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. DOI: 10.3389/fphys.2014.00444


E. R. Shellman, Y. Chen, X. Lin, S. Schnell* and C.F. Burant* (2014). Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. Computational Biology & Chemistry 35, 242-250. DOI: 10.1016/j.compbiolchem.2014.09.006


M. Mourão, J. B. Hakim and S. Schnell (2014). Connecting the dots: The effects of macromolecular crowding on cell physiology. Biophysical Journal, in press. (review) DOI: 10.1016/j.bpj.2014.10.051




E. R. Shellman, C.F. Burant and S. Schnell (2013). Network motifs provide signatures that characterize metabolism. Molecular BioSystems 9, 352-360. DOI: 10.1039/C2MB25346A (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. DOI: 10.11145/j.biomath.2013.03.027


L. Zheng, Y. J. Seon, M. A. Mourão, S. Schnell, D. Kim, H. Harada, S. Papagerakis and P. Papagerakis (2013). Circadian rhythms control ameloblasts differentiation. Bone 55, 158–165. DOI: 10.1016/j.bone.2013.02.011


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. DOI: 10.1088/1478-3975/10/3/035003


C. I. Sandefur, M. Mincheva, S. Schnell (2013). Network representations and methods for the analysis of chemical and biochemical pathways. Molecular BioSystems 9, 2189-2200. (review) DOI: 10.1039/C3MB70052F


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. DOI:10.1371/journal.pone.0072103




M. L. Wynn, S. D. Merajver and S. Schnell (2012). Unraveling the complex regulatory relationships between metabolism and signal transduction in cancer. Advances in Experimental Medicine and Biology 376, 179-189. (review) DOI:10.1007/978-1-4419-7210-1_9


M. L. Wynn, P. M. Kulesa* and S. Schnell* (2012). Computational modeling of collective cell migration reveals mechanisms that sustain follow-the-leader chain behavior. Journal of the Royal Society Interface 9, 1576-1588. DOI: 10.1098/rsif.2011.0726


K. D. Walton, A. Kolterud, M. J. Czerwinski, M. J. Bell, A. Prakash, J. Kushwaha, A. S. Grosse, S. Schnell, D. L. Gumucio (2012). Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi. Proceedings of the National Academy of Sciences of United States of America 109, 15817-15822. DOI: 10.1073/pnas.1205669109


M. L. Wynn, N. Consul, S. D. Merajver and S. Schnell (2012). Logic-based models in systems biology: a predictive and parameter-free network analysis method. Integrative Biology 4, 1323-1337. (review, cover article) DOI:10.1039/C2IB20193C




L. Zheng, S. Papagerakis, S. Schnell, W.A. Hoogerwerf and P. Papagerakis (2011). Expression of clock proteins in developing tooth. Gene Expression Patterns 11, 202-206. DOI: 10.1016/j.gep.2010.12.002


C. I. Sandefur, S. Schnell (2011). A model of threshold behavior reveals rescue mechanisms of bystander proteins in conformational diseases. Biophysical Journal 100, 1864-1873. (cover article) DOI: 10.1016/j.bpj.2011.03.006


M. Mourão, S. Schnell*, S. L. Shaw* (2011). Macroscopic simulations of microtubule dynamics predict two steady-state processes governing array morphology. Computational Biology & Chemistry 35, 269-281. DOI: 10.1016/j.compbiolchem.2011.06.002


M. A. Mourão, 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 6, e27534. DOI: 10.1371/journal.pone.0027534


M. Athanassiou-Papaefthymiou, D. Kim, L. Harbon, S. Papagerakis, S. Schnell, H. Harada,  P. Papagerakis (2011). Developmental and circadian control of enamel formation. European Journal of Oral Sciences 119, 35-40. DOI: 10.1111/j.1600-0722.2011.00918.x




J. Srividhya, M. A. Mourão, E. J. Crampin, S. Schnell (2010). Enzyme catalyzed reactions: from experiments to computational mechanism reconstruction. Computational Biology & Chemistry 34, 11-18. DOI: 10.1016/j.compbiolchem.2009.10.007


E. J. Flach, S. Schnell (2010). Stability of open pathways. Mathematical Biosciences 228, 147-152. DOI: 10.1016/j.mbs.2010.09.002




S. Schnell and R. 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. (review) DOI: 10.1186/1476-7961-7-1.


S. Schnell (2009). A model of the unfolded protein response: Pancreatic beta-cell as a case study. Cellular Physiology and Biochemistry 23, 233-244. DOI:10.1159/000218170.


