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:

 

  • (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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