Papers

For papers in a particular topic, try subpages under “Papers” on the toolbar. For a nearly complete bibliography but no actual papers, try the CV. Older papers from 2010 and earlier can be found here. Otherwise, here is a (currently very incomplete) mixture of somewhat newer papers on all topics:

  • (2019) C. B. Scott and Eric Mjolsness. Multilevel artificial Neural Network Training for Spatially Correlated Learning . SIAM J. Sci. Comput., vol 41 no. 5, pp. S297-S320, October 2019. https://doi.org/10.1137/18M1191506 .
  • (2019) Mark Alber, Christophe Godin, Philip Maini, Roeland Merks, and Eric Mjolsness. Introduction. Editorial introduction to the Special Issue on Modeling Tissue Growth and Shape, Bulletin of Mathematical Biology, vol. 81 no. 8, August 2019. https://doi.org/10.1007/s11538-019-00649-2
  • (2019) Oliver K. Ernst, Tom Bartol, Terrence Sejnowski, Eric Mjolsness.  Learning Moment Closure Approximations in Reaction-Diffusion Systems with Spatial Dynamic Boltzmann Distributions. Physical Review E, v.99, 063315, 26 June 2019. DOI: 10.1103/PhysRevE.99.063315 .
  • (2019) Eric Mjolsness. Prospects for Declarative Mathematical Modeling of Complex Biological Systems. Bulletin of Mathematical Biology, Volume 81, Issue 8, pp 3385–3420, August 2019. https://doi.org/10.1007/s11538-019-00628-7. Also preprint http://arxiv.org/abs/1804.11044 in a different format.
  • (2019) Olivier Hamant, Daisuke Inoue, David Bouchez, Jacques Dumais, and Eric Mjolsness. Are microtubules tension sensors? Nature Communications, v10 article no. 2360, 29 May 2019.
  • (2018) Oliver K. Ernst, Tom Bartol, Terrence Sejnowski, and Eric Mjolsness.Learning Dynamic Boltzmann Distributions as Reduced Models of Spatial Chemical Kinetics.  Journal of Chemical Physics 149, 034107, July 2018. Also arXiv 1803.01063, March 2018.
  • (2015) Bruce E. Shapiro and Eric Mjolsness. Pycellerator: An arrow-based reaction-like modelling language for biological simulations, Bioinformatics, Oct 26. 2015. DOI: 10.1093/bioinformatics/btv596.
  • (2015) Todd Johnson, Thomas Bartol, Terrence Sejnowski, and Eric Mjolsness. Model Reduction for Stochastic CaMKII Reaction Kinetics in Synapses by Graph-Constrained Correlation Dynamics.  Physical Biology 12:4, July 2015.
  • (2015) Bruce E. Shapiro, Cory Tobin, Eric Mjolsness, and Elliot M. Meyerowitz. Analysis of Cell Divisions Patterns in the Arabidopsis Shoot Apical Meristem. Proceedings of the National Academy of Sciences 112:15 pp 4815–4820, 2015.
  • (2013) “Using Cellzilla for Plant Growth Simulations at the Cellular Level”, Bruce E. Shapiro, Elliot Meyerowitz, Eric Mjolsness. Frontiers in Plant Biophysics and Modeling, 4:00408, 2013.
  • (2013) “Model of Structuring the Stem Cell Niche in Shoot Apical Meristem of Arabidopsis thaliana”, S.V. Nikolaev, U.S. Zubairova, A.V. Penenko, E.D. Mjolsness, B.E. Shapiro, N.A. Kolchanov., Doklady Akademii Nauk, 2013, Vol. 452, No. 3, pp. 336–338, September 2013. Original in Russian. English version is Doklady Biological Sciences, 2013, Vol. 452, pp. 316–319. (Pleiades Publishing)
  • (2013) Eric Mjolsness. Time-ordered product expansions for computational stochastic systems biology. Physical Biology 10 035009, 2013. [Journal paper, open access.]
