OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

(2017) Zhuo Wang et al.   PLoS Computational Biology

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models

(2016) R.P. Vivek-Ananth et al.   BIOSYSTEMS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Efficient production of 2,3-butanediol in Saccharomyces cerevisiae by eliminating ethanol and glycerol production and redox rebalancing

(2015) Sujin Kim et al.   METABOLIC ENGINEERING

De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae

(2015) Mingji Li et al.   METABOLIC ENGINEERING

In SilicoConstraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

(2015) Paulo Maia et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

(2015) Shuyi Ma et al.   PLoS Computational Biology

Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

(2015) Benjamin D. Heavner et al.   PLoS Computational Biology

Data-driven integration of genome-scale regulatory and metabolic network models

(2015) Saheed Imam et al.   Frontiers in Microbiology

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Dynamic flux balance analysis of batch fermentation: effect of genetic manipulations on ethanol production

(2013) K. P. Lisha et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Molecular mechanisms of system responses to novel stimuli are predictable from public data

(2013) Samuel A. Danziger et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements: Table 1.

(2013) Hao Luo et al.   NUCLEIC ACIDS RESEARCH

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

(2013) José Manuel Otero et al.   PLoS One

Implementation of a transhydrogenase-like shunt to counter redox imbalance during xylose fermentation in Saccharomyces cerevisiae

(2012) Hiroyuki Suga et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Designing optimal cell factories: integer programming couples elementary mode analysis with regulation

(2012) Christian Jungreuthmayer et al.   BMC Systems Biology

Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae

(2012) Hang Zhou et al.   METABOLIC ENGINEERING

Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering

(2012) Chiam Yu Ng et al.   Microbial Cell Factories

Rational improvement of the engineered isobutanol-producing Bacillus subtilis by elementary mode analysis

(2012) Shanshan Li et al.   Microbial Cell Factories

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production

(2010) H. S. Choi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information

(2010) Paulo Vilaça et al.   BIOSYSTEMS

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

Metabolic engineering of Saccharomyces cerevisiae for the biotechnological production of succinic acid

(2010) Andreas M. Raab et al.   METABOLIC ENGINEERING

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. Tepper et al.   BIOINFORMATICS

Systems biology of lipid metabolism: From yeast to human

(2009) Jens Nielsen   FEBS LETTERS