The Computable Plant

(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 ]

(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) 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 ]

(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 ]

(2009) Yosiphon G, Mjolsness E. Towards the Inference of Stochastic Biochemical Network and Parameterized Grammar Models, Learning and Inference in Computational Systems Biology (in press) [Download PDF Preprint]

(2009) Mjolsness E, Orendorff D, Chatelain P, Koumoutsakos P. An Exact Accelerated Stochastic Simulation Algorithm. Journal of Chemical Physics (in press) [ Download PDF Preprint ]

(2009) Demidenko GV, Likhoshvai VA, Mudrov AV. On the Relationship Between Solutions of Delay Differential Equations and Infinite-Dimensional Systems of Equations. Differential Equations, 45(1):33-45 (2009), translation of of original Russian Differentsial'nye Uravneniya,45(1):34-46 (2009). [ Download PDF Preprint of English Translation ]

(2008)  Hamant O, Heisler MG, Jonsson H, Krupinski P, Uyttewall M, Bokov P, Corson F, Sahlin P, Boudaoud A, Meyerowitz EM. Developmental Patterning by Mechanical Signals in Arabidopsis. Science, 322(5908):1650-1655; Journal Web Site

(2007)  Michniewicz M, Zago MK, Abas L, Weijers D, Schweighofer A, Meskiene I, Heisler MG, Ohno C, Zhang J, Huang F, Schwab R, Weigel D, Meyerowitz EM, Luschnig C, Offringa R, Firiml J. Antagonistic Regulation of PIN Phosphorylation by PP2A and PINOID Directs Auxin Flux Cell. 130: 1-13; View at Journal Web Page

(2007)  Gordon SP, Heisler MG, Reddy GV, Ohno C, Das P, Meyerowitz EM Pattern formation during de novo assemply of the Arabidopsis shoot meristem, Development 134:3539-3548,doi:10.1242/dev.010298 Download PDF Preprint

(2007)  Akberdin IR, Ozonov EA, Mironova VV, Omelyanchuk NA, Likhoshvai VA, Gorpinchenko DN, Kolchanov NA A cellular automaton to model the development of primary shoot meristems of arabidopsis thaliana, J. Bioinf. Comp. Biol. 5(4): 1-10. Download PDF preprint

(2007)  Nikolaev SV, Penenko AV, Lavreha VV, Mjolsness ED, Kolchanov NA A Model Study of the Role of Proteins CLV1, CLV2, CLV3, and WUS in Regulation of the Structure of the Shoot Apical Meristem, Originally published in Russian, Ontogenez 2007, 38(6):457-462. Download PDF preprint

(2007)  V. A. Likhoshvai VA, Omel'yanchuk NA, Mironova VV, Fadeev SI, Mjolsness ED and Kolchanov NA Mathematical Model of Auxin Distribution in the Plant Root Russian Journal of Developmental Biology, 38(6):374-384; Original Russian Verison published in Ontogenez 38(6):446-456(2007). Download PDF

(2007)  Heisler MG, Jönsson H Modeling meristem development in plants, Current Opinion in Plant Biology 10:92-97. Download PDF

(2007) Kirouac M. Experience, Confidence, and Tools: The 'Grounding in Botany' Program. ASTC (Association of Science-Technology Centers) Dimensions, May/June 2007.

(2007) Mjolsness E. On Cooperative Quasi-Equilibrium Models of Transcriptional Regulation. Journal of Bioinformatics and Computational Biology, (in press)Journal Web Site [Preprint Version as UCI TR ]

(2007) Mjolsness E. Towards a Calculus of Biomolecular Complexes at Equilibrium Brief Bioinform 2007 8: 226-233; doi:10.1093/bib/bbm034 Journal Web Site [Preprint Version as UCI TR ]

(2006) Mjolsness E, Yosiphon G Stochastic process semantics for dynamical grammars , Annals of Mathematics and Artificial Intelligence 47(3-4):329-395, August 2006. [Publishers Web Site | Preprint as UCI TR ]

(2006) Mjolsness E. The Growth and Development of Some Recent Plant Models: A Viewpoint. Journal of Plant Growth Regulation, 25:270-277, DOI: 10.1007/s00344-006-0069-7, Publisher's Web Site.