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. International Journal of Developmental Biology 53, 783-794. DOI:10.1387/ijdb.072493rd




E. H. Flach, S. Schnell and J. Norbury (2008). Limit cycles in the presence of convection, a first order analysis. Journal of Mathematical Chemistry 43, 101-110. DOI: 10.1007/s10910-006-9182-x


R. E. Baker, S. Schnell and P. K. Maini (2008). Mathematical models for somite formation. Current Topics in Developmental Biology 81, 183-203. (review) DOI:10.1016/S0070-2153(07)81006-4


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 structures during somitogenesis in chick. Current Topics in Developmental Biology 81, 205-247. DOI: 10.1016/S0070-2153(07)81007-6


S. Schnell and R. Hancock (2008). The intranuclear environment. Methods in Molecular Biology 463, 3-22. (review) DOI: 10.1007/978-1-59745-406-3_1.


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. DOI: 10.1016/j.susc.2007.12.031.


R. Grima and S. Schnell (2008). Modelling reaction kinetics inside cells. Essays in Biochemistry 45, 41-56. (review) DOI: 10.1042/BSE0450041


S. M Hanson, S. Schnell (2008). The reactant stationary approximation in enzyme kinetics. The Journal of Physical Chemistry A 112, 8654-8658. DOI: 10.1021/jp8026226.




S. Schnell and S. M. Hanson (2007). A test for measuring the effects of enzyme inactivation. Biophysical Chemistry 125, 269-274. DOI: 10.1016/j.bpc.2006.08.010


J. Srividhya, M. S. Gopinathan and S. Schnell (2007). The effects of time delays in a phosphorylation-dephosphorylation pathway. Biophysical Chemistry 125, 286-297. DOI: 10.1016/j.bpc.2006.09.001


J. Srividhya, E. J. Crampin, P. E. McSharry and S. Schnell (2007). Reconstructing biochemical pathways from time course data. Proteomics 7, 828-838. DOI: 10.1002/pmic.200600428


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. DOI: 10.1002/pmic.200600455


P. 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. (review) DOI: 10.1002/dvdy.21199


R. Grima and S. Schnell (2007). A mesoscopic simulation approach for modeling intracellular reactions. Journal of Statistical Physics 128, 139-164. DOI: 10.1007/s10955-006-9202-z


E. H. Flach, S. Schnell and J. Norbury (2007). Turing pattern outside of the Turing domain. Applied Mathematics Letters 20, 959-963. DOI: 10.1016/j.aml.2006.09.009


R. Grima and S. Schnell (2007). Can tissue surface tension drive somite formation? Developmental Biology 307, 248-257. DOI: 10.1016/j.ydbio.2007.04.032


E. H. Flach, S. Schnell and J. Norbury (2007). Limit cycles in the presence of convection, travelling wave analysis. Physical Review E 76, 036216. DOI: 10.1103/PhysRevE.76.036216




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. (highlighted paper)  DOI: 10.1016/j.crvi.2005.09.005


B. Ribba, T. Collin and S. Schnell (2006). A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies. Theoretical Biology and Medical Modelling 3, 7. DOI: 10.1186/1742-4682-3-7


R. E. Baker, S. Schnell and P. K. Maini (2006). A mathematical investigation of a clock and wavefront for somitogenesis. Journal of Mathematical Biology 52, 458-482. DOI: 10.1007/s00285-005-0362-2


R. E. Baker, S. Schnell and P. K. Maini (2006). A clock and wavefront mechanism for somite formation. Developmental Biology 293, 116-126. DOI:10.1016/j.dbio.2006.01.018


J. Srividhya and S. Schnell (2006). Why substrate depletion has apparent first-order kinetics in enzymatic digestion. Computational Biology & Chemistry 30, 209-214. DOI: 10.1016/j.compbiolchem.2006.03.003


R. Grima and S. Schnell (2006). How reaction kinetics with time-dependent rate coefficients differs from generalized mass action. ChemPhysChem 7, 1422-1424. (communication)  DOI: 10.1002/cphc.200600081


E. H. Flach and S. Schnell (2006). On the use and abuse of the Quasi-Steady-State Approximation. IEE Proceedings Systems Biology 153, 187-191. DOI:10.1049/ip-syb:20050104


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 & Chemistry 30, 241-248. DOI:10.1016/j.compbiolchem.2006.04.005


R. Grima and S. Schnell (2006). A systematic investigation of the rate laws valid in intracellular environments. Biophysical Chemistry 124, 1-10. DOI:0.1016/j.bpc.2006.04.019




