PubMed Mentions
The links below are to publications on PubMed referring to libSBML. This list is gathered weekly from PubMed automatically.
| Publication/References | |
| BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. Description: Li, Chen, et al. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. ''BMC Syst Biol''. 2010 Jun 29; '''4''': 92 | |
| Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. Description: Radrich, Karin, et al. Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. ''BMC Syst Biol''. 2010 Aug 16; '''4''': 114 | |
| Integrating systems biology models and biomedical ontologies. Description: Hoehndorf, Robert, et al. Integrating systems biology models and biomedical ontologies. ''BMC Syst Biol''. 2011 Aug 11; '''5''': 124 | |
| Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo. Description: Takizawa, Hiromu, et al. Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo. ''PLoS One''. 2012; '''7''' (12):e51000 | |
| LibSBMLSim: a reference implementation of fully functional SBML simulator. Description: Takizawa, Hiromu, et al. LibSBMLSim: a reference implementation of fully functional SBML simulator. ''Bioinformatics''. 2013 Jun 1; '''29''' (11):1474-6 | |
| SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. Description: Chaouiya, Claudine, et al. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. ''BMC Syst Biol''. 2013 Dec 10; '''7''': 135 | |
| R-based software for the integration of pathway data into bioinformatic algorithms. Description: Kramer, Frank, et al. R-based software for the integration of pathway data into bioinformatic algorithms. ''Biology (Basel)''. 2014 Feb 7; '''3''' (1):85-100 | |
| A novel mathematical model describing adaptive cellular drug metabolism and toxicity in the chemoimmune system. Description: Toth, Attila, et al. A novel mathematical model describing adaptive cellular drug metabolism and toxicity in the chemoimmune system. ''PLoS One''. 2015; '''10''' (2):e0115533 | |
| Biomass composition: the "elephant in the room" of metabolic modelling. Description: Dikicioglu, Duygu, et al. Biomass composition: the "elephant in the room" of metabolic modelling. ''Metabolomics''. 2015; '''11''' (6):1690-1701 | |
| Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. Description: Lai, Massimo, et al. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. ''PLoS Comput Biol''. 2015 Jan; '''11''' (1):e1004063 | |
| Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris. Description: Saitua, Francisco, et al. Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris. ''BMC Syst Biol''. 2017 Feb 21; '''11''' (1):27 | |
| Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. Description: Cankorur-Cetinkaya, Ayca, et al. Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. ''Biotechnol Bioeng''. 2017 Nov; '''114''' (11):2605-2615 | |
| A Glutamatergic Spine Model to Enable Multi-Scale Modeling of Nonlinear Calcium Dynamics. Description: Hu, Eric, et al. A Glutamatergic Spine Model to Enable Multi-Scale Modeling of Nonlinear Calcium Dynamics. ''Front Comput Neurosci''. 2018; '''12''': 58 | |
| Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti. Description: diCenzo, George C, et al. Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti. ''PLoS Genet''. 2018 Apr; '''14''' (4):e1007357 | |
| Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi. Description: Mellbye, Brett L, et al. Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi. ''mSystems''. 2018 May-Jun; '''3''' (3): | |
| DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. Description: Smith, Robert W, et al. DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. ''BMC Syst Biol''. 2018 Jun 19; '''12''' (1):72 | |
| Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. Description: diCenzo, George C, et al. Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. ''Genes (Basel)''. 2018 Jul 27; '''9''' (8): | |
| Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae. Description: Papapetridis, Ioannis, et al. Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae. ''FEMS Yeast Res''. 2018 Sep 1; '''18''' (6): | |
| RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. Description: Wang, Hao, et al. RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. ''PLoS Comput Biol''. 2018 Oct; '''14''' (10):e1006541 | |
| Process development for the continuous production of heterologous proteins by the industrial yeast, Komagataella phaffii. Description: Cankorur-Cetinkaya, Ayca, et al. Process development for the continuous production of heterologous proteins by the industrial yeast, Komagataella phaffii. ''Biotechnol Bioeng''. 2018 Dec; '''115''' (12):2962-2973 | |
| Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria. Description: Zoledowska, Sabina, et al. Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria. ''Microorganisms''. 2019 Apr 5; '''7''' (4): | |
| Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development. Description: Larsson, Ida, et al. Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development. ''Front Genet''. 2020; '''11''': 381 | |
| Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium. Description: diCenzo, George C, et al. Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium. ''Nat Commun''. 2020 May 22; '''11''' (1):2574 | |
| BioModels Parameters: a treasure trove of parameter values from published systems biology models. Description: Glont, Mihai, et al. BioModels Parameters: a treasure trove of parameter values from published systems biology models. ''Bioinformatics''. 2020 Nov 1; '''36''' (17):4649-4654 | |
| MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. Description: Moretti, Sebastien, et al. MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. ''Nucleic Acids Res''. 2021 Jan 8; '''49''' (D1):D570-D574 | |
| First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. Description: Renz, Alina, et al. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. ''Metabolites''. 2021 Apr 9; '''11''' (4): | |
| A Spatial Quantitative Systems Pharmacology Platform spQSP-IO for Simulations of Tumor-Immune Interactions and Effects of Checkpoint Inhibitor Immunotherapy. Description: Gong, Chang, et al. A Spatial Quantitative Systems Pharmacology Platform spQSP-IO for Simulations of Tumor-Immune Interactions and Effects of Checkpoint Inhibitor Immunotherapy. ''Cancers (Basel)''. 2021 Jul 26; '''13''' (15): | |
| An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. Description: Payne, Dawson D, et al. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. ''NPJ Syst Biol Appl''. 2021 Oct 8; '''7''' (1):37 | |
| A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Description: Santos, Joao P G, et al. A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. ''Neuroinformatics''. 2022 Jan; '''20''' (1):241-259 | |
| A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota. Description: Versluis, David M, et al. A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota. ''mSystems''. 2022 Oct 26; '''7''' (5):e0044622 | |
| Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism? Description: Negre, Delphine, et al. Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism? ''PLoS One''. 2023; '''18''' (8):e0289757 | |
| SBML2HYB: a Python interface for SBML compatible hybrid modeling. Description: Pinto, Jose, et al. SBML2HYB: a Python interface for SBML compatible hybrid modeling. ''Bioinformatics''. 2023 Jan 1; '''39''' (1): | |
| 2'-Fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations. Description: Versluis, David M, et al. 2'-Fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations. ''iScience''. 2024 Mar 15; '''27''' (3):109085 | |
| Curating models from BioModels: Developing a workflow for creating OMEX files. Description: Xu, Jin, et al. Curating models from BioModels: Developing a workflow for creating OMEX files. ''bioRxiv''. 2024 Mar 17; | |
| Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities. Description: Leonidou, Nantia, et al. Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities. ''Microbiol Spectr''. 2024 Jun 4; '''12''' (6):e0400623 | |
| Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses. Description: Bleker, Carissa, et al. Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses. ''Plant Commun''. 2024 Jun 10; '''5''' (6):100920 | |
| Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling. Description: Leonidou, Nantia, et al. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling. ''PLoS Pathog''. 2024 Sep; '''20''' (9):e1012528 |