(2006) Heisler MG & Jönsson H, Modeling Auxin Transport and Plant Development. Journal of Plant Growth Regulation, 25:302-312, DOI: 10.1007/s00344-006-0066-x, Publisher's Web Site.

(2006) Mjolsness E. Modeling transcriptional regulation with equilibrium molecular complex composition, 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 1, pp. 118-121. Download PDF

(2006) Nikolaev SV, Fadeev SI, Kogai VV, Mjolsness E, Kolchanov NA. A one-dimensional model for the regulation of the size of the renewable zone in biological tissue, 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 2, pp. 213-217. Download pdf

(2006) Nikolaev SV, Penenko AV, Belavskaya VV, Mjolsness E, Kolchanov NA. A system for simulation of 2D plant tissue growth and development, 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 2, pp. 218-22. Download pdf

(2006) Omelianchuk NA, Mironova VV, Poplavsky AS, Pavlov KS, Savinskaya SA, Podkolodny NL, Mjolsness ED, Meyerowitz EM, Kolchanov NA. AGNS (Arabidopsis GenNet Supplementary Database), release 3.0, 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 2, pp. 223-226. Download pdf

(2006) Ponomaryov D, Omelianchuk N, Kolchanov N, Mjolsness E, Meyerowitz E. Semantically rich ontology of anatomical structure and development for arabidopsis thaliana l. , 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 2, pp. 227-230. Download pdf

(2006) Ponomaryov D, Omelianchuk N, Mironova V, Kolchanov N, Mjolsness E, Meyerowitz E. A program method of constructing ontology of phenotypic abnormalities for arabidopsis thaliana., 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 2, pp. 231-234. Download pdf

(2006) Podkolodny NL, Podkolodnaya NN, Miginsky DS, Poplavsky AS, Likhoshvai VA, Compani B, Mjolsness E. An integration of the descriptions of gene networks and their models presented in Sigmoid (Cellerator) and GeneNet, 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 3, pp. 86-90. Download pdf

(2006) Bhan, A. and Mjolsness, E. Static and Dynamic Models of Biological Networks. Complexity 11(6): 57-63. Download from Journal Website

(2006) Jönsson H, Heisler M, Shapiro BE, Meyerowitz EM, Mjolsness ED. An Auxin-driven polarized transport model for phyllotaxis. Proc. Natl. Acad. Sci., U.S.A., 103(5):1633-1638. [ Abstract & Full Paper from Publisher | Supplementary Information at Publisher's Web Site | Additional Supplementary Informaton]

(2006) Mjolsness, E. Stochastic Process Semantics for Dynamical Grammer Syntax: An Overview . 9th International Symposium on Artificial Intelligence and Mathematics, Jan 2006. [ Preprint from arXiv.org]

(2006) Fadeev SI, Nikolaev SV, Kogay VV, Mjolsness E, Kolchanov NA. [Analysis of a one-dimensional model for the regulation of the size of the renewable zone in biological tissue (in Russian)], Computational Technologies 11(2) [ Publisher's Web Site | Partial English Translation]

(2006) Demidenko GV, Likhoshvai VA, Khropova Yu.E. On one class of systems of differential equations and on retarded systems, Siberian Mathematical Journal, 47(1):58-68. [ Abstract/Paper ]

(2006) Demidenko GV, Likhoshvai VA. On Differential Equations with Retarded Argument, Siberian Mathematical Journal , 46(3):417-430. [ Abstract/Paper ]

(2006) Gor V, Shapiro BE, Jönsson H, Heisler M, Reddy GV,Meyerowitz EM, Mjolsness E A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project. In: Bioinformatics of Genome Regulation and Structure II,(Eds. N.Kolchanov, R. Hofestaedt, L. Milanesi) Springer, pp. 345-354.  [ Abstract | Preprint ]

(2006)  Omelyanchuk N, Mironova V, Poplavsky A, Podkoldny N, Kolchanov N, Mjolsness E, Meyerowitz E AGNS-A Database on expression of Arabidopsis Genes. In: Bioinformatics of Genome Regulation and Structure II (Eds. N.Kolchanov, R. Hofestaedt, L. Milanesi) Springer. 

