Improving lysine production through construction of an Escherichia coli enzyme‐constrained model

Comprehensive understanding of Saccharomyces cerevisiae phenotypes with whole‐cell model WM_S288C

(2020) Chao Ye et al.   BIOTECHNOLOGY AND BIOENGINEERING

Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

(2019) Ilaria Massaiu et al.   Microbial Cell Factories

Growth strategy of microbes on mixed carbon sources

(2019) Xin Wang et al.   Nature Communications

L-lysine production improvement: a review of the state of the art and patent landscape focusing on strain development and fermentation technologies

(2019) Fernanda Karine do Carmo Félix et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

(2019) Troy E. Sandberg et al.   METABOLIC ENGINEERING

Enhancement of malate production through engineering of the periplasmic rTCA pathway in Escherichia coli

(2018) Liang Guo et al.   BIOTECHNOLOGY AND BIOENGINEERING

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Enhancing fructosylated chondroitin production in Escherichia coli K4 by balancing the UDP-precursors

(2018) Quan Zhang et al.   METABOLIC ENGINEERING

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

BRENDA in 2019: a European ELIXIR core data resource

(2018) Lisa Jeske et al.   NUCLEIC ACIDS RESEARCH

Synthetic Consortium of Escherichia coli for n-Butanol Production by Fermentation of the Glucose–Xylose Mixture

(2017) Mukesh Saini et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Metabolic engineering of Escherichia coli for the production of four-, five- and six-carbon lactams

(2017) Tong Un Chae et al.   METABOLIC ENGINEERING

Metabolomics-driven approach to solving a CoA imbalance for improved 1-butanol production in Escherichia coli

(2017) Toshiyuki Ohtake et al.   METABOLIC ENGINEERING

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

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

(2017) Ulrike Wittig et al.   NUCLEIC ACIDS RESEARCH

Evolving the l-lysine high-producing strain of Escherichia coli using a newly developed high-throughput screening method

(2016) Yan Wang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

(2016) Ali Khodayari et al.   Nature Communications

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines

(2015) Mingcong Wang et al.   PROTEOMICS

Ethylene-forming enzyme and bioethylene production

(2014) Carrie Eckert et al.   Biotechnology for Biofuels

Synthesis and Accumulation of Aromatic Aldehydes in an Engineered Strain of Escherichia coli

(2014) Aditya M. Kunjapur et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A de novo NADPH generation pathway for improving lysine production of Corynebacterium glutamicum by rational design of the coenzyme specificity of glyceraldehyde 3-phosphate dehydrogenase

(2014) Rajesh Reddy Bommareddy et al.   METABOLIC ENGINEERING

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

(2014) J. Carrera et al.   Molecular Systems Biology

Metabolic Engineering of Escherichia coli for Production of 2-phenylethanol from Renewable Glucose

(2013) Zhen Kang et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis

(2013) Xueyang Feng et al.   Microbial Cell Factories

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Redox balance is key to explaining full vs. partial switching to low-yield metabolism

(2012) Milan JA van Hoek et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

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

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

Engineering of Corynebacterium glutamicum with an NADPH-Generating Glycolytic Pathway for L-Lysine Production

(2010) S. Takeno et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli

(2010) Xuewen Chen et al.   METABOLIC ENGINEERING

Genotype to Phenotype: A Complex Problem

(2010) R. D. Dowell et al.   SCIENCE

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE