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1.

Approximate simulation of cortical microtubule models using dynamical graph grammars.

Medwedeff, Eric; Mjolsness, Eric.

Phys Biol ; 20(5)2023 Jul 07.

Article in English | MEDLINE | ID: mdl-37279763

2.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Keating, Sarah M; Waltemath, Dagmar; König, Matthias; Zhang, Fengkai; Dräger, Andreas; Chaouiya, Claudine; Bergmann, Frank T; Finney, Andrew; Gillespie, Colin S; Helikar, Tomás; Hoops, Stefan; Malik-Sheriff, Rahuman S; Moodie, Stuart L; Moraru, Ion I; Myers, Chris J; Naldi, Aurélien; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Swat, Maciej J; Thieffry, Denis; Watanabe, Leandro; Wilkinson, Darren J; Blinov, Michael L; Begley, Kimberly; Faeder, James R; Gómez, Harold F; Hamm, Thomas M; Inagaki, Yuichiro; Liebermeister, Wolfram; Lister, Allyson L; Lucio, Daniel; Mjolsness, Eric; Proctor, Carole J; Raman, Karthik; Rodriguez, Nicolas; Shaffer, Clifford A; Shapiro, Bruce E; Stelling, Joerg; Swainston, Neil; Tanimura, Naoki; Wagner, John; Meier-Schellersheim, Martin; Sauro, Herbert M; Palsson, Bernhard; Bolouri, Hamid; Kitano, Hiroaki; Funahashi, Akira; Hermjakob, Henning.

Mol Syst Biol ; 16(8): e9110, 2020 08.

Article in English | MEDLINE | ID: mdl-32845085

3.

Prospects for Declarative Mathematical Modeling of Complex Biological Systems.

Mjolsness, Eric.

Bull Math Biol ; 81(8): 3385-3420, 2019 08.

Article in English | MEDLINE | ID: mdl-31175549

4.

Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics.

Ernst, Oliver K; Bartol, Thomas; Sejnowski, Terrence; Mjolsness, Eric.

J Chem Phys ; 149(3): 034107, 2018 Jul 21.

Article in English | MEDLINE | ID: mdl-30037235

5.

Analysis of cell division patterns in the Arabidopsis shoot apical meristem.

Shapiro, Bruce E; Tobin, Cory; Mjolsness, Eric; Meyerowitz, Elliot M.

Proc Natl Acad Sci U S A ; 112(15): 4815-20, 2015 Apr 14.

Article in English | MEDLINE | ID: mdl-25825722

6.

Pycellerator: an arrow-based reaction-like modelling language for biological simulations.

Shapiro, Bruce E; Mjolsness, Eric.

Bioinformatics ; 32(4): 629-31, 2016 Feb 15.

Article in English | MEDLINE | ID: mdl-26504142

7.

Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics.

Johnson, Todd; Bartol, Tom; Sejnowski, Terrence; Mjolsness, Eric.

Phys Biol ; 12(4): 045005, 2015 Jun 18.

Article in English | MEDLINE | ID: mdl-26086598

8.

Introduction.

Alber, Mark; Godin, Christophe; Maini, Philip K; Merks, Roeland; Mjolsness, Eric.

Bull Math Biol ; 81(8): 3214-3218, 2019 08.

Article in English | MEDLINE | ID: mdl-31332600

9.

Time-ordered product expansions for computational stochastic system biology.

Mjolsness, Eric.

Phys Biol ; 10(3): 035009, 2013 Jun.

Article in English | MEDLINE | ID: mdl-23735739

10.

Mathematics of small stochastic reaction networks: a boundary layer theory for eigenstate analysis.

Mjolsness, Eric; Prasad, Upendra.

J Chem Phys ; 138(10): 104111, 2013 Mar 14.

Article in English | MEDLINE | ID: mdl-23514469

11.

A hierarchical exact accelerated stochastic simulation algorithm.

Orendorff, David; Mjolsness, Eric.

J Chem Phys ; 137(21): 214104, 2012 Dec 07.

Article in English | MEDLINE | ID: mdl-23231214

12.

