Eric Mjolsness - Publications

Affiliations: 
University of California, Irvine, Irvine, CA 
Area:
Computer Science

47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Shapiro BE, Mjolsness E. Pycellerator: an arrow-based reaction-like modelling language for biological simulations. Bioinformatics (Oxford, England). 32: 629-31. PMID 26504142 DOI: 10.1093/bioinformatics/btv596  1
2015 Johnson T, Bartol T, Sejnowski T, Mjolsness E. Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics. Physical Biology. 12: 045005. PMID 26086598 DOI: 10.1088/1478-3975/12/4/045005  1
2015 Shapiro BE, Tobin C, Mjolsness E, Meyerowitz EM. Analysis of cell division patterns in the Arabidopsis shoot apical meristem. Proceedings of the National Academy of Sciences of the United States of America. 112: 4815-20. PMID 25825722 DOI: 10.1073/pnas.1502588112  1
2013 Nikolaev SV, Zubairova US, Penenko AV, Mjolsness ED, Shapiro BE, Kolchanov NA. Model of structuring the stem cell niche in shoot apical meristem of Arabidopsis thaliana. Doklady Biological Sciences : Proceedings of the Academy of Sciences of the Ussr, Biological Sciences Sections / Translated From Russian. 452: 316-9. PMID 24150656 DOI: 10.1134/S0012496613050104  1
2013 Shapiro BE, Meyerowitz EM, Mjolsness E. Using cellzilla for plant growth simulations at the cellular level. Frontiers in Plant Science. 4: 408. PMID 24137172 DOI: 10.3389/fpls.2013.00408  1
2013 Mjolsness E. Time-ordered product expansions for computational stochastic system biology. Physical Biology. 10: 035009. PMID 23735739 DOI: 10.1088/1478-3975/10/3/035009  1
2013 Mjolsness E, Prasad U. Mathematics of small stochastic reaction networks: a boundary layer theory for eigenstate analysis. The Journal of Chemical Physics. 138: 104111. PMID 23514469 DOI: 10.1063/1.4794128  1
2013 Mjolsness E. Quantitative symbolic process models: How a fair fraction of intelligence could be abstracted in AI research Aaai Fall Symposium - Technical Report. 50-51.  1
2012 Orendorff D, Mjolsness E. A hierarchical exact accelerated stochastic simulation algorithm. The Journal of Chemical Physics. 137: 214104. PMID 23231214 DOI: 10.1063/1.4766353  1
2012 Cunha A, Tarr PT, Roeder AH, Altinok A, Mjolsness E, Meyerowitz EM. Computational analysis of live cell images of the Arabidopsis thaliana plant. Methods in Cell Biology. 110: 285-323. PMID 22482954 DOI: 10.1016/B978-0-12-388403-9.00012-6  1
2012 Young JW, Locke JC, Altinok A, Rosenfeld N, Bacarian T, Swain PS, Mjolsness E, Elowitz MB. Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nature Protocols. 7: 80-8. PMID 22179594 DOI: 10.1038/nprot.2011.432  1
2012 Mjolsness E, Cunha A. Topological object types for morphodynamic modeling languages Proceedings - 2012 Ieee 4th International Symposium On Plant Growth Modeling, Simulation, Visualization and Applications, Pma 2012. 8-14. DOI: 10.1109/PMA.2012.6524805  1
2011 Nikolaev SV, Zubairova US, Fadeev SI, Mjolsness E, Kolchanov NA. Study of a one-dimensional model, accounting for cell division, of regulation of the renewing zone size in a biological tissue Journal of Applied and Industrial Mathematics. 5: 601-611. DOI: 10.1134/S1990478911040156  1
2011 Ponomaryov D, Omelianchuk N, Mironova V, Zalevsky E, Podkolodny N, Mjolsness E, Kolchanov N. From published expression and phenotype data to structured knowledge: The arabidopsis gene net supplementary database and its applications Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6581: 101-120. DOI: 10.1007/978-3-642-22140-8_7  1
2010 Mjolsness E. Towards Measurable Types for Dynamical Process Modeling Languages. Electronic Notes in Theoretical Computer Science. 265: 123-144. PMID 21572536 DOI: 10.1016/j.entcs.2010.08.008  1
2010 Compani B, Su T, Chang I, Cheng J, Shah KH, Whisenant T, Dou Y, Bergmann A, Cheong R, Wold B, Bardwell L, Levchenko A, Baldi P, Mjolsness E. A scalable and integrative system for pathway bioinformatics and systems biology. Advances in Experimental Medicine and Biology. 680: 523-34. PMID 20865537 DOI: 10.1007/978-1-4419-5913-3_58  1
2010 Wang Y, Christley S, Mjolsness E, Xie X. Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. Bmc Systems Biology. 4: 99. PMID 20663171 DOI: 10.1186/1752-0509-4-99  1
2010 Mironova VV, Omelyanchuk NA, Yosiphon G, Fadeev SI, Kolchanov NA, Mjolsness E, Likhoshvai VA. A plausible mechanism for auxin patterning along the developing root. Bmc Systems Biology. 4: 98. PMID 20663170 DOI: 10.1186/1752-0509-4-98  1
2010 Najdi TS, Hatfield GW, Mjolsness ED. A 'random steady-state' model for the pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase enzyme complexes. Physical Biology. 7: 16016. PMID 20228444 DOI: 10.1088/1478-3975/7/1/016016  1
2009 Mjolsness E, Orendorff D, Chatelain P, Koumoutsakos P. An exact accelerated stochastic simulation algorithm. The Journal of Chemical Physics. 130: 144110. PMID 19368432 DOI: 10.1063/1.3078490  1
2007 Mjolsness E. Towards a calculus of biomolecular complexes at equilibrium. Briefings in Bioinformatics. 8: 226-33. PMID 17640924 DOI: 10.1093/bib/bbm034  1
