Logical transformation of genome-scale metabolic models for gene level applications and analysis

New paradigms for metabolic modeling of human cells

(2015) Adil Mardinoglu et al.   CURRENT OPINION IN BIOTECHNOLOGY

DAISY: Picking Synthetic Lethals from Cancer Genomes

(2014) Colm J. Ryan et al.   CANCER CELL

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality

(2014) Livnat Jerby-Arnon et al.   CELL

A hybrid of ant colony optimization and minimization of metabolic adjustment to improve the production of succinic acid in Escherichia coli

(2014) Shiue Kee Chong et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production

(2014) Justyna Nocon et al.   METABOLIC ENGINEERING

A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration

(2014) K. Yizhak et al.   Molecular Systems Biology

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

(2014) R. Agren et al.   Molecular Systems Biology

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

(2014) Hojung Nam et al.   PLoS Computational Biology

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

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

A hybrid of bees algorithm and flux balance analysis with OptKnock as a platform for in silico optimization of microbial strains

(2013) Yee Wen Choon et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Genome-scale modeling of human metabolism - a systems biology approach

(2013) Adil Mardinoglu et al.   Biotechnology Journal

Genome-wide analysis of redox reactions reveals metabolic engineering targets for d-lactate overproduction in Escherichia coli

(2013) Hyun Ju Kim et al.   METABOLIC ENGINEERING

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

(2013) Seung Woo Cho et al.   NATURE BIOTECHNOLOGY

Steady-State Metabolite Concentrations Reflect a Balance between Maximizing Enzyme Efficiency and Minimizing Total Metabolite Load

(2013) Naama Tepper et al.   PLoS One

Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools

(2013) Ed Reznik et al.   PLoS Computational Biology

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Truncated branch and bound achieves efficient constraint-based genetic design

(2012) Dennis Egen et al.   BIOINFORMATICS

An integrated computational and experimental study for overproducing fatty acids in Escherichia coli

(2012) Sridhar Ranganathan et al.   METABOLIC ENGINEERING

Systems medicine and metabolic modelling

(2011) A. Mardinoglu et al.   JOURNAL OF INTERNAL MEDICINE

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

(2011) Peng Xu et al.   METABOLIC ENGINEERING

Engineering strategy of yeast metabolism for higher alcohol production

(2011) Fumio Matsuda et al.   Microbial Cell Factories

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

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

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

Microbial 1-butanol production: Identification of non-native production routes andin silicoengineering interventions

(2010) Sridhar Ranganathan et al.   Biotechnology Journal

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

(2010) Joonhoon Kim et al.   BMC Systems Biology

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Fatty acid synthase as a potential therapeutic target in cancer

(2010) Richard Flavin et al.   Future Oncology

Improved vanillin production in baker's yeast through in silico design

(2010) Ana Brochado et al.   Microbial Cell Factories

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

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

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

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Increased Malonyl Coenzyme A Biosynthesis by Tuning the Escherichia coli Metabolic Network and Its Application to Flavanone Production

(2009) Z. L. Fowler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-scale gene/reaction essentiality and synthetic lethality analysis

(2009) Patrick F Suthers et al.   Molecular Systems Biology

Large-scale identification of genetic design strategies using local search

(2009) Desmond S Lun et al.   Molecular Systems Biology

Context-Specific Metabolic Networks Are Consistent with Experiments

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