Explicit Calculation of Structural Commutation Relations for Stochastic and Dynamical Graph Grammar Rule Operators in Biological Morphodynamics.

Mjolsness, Eric.

Front Syst Biol ; 22022 Sep.

Article in English | MEDLINE | ID: mdl-36712785

13.

Graph diffusion distance: Properties and efficient computation.

Scott, C B; Mjolsness, Eric.

PLoS One ; 16(4): e0249624, 2021.

Article in English | MEDLINE | ID: mdl-33905423

14.

A scalable and integrative system for pathway bioinformatics and systems biology.

Compani, Behnam; Su, Trent; Chang, Ivan; Cheng, Jianlin; Shah, Kandarp H; Whisenant, Thomas; Dou, Yimeng; Bergmann, Adriel; Cheong, Raymond; Wold, Barbara; Bardwell, Lee; Levchenko, Andre; Baldi, Pierre; Mjolsness, Eric.

Adv Exp Med Biol ; 680: 523-34, 2010.

Article in English | MEDLINE | ID: mdl-20865537

15.

Towards Measurable Types for Dynamical Process Modeling Languages.

Mjolsness, Eric.

Electron Notes Theor Comput Sci ; 265: 123-144, 2010 Sep 06.

Article in English | MEDLINE | ID: mdl-21572536

16.

Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing.

Davis, Ryan T; Blake, Kerrigan; Ma, Dennis; Gabra, Mari B Ishak; Hernandez, Grace A; Phung, Anh T; Yang, Ying; Maurer, Dustin; Lefebvre, Austin E Y T; Alshetaiwi, Hamad; Xiao, Zhengtao; Liu, Juan; Locasale, Jason W; Digman, Michelle A; Mjolsness, Eric; Kong, Mei; Werb, Zena; Lawson, Devon A.

Nat Cell Biol ; 22(3): 310-320, 2020 03.

Article in English | MEDLINE | ID: mdl-32144411

17.

An exact accelerated stochastic simulation algorithm.

Mjolsness, Eric; Orendorff, David; Chatelain, Philippe; Koumoutsakos, Petros.

J Chem Phys ; 130(14): 144110, 2009 Apr 14.

Article in English | MEDLINE | ID: mdl-19368432

18.

A Pycellerator Tutorial.

Shapiro, Bruce E; Mjolsness, Eric.

Methods Mol Biol ; 1945: 1-32, 2019.

Article in English | MEDLINE | ID: mdl-30945240

19.

Are microtubules tension sensors?

Hamant, Olivier; Inoue, Daisuke; Bouchez, David; Dumais, Jacques; Mjolsness, Eric.

Nat Commun ; 10(1): 2360, 2019 05 29.

Article in English | MEDLINE | ID: mdl-31142740

20.

Learning moment closure in reaction-diffusion systems with spatial dynamic Boltzmann distributions.

Ernst, Oliver K; Bartol, Thomas M; Sejnowski, Terrence J; Mjolsness, Eric.

Phys Rev E ; 99(6-1): 063315, 2019 Jun.

Article in English | MEDLINE | ID: mdl-31330605

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Approximate simulation of cortical microtubule models using dynamical graph grammars.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Prospects for Declarative Mathematical Modeling of Complex Biological Systems.

Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics.

Analysis of cell division patterns in the Arabidopsis shoot apical meristem.

Pycellerator: an arrow-based reaction-like modelling language for biological simulations.

Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics.

Introduction.

Time-ordered product expansions for computational stochastic system biology.

Mathematics of small stochastic reaction networks: a boundary layer theory for eigenstate analysis.

A hierarchical exact accelerated stochastic simulation algorithm.

Explicit Calculation of Structural Commutation Relations for Stochastic and Dynamical Graph Grammar Rule Operators in Biological Morphodynamics.

Graph diffusion distance: Properties and efficient computation.

A scalable and integrative system for pathway bioinformatics and systems biology.

Towards Measurable Types for Dynamical Process Modeling Languages.

Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing.

An exact accelerated stochastic simulation algorithm.

A Pycellerator Tutorial.

Are microtubules tension sensors?

Learning moment closure in reaction-diffusion systems with spatial dynamic Boltzmann distributions.