BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

41 related articles for article (PubMed ID: 30945247)

  • 1. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.
    Chylek LA; Harris LA; Tung CS; Faeder JR; Lopez CF; Hlavacek WS
    Wiley Interdiscip Rev Syst Biol Med; 2014; 6(1):13-36. PubMed ID: 24123887
    [TBL] [Abstract][Full Text] [Related]  

  • 2. bnglViz: online visualization of rule-based models.
    Liguori-Bills N; Blinov ML
    Bioinformatics; 2024 Jun; 40(6):. PubMed ID: 38814806
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.
    Schaff JC; Gao F; Li Y; Novak IL; Slepchenko BM
    PLoS Comput Biol; 2016 Dec; 12(12):e1005236. PubMed ID: 27959915
    [TBL] [Abstract][Full Text] [Related]  

  • 4. MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.
    Husar A; Ordyan M; Garcia GC; Yancey JG; Saglam AS; Faeder JR; Bartol TM; Kennedy MB; Sejnowski TJ
    PLoS Comput Biol; 2024 Apr; 20(4):e1011800. PubMed ID: 38656994
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Simulation of large-scale rule-based models.
    Colvin J; Monine MI; Faeder JR; Hlavacek WS; Von Hoff DD; Posner RG
    Bioinformatics; 2009 Apr; 25(7):910-7. PubMed ID: 19213740
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Detailed simulations of cell biology with Smoldyn 2.1.
    Andrews SS; Addy NJ; Brent R; Arkin AP
    PLoS Comput Biol; 2010 Mar; 6(3):e1000705. PubMed ID: 20300644
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Potential based, spatial simulation of dynamically nested particles.
    Köster T; Henning P; Uhrmacher AM
    BMC Bioinformatics; 2019 Nov; 20(1):607. PubMed ID: 31775608
    [TBL] [Abstract][Full Text] [Related]  

  • 8. PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems.
    Ghaffarizadeh A; Heiland R; Friedman SH; Mumenthaler SM; Macklin P
    PLoS Comput Biol; 2018 Feb; 14(2):e1005991. PubMed ID: 29474446
    [TBL] [Abstract][Full Text] [Related]  

  • 9. The Kappa platform for rule-based modeling.
    Boutillier P; Maasha M; Li X; Medina-Abarca HF; Krivine J; Feret J; Cristescu I; Forbes AG; Fontana W
    Bioinformatics; 2018 Jul; 34(13):i583-i592. PubMed ID: 29950016
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Kinetic Monte Carlo method for rule-based modeling of biochemical networks.
    Yang J; Monine MI; Faeder JR; Hlavacek WS
    Phys Rev E Stat Nonlin Soft Matter Phys; 2008 Sep; 78(3 Pt 1):031910. PubMed ID: 18851068
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Rule-based multi-level modeling of cell biological systems.
    Maus C; Rybacki S; Uhrmacher AM
    BMC Syst Biol; 2011 Oct; 5():166. PubMed ID: 22005019
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Modeling for (physical) biologists: an introduction to the rule-based approach.
    Chylek LA; Harris LA; Faeder JR; Hlavacek WS
    Phys Biol; 2015 Jul; 12(4):045007. PubMed ID: 26178138
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Automated visualization of rule-based models.
    Sekar JAP; Tapia JJ; Faeder JR
    PLoS Comput Biol; 2017 Nov; 13(11):e1005857. PubMed ID: 29131816
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Correction to: Python interfaces for the Smoldyn simulator.
    Bioinformatics; 2023 Sep; 39(9):. PubMed ID: 37776564
    [No Abstract]   [Full Text] [Related]  

  • 15. Simulation of receptor triggering by kinetic segregation shows role of oligomers and close contacts.
    Taylor R; Allard J; Read EL
    Biophys J; 2022 May; 121(9):1660-1674. PubMed ID: 35367423
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Rule-Based Modeling Using Wildcards in the Smoldyn Simulator.
    Andrews SS
    Methods Mol Biol; 2019; 1945():179-202. PubMed ID: 30945247
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Spatial and stochastic cellular modeling with the Smoldyn simulator.
    Andrews SS
    Methods Mol Biol; 2012; 804():519-42. PubMed ID: 22144170
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface.
    Andrews SS
    Bioinformatics; 2017 Mar; 33(5):710-717. PubMed ID: 28365760
    [TBL] [Abstract][Full Text] [Related]  

  • 19. MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.
    Tapia JJ; Saglam AS; Czech J; Kuczewski R; Bartol TM; Sejnowski TJ; Faeder JR
    Methods Mol Biol; 2019; 1945():203-229. PubMed ID: 30945248
    [TBL] [Abstract][Full Text] [Related]  

  • 20.
    ; ; . PubMed ID:
    [No Abstract]   [Full Text] [Related]  

    [Next]    [New Search]
    of 3.