S. Schnell and C. Mendoza (2004). The condition for pseudo-first-order kinetics to be valid in transient-phase studies of enzymatic reactions is independent of the initial enzyme concentration. Biophysical Chemistry 107, 165-174. DOI:10.1016/j.bpc.2003.09.003


D. McInerney, S. Schnell, R. E. Baker and 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. DOI: 10.1093/imammb/21.2.85


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. DOI:10.1016/j.pbiomolbio.2004.01.012


R. Hinch and S. Schnell (2004). Mechanism equivalence in enzyme-substrate reactions: Distributed differential delay in enzyme kinetics. Journal of Mathematical Chemistry 35, 253-264. DOI:10.1023/B:JOMC.0000033258.42803.60


E. J. Crampin, S. Schnell and P. McSharry (2004). Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Progress in Biophysics and Molecular Biology 86, 77-112. (review) DOI:10.1016/j.pbiomolbio.2004.04.002


T. E. Turner, S. Schnell and K. Burrage (2004). Stochastic approaches for modelling in vivo reactions. Computational Biology and Chemistry 28, 165-178. (review) DOI: 10.1016/j.compbiolchem.2004.05.001


E. J. Crampin, P. McSharry and S. Schnell (2004). Extracting biochemical reaction kinetics from time series data. Lecture Notes in Artificial Intelligence 3214, 329-336. DOI: 10.1007/b100910




S. Schnell and P. K. Maini (2003). A century of enzyme kinetics: Reliability of the KM and vmax estimates. Comments on Theoretical Biology 8, 169-187. (review) DOI: 10.1080/08948550390206768


R. Baker, S. Schnell and P. K. Maini (2003). Formation of vertebral precursors: Past Models and Future Predictions. Journal of Theoretical Medicine 5, 23-35. DOI: 10.1080/10273660310001628365




S. Schnell and P. K. Maini (2002). Enzyme kinetics far from quasi-steady-state and equilibrium approximations. Mathematical and Computer Modelling 35, 137-144. DOI: 10.1016/S0895-7177(01)00156-X


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. (review) DOI:10.1016/S1631-0691(01)01418-4




S. Schnell and C. Mendoza (2001). A fast method to estimate kinetic constants for enzyme inhibitors. Acta Biotheoretica 49, 109-113. DOI:10.1023/A:1010219527831




S. Schnell and C. Mendoza (2000). A formula for integrating inverse functions. The Mathematical Gazette 84, 103-104. Link


S. Schnell and C. Mendoza (2000). Time-dependent closed form solution for fully competitive enzyme kinetics. Bulletin of Mathematical Biology 62, 321-336. DOI:10.1006/bulm.1999.0156


S. Schnell and P. K. Maini (2000). Clock and induction model for somitogenesis. Developmental Dynamics 217, 415-420. DOI: 10.1002/(SICI)1097-0177(200004)217:4<415::AID-DVDY8>3.0.CO;2-3


S. Schnell and P. K. Maini (2000). Enzyme kinetics at high enzyme concentration. Bulletin of Mathematical Biology 62, 483-499. DOI:10.1006/bulm.1999.0163


S. Schnell and C. Mendoza (2000). Enzyme kinetics of multiple alternative substrates. Journal of Mathematical Chemistry 27, 155-170. DOI:10.1023/A:1019139423811


J. R. Collier, D. McInerney, S. Schnell, P. K. Maini, D. J. Gavaghan, P. Houston and C. D. Stern (2000). A cell cycle model for somitogenesis: mathematical formulation and numerical simulation. Journal of theoretical Biology 207, 305-316. DOI: 10.1006/jtbi.2000.2172




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. DOI:10.1006/jtbi.1996.0283


S. Schnell and C. Mendoza (1997). A closed-form solution for time-dependent enzyme kinetic. Journal of theoretical  Biology 187, 207-212. DOI:10.1006/jtbi.1997.0425


S. Schnell and C. Mendoza (1997). Theoretical description of polymerase chain reaction. Journal of theoretical Biology 188, 313-318. DOI:10.1006/jtbi.1997.0473




R. Villegas, C. Castillo, M. E. Póo, S. Schnell, C. Piernavieja, D. Balbi and G. M. Villegas (1994). Expression of sodium channels with different saxitoxin affinity during rat forebrain development. Developmental Brain Research 81, 26-40. DOI: 10.1016/0165-3806(94)90065-5






The Schnell Lab, University of Michigan Medical School

All Rights Reserved