2007 Mjolsness E. On cooperative quasi-equilibrium models of transcriptional regulation. Journal of Bioinformatics and Computational Biology. 5: 467-90. PMID 17636856  1
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 Russian Journal of Developmental Biology. 38: 383-388. DOI: 10.1134/S1062360407060069  1
2007 Likhoshvai VA, Omel'yanchuk NA, Mironova VV, Fadeev SI, Mjolsness ED, Kolchanov NA. Mathematical model of auxin distribution in the plant root Russian Journal of Developmental Biology. 38: 374-382. DOI: 10.1134/S1062360407060057  1
2006 Hart CE, Mjolsness E, Wold BJ. Connectivity in the yeast cell cycle transcription network: inferences from neural networks. Plos Computational Biology. 2: e169. PMID 17194216 DOI: 10.1371/journal.pcbi.0020169  1
2006 Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. Journal of Bioinformatics and Computational Biology. 4: 335-55. PMID 16819787 DOI: 10.1142/S0219720006001862  1
2006 Jönsson H, Heisler MG, Shapiro BE, Meyerowitz EM, Mjolsness E. An auxin-driven polarized transport model for phyllotaxis. Proceedings of the National Academy of Sciences of the United States of America. 103: 1633-8. PMID 16415160 DOI: 10.1073/pnas.0509839103  1
2006 Nikolaev SV, Fadeev SI, Penenko AV, Lavrekha VV, Mironova VV, Omelyanchuk NA, Mjolsness ED, Kolchanov NA. A systems approach to morphogenesis in Arabidopsis thaliana: II. Modeling the regulation of shoot apical meristem structure Biophysics. 51: 83-90. DOI: 10.1134/S0006350906070177  1
2006 Omelyanchuk NA, Mironova VV, Zalevsky EM, Shamov IS, Poplavsky AS, Podkolodny NL, Ponomaryov DK, Nikolaev SV, Mjolsness ED, Meyerowitz EM, Kolchanov NA. A systems approach to morphogenesis in Arabidopsis thaliana: I. AGNS database Biophysics. 51: 75-82. DOI: 10.1134/S0006350906070165  1
2006 Mjolsness E, Yosiphon G. Stochastic process semantics for dynamical grammars Annals of Mathematics and Artificial Intelligence. 47: 329-395. DOI: 10.1007/s10472-006-9034-1  1
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  1
2006 Howard A, Turmon M, Matthies L, Tang B, Angelova A, Mjolsness E. Towards learned traversability for robot navigation: From underfoot to the far field Journal of Field Robotics. 23: 1005-1017. DOI: 10.1002/rob.20168  1
2006 Bhan A, Mjolsness E. Static and dynamic models of biological networks Complexity. 11: 57-63. DOI: 10.1002/cplx.20140  1
2006 Mjolsness E. Stochastic process semantics for dynamical grammar syntax: An overview 9th International Symposium On Artificial Intelligence and Mathematics, Isaim 2006 1
2005 Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 279-88. PMID 16447985 DOI: 10.1109/CSB.2005.15  1
2005 Jönsson H, Heisler M, Reddy GV, Agrawal V, Gor V, Shapiro BE, Mjolsness E, Meyerowitz EM. Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. Bioinformatics (Oxford, England). 21: i232-40. PMID 15961462 DOI: 10.1093/bioinformatics/bti1036  1
2005 Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ. A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data. Nucleic Acids Research. 33: 2580-94. PMID 15886390 DOI: 10.1093/nar/gki536  1
2005 Yang CR, Shapiro BE, Hung SP, Mjolsness ED, Hatfield GW. A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12. The Journal of Biological Chemistry. 280: 11224-32. PMID 15657047 DOI: 10.1074/jbc.M411471200  1
2005 Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW. An enzyme mechanism language for the mathematical modeling of metabolic pathways. Bioinformatics (Oxford, England). 21: 774-80. PMID 15509612 DOI: 10.1093/bioinformatics/bti068  1
2005 Cheng J, Scharenbroich L, Baldi P, Mjolsness E. Sigmoid: A software infrastructure for pathway bioinformatics and systems biology Ieee Intelligent Systems. 20: 68-75. DOI: 10.1109/MIS.2005.51  1
2004 Chudova D, Hart C, Mjolsness E, Smyth P. Gene expression clustering with functional mixture models Advances in Neural Information Processing Systems 1
2003 Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics (Oxford, England). 19: 677-8. PMID 12651737 DOI: 10.1093/bioinformatics/btg042  1
2003 Chudova D, Gaffney S, Mjolsness E, Smyth P. Translation-invariant mixture models for curve clustering Proceedings of the Acm Sigkdd International Conference On Knowledge Discovery and Data Mining. 79-88. DOI: 10.1145/956750.956763  1
2003 Wang R, Scharenbroich L, Hart C, Wold B, Mjolsness E. Clustering analysis of microarray gene expression data by splitting algorithm Journal of Parallel and Distributed Computing. 63: 692-706. DOI: 10.1016/S0743-7315(03)00085-6  1
2003 Jönsson H, Shapiro BE, Meyerowitz EM, Mjolsness E. Signalling in multicellular models of plant development On Growth, Form and Computers. 156-161. DOI: 10.1016/B978-012428765-5/50041-4  1
1998 Marnellos G, Mjolsness E. A gene network approach to modeling early neurogenesis in Drosophila Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 30-41. PMID 9697169  1
1993 Prusinkiewicz P, Hammel MS, Mjolsness E. Animation of plant development Proceedings of the 20th Annual Conference On Computer Graphics and Interactive Techniques, Siggraph 1993. 351-360. DOI: 10.1145/166117.166161  1
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