  • (2013) Eric Mjolsness and Upendra Prasad. Mathematics of small stochastic reaction networks: A boundary layer theory for eigenstate analysis, Journal of Chemical Physics 138, 104111 March 2013. [Journal Paper]
  • (2012) David Orendorff and Eric Mjolsness. A hierarchical exact accelerated stochastic simulation algorithm, Journal of Chemical Physics 137, 214104, December 2012. DOI: 10.1063/1.4766353 ; arXiv:1212.4080. [Journal Paper | Technical Report]
  • (2012)  Eric Mjolsness, Compositional stochastic modeling and probabilistic programming. Workshop on Probabilistic Programming, Neural Information Processing Systems Conference Workshops, extended abstract, December 2012. [Mjolsness_1212.0582] Also available as [arXiv:1212.0582]
  • (2012) Mironova VV, Novoselova ES, Doroshkov AV, Kazantsev FV, Omelyanchuk NA, Kochetov AV, Kolchanov NA, Mjolsness E. , Likhoshvai VA. Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance , Annals of Botany 110:2 pp 349-360, July 2012; doi: 10.1093/aob/mcs069.
  • (2012) Eric Mjolsness and Alexandre Cunha. “Topological object types for morphodynamic modeling languages”, PMA 2012 : IEEE Fourth International Symposium on Plant Growth Modeling, Visualization and Applications. Shanghai China, October 2012. IEEE Press. [Technical Report]
  • (2011) Jonathan Young, James Locke, Alphan Altinok, Nitzan Rosenfeld, Tigran Bacarian, Peter Swain, Eric Mjolsness, and Michael Elowitz. Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy, Nature Protocols 7:1, pp. 80-88, 2012. Published online December 15, 2011. [Paper]
  • (2010)  Mironova, V.V., Omelyanchuk, N.A., Yosiphon, G. Fadeev, S.I., Kolchanov, N.A., Mjolsness, E. and Likhoshvai, V.A. A plausible mechanism for auxin patterning along the developing root , BMC Systems Biology 4:98. [Published PDF ]
  • (2010)  Mjolsness, E. Towards Measurable Types for Dynamical Process Modeling Languages , To appear in Electronic Notes in Theoretical Computer Science (ENTCS), Elsevier. [ Author’s technical report version, PDF ]
  • Wang, Y., Christley, S., Mjolsness, E., and Xie, X. Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent, BMC Systems Biology 4:99 . [ Published PDF ]
  • (2010)  Najdi, T.S., Hatfield, G. W. and Mjolsness, E. D. A `Random Steady State` Model for the Pyruvate Dehydrogenase and Alpha-Ketogluterate Dehydrogenase Enzyme Complexes , Physical Biology, 7 (2010) 016016 [ Author’s version, PDF | View published paper at publisher`s web site ]
  • (2009)  Golubyatnikov, V.P., Mjolsness, E., Gaidov, Yu.A. Topological index of the p53-Mdm2 circuit , The Herald of Vavilov Society for geneticists and breeding scientists (Informatzionnyi Vestnik Vavilovskogo obshchestva genetikov i selektzionerov) v. 13, N 1, 2009, pp 160 – 162. In English, 2009. [ Published PDF ]
  • (2009)  Mjolsness E, Orendorff D, Chatelain P, Koumoutsakos P. An Exact Accelerated Stochastic Simulation Algorithm, Journal of Chemical Physics 130:144110, 2009. Technical Report UCI-ICS 08-09 [Journal paper View paper at publisher’s web site |Technical report ]
  • (2008)  Yosiphon G, Mjolsness E. Towards the Inference of Stochastic Biochemical Network and Parameterized Grammar Models, In N. Lawrence , M. Girolami, M. Rattray, and G. Sanguinetti eds., Learning and Inference in Computational Systems Biology, MIT Press, 2010. Also Technical Report UCI-ICS 08-07 [ Authors’ version, PDF ]

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