Application of theoretical methods to increase succinate production in engineered strains

Highly selective production of succinic acid by metabolically engineered Mannheimia succiniciproducens and its efficient purification

(2016) Sol Choi et al.   BIOTECHNOLOGY AND BIOENGINEERING

solveME: fast and reliable solution of nonlinear ME models

(2016) Laurence Yang et al.   BMC BIOINFORMATICS

Production of succinic acid by metabolically engineered microorganisms

(2016) Jung Ho Ahn et al.   CURRENT OPINION IN BIOTECHNOLOGY

CRISPR/Cas9 advances engineering of microbial cell factories

(2016) Tadas Jakočiūnas et al.   METABOLIC ENGINEERING

Systematic engineering of TCA cycle for optimal production of a four-carbon platform chemical 4-hydroxybutyric acid in Escherichia coli

(2016) Sol Choi et al.   METABOLIC ENGINEERING

Homo-succinic acid production by metabolically engineered Mannheimia succiniciproducens

(2016) Jeong Wook Lee et al.   METABOLIC ENGINEERING

Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli

(2016) Björn-Johannes Harder et al.   METABOLIC ENGINEERING

Designing intracellular metabolism for production of target compounds by introducing a heterologous metabolic reaction based on a Synechosystis sp. 6803 genome-scale model

(2016) Tomokazu Shirai et al.   Microbial Cell Factories

High-yield anaerobic succinate production by strategically regulating multiple metabolic pathways based on stoichiometric maximum in Escherichia coli

(2016) Jiao Meng et al.   Microbial Cell Factories

Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

(2016) Pablo Carbonell et al.   NATURAL PRODUCT REPORTS

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Redox State of Flavin Adenine Dinucleotide Drives Substrate Binding and Product Release in Escherichia coli Succinate Dehydrogenase

(2015) Victor W. T. Cheng et al.   BIOCHEMISTRY

tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks

(2015) Matthias P. Gerstl et al.   BIOINFORMATICS

Flux-sum analysis identifies metabolite targets for strain improvement

(2015) Meiyappan Lakshmanan et al.   BMC Systems Biology

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

(2015) Meric Ataman et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational methods in metabolic engineering for strain design

(2015) Matthew R Long et al.   CURRENT OPINION IN BIOTECHNOLOGY

Manipulating pyruvate to acetyl-CoA conversion in Escherichia coli for anaerobic succinate biosynthesis from glucose with the yield close to the stoichiometric maximum

(2015) Alexandra Yu. Skorokhodova et al.   JOURNAL OF BIOTECHNOLOGY

Design of homo-organic acid producing strains using multi-objective optimization

(2015) Tae Yong Kim et al.   METABOLIC ENGINEERING

Characterizing metabolic pathway diversification in the context of perturbation size

(2015) Laurence Yang et al.   METABOLIC ENGINEERING

On the feasibility of growth-coupled product synthesis in microbial strains

(2015) Steffen Klamt et al.   METABOLIC ENGINEERING

Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis

(2015) Yee Wen Choon et al.   Biomed Research International

SSDesign: Computational metabolic pathway design based on flux variability using elementary flux modes

(2014) Yoshihiro Toya et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

Towards large scale fermentative production of succinic acid

(2014) Mickel LA Jansen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic engineering of carbon and redox flow in the production of small organic acids

(2014) Chandresh Thakker et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli

(2014) Xinna Zhu et al.   METABOLIC ENGINEERING

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

(2014) Ali Khodayari et al.   METABOLIC ENGINEERING

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization

(2014) Yee Wen Choon et al.   PLoS One

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

FastPros: screening of reaction knockout strategies for metabolic engineering

(2013) Satoshi Ohno et al.   BIOINFORMATICS

Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

(2013) Joshua J. Hamilton et al.   BIOPHYSICAL JOURNAL

Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints

(2013) Shaogang Ren et al.   BMC BIOINFORMATICS

Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design

(2013) Kai Zhuang et al.   BMC BIOTECHNOLOGY

Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production

(2013) Rasmus Agren et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Metabolic engineering of Escherichia coli to minimize byproduct formate and improving succinate productivity through increasing NADH availability by heterologous expression of NAD+-dependent formate dehydrogenase

(2013) Grant J. Balzer et al.   METABOLIC ENGINEERING

Metabolic engineering of Escherichia coli and in silico comparing of carboxylation pathways for high succinate productivity under aerobic conditions

(2013) Jiangang Yang et al.   MICROBIOLOGICAL RESEARCH

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

(2013) José Manuel Otero et al.   PLoS One

Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes

(2013) Zita I. T. A. Soons et al.   PLoS One

ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

(2013) Zixiang Xu et al.   PLoS One

Truncated branch and bound achieves efficient constraint-based genetic design

(2012) Dennis Egen et al.   BIOINFORMATICS

Robust design of microbial strains

(2012) Jole Costanza et al.   BIOINFORMATICS

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Computational identification of gene over-expression targets for metabolic engineering of taxadiene production

(2011) Brett A. Boghigian et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metabolic ensemble modeling for strain engineers

(2011) Yikun Tan et al.   Biotechnology Journal

Succinate production in Escherichia coli

(2011) Chandresh Thakker et al.   Biotechnology Journal

Perspective on opportunities in industrial biotechnology in renewable chemicals

(2011) Brent Erickson et al.   Biotechnology Journal

Succinate production from sucrose by metabolic engineered escherichia coli strains under aerobic conditions

(2011) Jian Wang et al.   BIOTECHNOLOGY PROGRESS

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

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

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

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques

(2011) Joonhoon Kim et al.   PLoS One

Metabolic engineering of Escherichia coli for biotechnological production of high-value organic acids and alcohols

(2010) Chao Yu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

CASOP: A Computational Approach for Strain Optimization aiming at high Productivity

(2010) Oliver Hädicke et al.   JOURNAL OF BIOTECHNOLOGY

Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux

(2010) Yikun Tan et al.   METABOLIC ENGINEERING

Manipulating redox and ATP balancing for improved production of succinate in E. coli

(2010) Amarjeet Singh et al.   METABOLIC ENGINEERING

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Production of succinate by a pflB ldhA double mutant of Escherichia coli overexpressing malate dehydrogenase

(2009) Wei Wang et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Multiobjective flux balancing using the NISE method for metabolic network analysis

(2009) Young-Gyun Oh et al.   BIOTECHNOLOGY PROGRESS

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Metabolic evolution of energy-conserving pathways for succinate production in Escherichia coli

(2009) X. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Feasibility of production methods for succinic acid derivatives: a marriage of renewable resources and chemical technology

(2008) Ana Cukalovic et al.   Biofuels Bioproducts & Biorefining-Biofpr

Ensemble Modeling of Metabolic Networks

(2008) Linh M. Tran et al.   BIOPHYSICAL JOURNAL

Eliminating side products and increasing succinate yields in engineered strains ofEscherichia coliC

(2008) Kaemwich Jantama et al.   BIOTECHNOLOGY AND BIOENGINEERING

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

(2008) Nicola Zamboni et al.   BMC BIOINFORMATICS

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains ofEscherichia coli C that produce succinate and malate

(2007) Kaemwich Jantama et al.   BIOTECHNOLOGY AND BIOENGINEERING