Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

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

(2015) Cheng Zhang et al.   BIOINFORMATICS

Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks

(2015) Aditya Pratapa et al.   BIOINFORMATICS

Critical assessment of genome-scale metabolic networks: the need for a unified standard

(2015) A. Ravikrishnan et al.   BRIEFINGS IN BIOINFORMATICS

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

New paradigms for metabolic modeling of human cells

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

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

(2015) Ljubisa Miskovic et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational methods in metabolic engineering for strain design

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

Modeling cancer metabolism on a genome scale

(2015) K. Yizhak et al.   Molecular Systems Biology

The gut microbiota modulates host amino acid and glutathione metabolism in mice

(2015) A. Mardinoglu et al.   Molecular Systems Biology

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

In search for symmetries in the metabolism of cancer

(2015) Francesco Gatto et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

(2015) Francesco Gatto et al.   Scientific Reports

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes

(2015) Leif Väremo et al.   Cell Reports

A Method to Constrain Genome-Scale Models with 13C Labeling Data

(2015) Héctor García Martín et al.   PLoS Computational Biology

From next-generation sequencing to systematic modeling of the gut microbiome

(2015) Boyang Ji et al.   Frontiers in Genetics

Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production inStreptomyces coelicolorA3(2)

(2014) Minsuk Kim et al.   Biotechnology Journal

Efficiently gap-filling reaction networks

(2014) Mario Latendresse   BMC BIOINFORMATICS

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

(2014) Livnat Jerby-Arnon et al.   CELL

Applications of genome-scale metabolic network model in metabolic engineering

(2014) Byoungjin Kim et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

(2014) Justyna Nocon 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

Genome engineering for improved recombinant protein expression in Escherichia coli

(2014) Shubhashree Mahalik et al.   Microbial Cell Factories

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

Design of Optimally Constructed Metabolic Networks of Minimal Functionality

(2014) David E. Ruckerbauer et al.   PLoS One

Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma

(2014) Francesco Gatto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

(2014) Leonid Chindelevitch et al.   Nature Communications

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

(2014) Adil Mardinoglu et al.   Nature Communications

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

(2014) Daniel Machado et al.   PLoS Computational Biology

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

(2014) Axel von Kamp et al.   PLoS Computational Biology

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

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

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

(2013) Shaogang Ren et al.   BMC BIOINFORMATICS

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

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

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

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

(2013) José Manuel Otero et al.   PLoS One

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

(2013) Benjamin D. Heavner et al.   Database-The Journal of Biological Databases and Curation

Understanding the interactions between bacteria in the human gut through metabolic modeling

(2013) Saeed Shoaie et al.   Scientific Reports

Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

(2012) Ali Navid et al.   BMC Systems Biology

Flux variability scanning based on enforced objective flux for identifying gene amplification targets

(2012) Jong Park et al.   BMC Systems Biology

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

(2012) Sridhar Ranganathan 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

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

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

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

(2012) Xin Fang et al.   PLoS Computational Biology

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

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

(2011) Peng Xu et al.   METABOLIC ENGINEERING

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

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

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

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

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

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

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

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

Genome-scale gene/reaction essentiality and synthetic lethality analysis

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

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses

(2008) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Geobacter sulfurreducens strain engineered for increased rates of respiration

(2008) Mounir Izallalen et al.   METABOLIC ENGINEERING

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Context-Specific Metabolic Networks Are Consistent with Experiments

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