BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

244 related articles for article (PubMed ID: 33507922)

  • 1. MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.
    Haiman ZB; Zielinski DC; Koike Y; Yurkovich JT; Palsson BO
    PLoS Comput Biol; 2021 Jan; 17(1):e1008208. PubMed ID: 33507922
    [TBL] [Abstract][Full Text] [Related]  

  • 2. libRoadRunner: a high performance SBML simulation and analysis library.
    Somogyi ET; Bouteiller JM; Glazier JA; König M; Medley JK; Swat MH; Sauro HM
    Bioinformatics; 2015 Oct; 31(20):3315-21. PubMed ID: 26085503
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
    Becker SA; Feist AM; Mo ML; Hannum G; Palsson BØ; Herrgard MJ
    Nat Protoc; 2007; 2(3):727-38. PubMed ID: 17406635
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions.
    Medlock GL; Moutinho TJ; Papin JA
    PLoS Comput Biol; 2020 Apr; 16(4):e1007847. PubMed ID: 32348298
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Computational modeling of biochemical networks using COPASI.
    Mendes P; Hoops S; Sahle S; Gauges R; Dada J; Kummer U
    Methods Mol Biol; 2009; 500():17-59. PubMed ID: 19399433
    [TBL] [Abstract][Full Text] [Related]  

  • 6. libRoadRunner 2.0: a high performance SBML simulation and analysis library.
    Welsh C; Xu J; Smith L; König M; Choi K; Sauro HM
    Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36478036
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.
    Chakrabarti A; Miskovic L; Soh KC; Hatzimanikatis V
    Biotechnol J; 2013 Sep; 8(9):1043-57. PubMed ID: 23868566
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Constructing kinetic models of metabolism at genome-scales: A review.
    Srinivasan S; Cluett WR; Mahadevan R
    Biotechnol J; 2015 Sep; 10(9):1345-59. PubMed ID: 26332243
    [TBL] [Abstract][Full Text] [Related]  

  • 9. BioSANS: A software package for symbolic and numeric biological simulation.
    Fajiculay E; Hsu CP
    PLoS One; 2022; 17(4):e0256409. PubMed ID: 35436294
    [TBL] [Abstract][Full Text] [Related]  

  • 10. COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
    Ebrahim A; Lerman JA; Palsson BO; Hyduke DR
    BMC Syst Biol; 2013 Aug; 7():74. PubMed ID: 23927696
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Advanced Modeling of Cellular Proliferation: Toward a Multi-scale Framework Coupling Cell Cycle to Metabolism by Integrating Logical and Constraint-Based Models.
    van der Zee L; Barberis M
    Methods Mol Biol; 2019; 2049():365-385. PubMed ID: 31602622
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Use of randomized sampling for analysis of metabolic networks.
    Schellenberger J; Palsson BØ
    J Biol Chem; 2009 Feb; 284(9):5457-61. PubMed ID: 18940807
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain.
    Gavai AK; Supandi F; Hettling H; Murrell P; Leunissen JA; van Beek JH
    PLoS One; 2015; 10(3):e0119016. PubMed ID: 25806817
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Leveraging modeling approaches: reaction networks and rules.
    Blinov ML; Moraru II
    Adv Exp Med Biol; 2012; 736():517-30. PubMed ID: 22161349
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic Models.
    Dufault-Thompson K; Steffensen JL; Zhang Y
    Methods Mol Biol; 2018; 1716():131-150. PubMed ID: 29222752
    [TBL] [Abstract][Full Text] [Related]  

  • 16. A Computational Workflow for the Automated Generation of Models of Genetic Designs.
    Misirli G; Nguyen T; McLaughlin JA; Vaidyanathan P; Jones TS; Densmore D; Myers C; Wipat A
    ACS Synth Biol; 2019 Jul; 8(7):1548-1559. PubMed ID: 29782151
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Tellurium: An extensible python-based modeling environment for systems and synthetic biology.
    Choi K; Medley JK; König M; Stocking K; Smith L; Gu S; Sauro HM
    Biosystems; 2018 Sep; 171():74-79. PubMed ID: 30053414
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Constructing and analysing dynamic models with modelbase v1.2.3: a software update.
    van Aalst M; Ebenhöh O; Matuszyńska A
    BMC Bioinformatics; 2021 Apr; 22(1):203. PubMed ID: 33879053
    [TBL] [Abstract][Full Text] [Related]  

  • 19. SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
    Zi Z; Klipp E
    Bioinformatics; 2006 Nov; 22(21):2704-5. PubMed ID: 16926221
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Towards dynamic genome-scale models.
    Gilbert D; Heiner M; Jayaweera Y; Rohr C
    Brief Bioinform; 2019 Jul; 20(4):1167-1180. PubMed ID: 29040409
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 13.