(2005)  Venugopala Reddy G, Meyerowitz EM. Stem-Cell Homeostasis Growth Dynamics can be Uncoupled in the Arabidopsis Shoot Apex. Science 310(5748):663-667. [ Abstract or paper at publisher's web site. | Pubmed ]

(2005) Heisler M.G., Ohno, C., Das, P., Sieber, P., Reddy, G.V., Long, J.A., and Meyerowitz, E.M. Patterns of Auxin Transport and Gene Expression during Primordium Development Revealed by Live Imaging of the Arabidopsis Inflorescence Meristem. Curr. Biol. 15:1899-1911. [ Full Paper | Pubmed ]

(2005) Jönsson H, Heisler M, Reddy GV, Agrawal V, Gor V, Shapiro BE, Mjolsness E, and Meyerowitz E.M. Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. Bioinformatics 21(S1): i232-i240.[ View Abstract or Paper at Publisher's Web Site. | Supplementary Material]

(2005) Gor V. Bacarian T, Elowitz M, Mjolsness E. Tracking Cell Signlas in Fluorescent Images . Workshop on Computer Vision in Bioinformatics, IEEE CVPR Annual Meeting, 2005 [ Abstract | Paper ]

(2004) Reddy, G.V., Heisler, M.G., Ehrhardt, D.W. and Meyerowitz, E.M. Real-time analysis reveals oriented cell divisions associated with morphogenesis at the shoot apex of Arabidopsis thaliana. Development 131:4225-4237 [ View abstract or full paper at publiser's web site]

(2004) Gor V, Shapiro BE, Jönsson H, Heisler M, Venugopala Reddy G, Meyerowitz EM, Mjolsness E, A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project, presented at the 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2004), Novosibirsk, Russia, July 2004. [ Abstract | Preprint ].

(2004)  Jönsson, H., Shapiro, B.E., Meyerowitz, E.M., and Mjolsness, E. Modeling plant development with gene regulation networks including signaling and cell division. in Bioinformatics of Genome Regulation and Structure, eds R. Hofestaedt and N. Kolchanov, Kluwer Publications, pp 311-318. [ Abstract ]

(2003)  Jönsson, H., Shapiro, B.E., Meyerowitz, E.M. and Mjolsness, E. Signaling in Multicellular Models of Plant Development. In S. Kumar and P.J. Bentley (Eds.) On Growth, Form, and Computers, Academic Press, London, UK, pages 156-161. [ Abstract | Publisher's Web Site ]

(2003)  Shapiro, B.E., Levchenko, A., Meyerowitz, E.M., Wold, B.J., and Mjolsness, E.D. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics , 19(5):677-678. [View Abstract or Paper at Publisher's Web Site]

(2003)  M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano , A. P. Arkin , B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J.-H. Hofmey, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Nov` ere, L. M. Loew, D. Lucio , P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff , B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics Vol 19, no 4, 2003 pp 524-531.[View Abstract or Paper at Publisher's Web Site]

(2002)  Mjolsness E, Jönsson H, Shapiro BE, Meyerowitz EM. Modeling plant development with gene regulation networks including signaling and cell division. Paper presented at the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002), Novosibirsk, Russia, July 14-20, 2002. [ Abstract | Paper | Conference Proceedings ].

(2002)  Shapiro BE, Levchenko A, Mjolsness E. Automatic Model Generation for Signal Transduction with Applications to Map Kinase Pathways. In: Foundations of Systems Biology, H. Kitano, ed, MIT Press, pages 145-162) ISBN 0-262-11266-3 [ Publisher's web site].

(2001)  Shapiro BE, Mjolsness ED. Developmental Simulations with Cellerator. Paper presented at the Second International Conference on Systems Biology, Pasadena, CA, Novemeber 2001. [Download Preprint | On-line proceedings at conference web site.]

(1991)  Mjolsness E, Sharp DH, Reinitz J. A connectionist model of development. Journal of Theoretical Biology 152: 429-453. [Download pdf].