Genome-scale modeling for metabolic engineering

Halophiles, coming stars for industrial biotechnology

(2015) Jin Yin et al.   BIOTECHNOLOGY ADVANCES

Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine

(2015) Irina Borodina et al.   METABOLIC ENGINEERING

Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae

(2014) Zachary A. King et al.   METABOLIC ENGINEERING

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Identification of Novel Knockout Targets for Improving Terpenoids Biosynthesis in Saccharomyces cerevisiae

(2014) Zhiqiang Sun et al.   PLoS One

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

(2014) Daniel Machado et al.   PLoS Computational Biology

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

(2014) Matthew N. Benedict et al.   PLoS Computational Biology

Multi-scale modeling for sustainable chemical production

(2013) Kai Zhuang et al.   Biotechnology Journal

Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746

(2013) Matthew C. Gonnerman et al.   Biotechnology Journal

Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae

(2013) René H Wijffels et al.   CURRENT OPINION IN BIOTECHNOLOGY

Frontiers of yeast metabolic engineering: diversifying beyond ethanol and Saccharomyces

(2013) Leqian Liu et al.   CURRENT OPINION IN BIOTECHNOLOGY

Biobased chemicals: the convergence of green chemistry with industrial biotechnology

(2013) Jim C. Philp et al.   TRENDS IN BIOTECHNOLOGY

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

(2012) Xueyang Feng et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries

(2012) Kuk-Ki Hong et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites

(2012) Satoshi Ohno et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Automation on the Generation of Genome-Scale Metabolic Models

(2012) R. Reyes et al.   JOURNAL OF COMPUTATIONAL 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

The future of metabolic engineering and synthetic biology: Towards a systematic practice

(2012) Vikramaditya G. Yadav et al.   METABOLIC ENGINEERING

Mathematical optimization applications in metabolic networks

(2012) Ali R. Zomorrodi et al.   METABOLIC ENGINEERING

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

(2012) J. Nogales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803

(2011) Katsunori Yoshikawa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches

(2011) Yu-Sin Jang et al.   BIOTECHNOLOGY ADVANCES

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

Bio-based production of chemicals, materials and fuels – Corynebacterium glutamicum as versatile cell factory

(2011) Judith Becker et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A

(2011) M. N. Benedict et al.   JOURNAL OF BACTERIOLOGY

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae

(2011) Amit Ghosh et al.   PLoS One

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Systems metabolic engineering: Genome-scale models and beyond

(2010) John Blazeck et al.   Biotechnology Journal

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

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

Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture

(2010) C. K. Savile et al.   SCIENCE

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

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

Bacterial vitamin B2, B11 and B12 overproduction: An overview

(2009) Catherine M. Burgess et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger

(2009) Susan Meijer et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering

(2009) Mohammad A. Asadollahi et al.   METABOLIC ENGINEERING

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence

(2008) Hyohak Song et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Progress in Metabolic Engineering of Saccharomyces cerevisiae

(2008) E. Nevoigt   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology