KOPTIC: A novel approach for in silico prediction of enzyme kinetics and regulation
WL Schroeder, R Saha - bioRxiv, 2019 - biorxiv.org
Kinetic models of metabolism (kMMs) provide not only a more accurate method for
designing novel biological systems but also characterization of system regulations; however …
designing novel biological systems but also characterization of system regulations; however …
Reconstruction of an in silico metabolic model of Arabidopsis thaliana through database integration
K Radrich, Y Tsuruoka, P Dobson, A Gevorgyan… - Nature …, 2009 - nature.com
The number of genome-scale metabolic models has been rising quickly in recent years, and
the scope of their utilization encompasses a broad range of applications from metabolic …
the scope of their utilization encompasses a broad range of applications from metabolic …
A Computational Framework to Study the Primary Lifecycle Metabolism of Arabidopsis thaliana
WL Schroeder, R Saha - bioRxiv, 2019 - biorxiv.org
Stoichiometric Models of metabolism have proven valuable tools for increased
understanding of metabolism and accuracy of synthetic biology interventions to achieve …
understanding of metabolism and accuracy of synthetic biology interventions to achieve …
Kinetic modeling of metabolism: Present and future
Kinetic models of metabolism are predictors of temporal metabolic behavior of living
organisms that integrate multi-omics data sets with reaction network models to interpret …
organisms that integrate multi-omics data sets with reaction network models to interpret …
Critical assessment of genome-scale metabolic models of Arabidopsis thaliana
JZ Amirzakaria, SA Marashi, MA Malboobi… - Molecular …, 2022 - pubs.rsc.org
Genome-scale metabolic models (GEMs) have enabled researchers to perform systems-
level studies of living organisms. Flux balance analysis (FBA), as a constraint-based …
level studies of living organisms. Flux balance analysis (FBA), as a constraint-based …
[PDF][PDF] The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi …
For over ten years, ModelSEED has been a primary resource for the construction of draft
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
Modeling plant metabolism: from network reconstruction to mechanistic models
Mathematical modeling of plant metabolism enables the plant science community to
understand the organization of plant metabolism, obtain quantitative insights into metabolic …
understand the organization of plant metabolism, obtain quantitative insights into metabolic …
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants …
For over 10 years, ModelSEED has been a primary resource for the construction of draft
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
Geckopy 3.0: enzyme constraints, thermodynamics constraints and omics integration in python
JC Muriel, C Long, N Sonnenschein - bioRxiv, 2023 - biorxiv.org
GEnome-scale Metabolic (GEM) models are knowledge bases of the reactions and
metabolites of a particular organism. These GEM models allow for the simulation of the …
metabolites of a particular organism. These GEM models allow for the simulation of the …
Omics data input for metabolic modeling
Highlights•Metabolic modeling and its reconstruction.•Plant metabolic modeling, progress
and challenges.•Omics datasets as constraints to reconstruct plant metabolic models.Recent …
and challenges.•Omics datasets as constraints to reconstruct plant metabolic models.Recent …