Modeling the metabolic dynamics at the genome-scale by optimized yield analysis

CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention

(2021) Jun Geng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models

(2021) Xue Yang et al.   METABOLIC ENGINEERING

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Dynamic Modeling of CHO Cell Metabolism Using the Hybrid Cybernetic Approach With a Novel Elementary Mode Analysis Strategy

(2020) Juan A. Martínez et al.   Frontiers in Bioengineering and Biotechnology

Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments

(2020) Elena Perrin et al.   Nature Communications

Cybernetic modeling of biological processes in mammalian systems

(2020) Lina Aboulmouna et al.   Current Opinion in Chemical Engineering

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

(2019) Hongzhong Lu et al.   Nature Communications

A mathematical framework for yield ( vs. rate) optimization in constraint-based modeling and applications in metabolic engineering

(2018) Steffen Klamt et al.   METABOLIC ENGINEERING

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

(2017) Steffen Klamt et al.   PLoS Computational Biology

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Elementary Vectors and Conformal Sums in Polyhedral Geometry and their Relevance for Metabolic Pathway Analysis

(2016) Stefan Müller et al.   Frontiers in Genetics

Learning from the Steersman: A Natural History of Cybernetic Models

(2015) Jamey D. Young   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Dynamic models of metabolism: Review of the cybernetic approach

(2012) Doraiswami Ramkrishna et al.   AICHE JOURNAL

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

On enhancing productivity of bioethanol with multiple species

(2011) Jun Geng et al.   BIOTECHNOLOGY AND BIOENGINEERING

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Cybernetic models based on lumped elementary modes accurately predict strain-specific metabolic function

(2010) Hyun-Seob Song et al.   BIOTECHNOLOGY AND BIOENGINEERING

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Systematic development of hybrid cybernetic models: Application to recombinant yeast co-consuming glucose and xylose

(2009) Hyun-Seob Song et al.   BIOTECHNOLOGY AND BIOENGINEERING

Large-scale computation of elementary flux modes with bit pattern trees

(2008) Marco Terzer et al.   BIOINFORMATICS

Reduction of a set of elementary modes using yield analysis

(2008) Hyun-Seob Song et al.   BIOTECHNOLOGY AND BIOENGINEERING

A hybrid model of anaerobicE. coliGJT001: Combination of elementary flux modes and cybernetic variables

(2008) Jin Il Kim et al.   BIOTECHNOLOGY PROGRESS

Is maximization of molar yield in metabolic networks favoured by evolution?

(2007) Stefan Schuster et al.   JOURNAL OF THEORETICAL BIOLOGY