Genome-scale biological models for industrial microbial systems

Genome-scale metabolic modelling common cofactors metabolism in microorganisms

(2017) Nan Xu et al.   JOURNAL OF BIOTECHNOLOGY

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

(2017) ShengShee Thor et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

(2017) Kees C. H. van der Ark et al.   Microbiome

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models

(2017) Chao Ye et al.   Scientific Reports

Universal Poisson Statistics of mRNAs with Complex Decay Pathways

(2016) Mukund Thattai   BIOPHYSICAL JOURNAL

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

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

Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae

(2016) Yingying Chen et al.   Biotechnology for Biofuels

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Genome-scale metabolic models as platforms for strain design and biological discovery

(2016) Bashir Sajo Mienda   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

(2016) Cheng Zhang et al.   Frontiers in Physiology

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

(2016) Jose Utrilla et al.   Cell Systems

Engineering Synthetic Multistress Tolerance in Escherichia coli by Using a Deinococcal Response Regulator, DR1558

(2015) Deepti Appukuttan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exact quantification of cellular robustness in genome-scale metabolic networks

(2015) Matthias P. Gerstl et al.   BIOINFORMATICS

Modular design of metabolic network for robust production of n-butanol from galactose–glucose mixtures

(2015) Hyun Gyu Lim et al.   Biotechnology for Biofuels

Constructing kinetic models of metabolism at genome-scales: A review

(2015) Shyam Srinivasan et al.   Biotechnology Journal

Reconstruction and analysis of the genome-scale metabolic model of schizochytrium limacinum SR21 for docosahexaenoic acid production

(2015) Chao Ye et al.   BMC GENOMICS

Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina

(2015) Chao Ye et al.   BMC Systems Biology

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models

(2015) Philipp Erdrich et al.   BMC Systems Biology

Redox Homeostasis and Mitochondrial Dynamics

(2015) Peter H.G.M. Willems et al.   Cell Metabolism

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W

(2015) Nan Xu et al.   GENE

Genome-scale modeling for metabolic engineering

(2015) Evangelos Simeonidis et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Unraveling interactions in microbial communities - from co-cultures to microbiomes

(2015) Justin Tan et al.   JOURNAL OF MICROBIOLOGY

Compartmentalizing metabolic pathway in Candida glabrata for acetoin production

(2015) Shubo Li et al.   METABOLIC ENGINEERING

Protein–protein interaction predictions using text mining methods

(2015) Nikolas Papanikolaou et al.   METHODS

Twenty years of bacterial genome sequencing

(2015) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

(2015) Saheed Imam et al.   PLoS Computational Biology

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

(2015) Shuyi Ma et al.   PLoS Computational Biology

Constructing kinetic models of metabolism at genome-scales: A review

(2015) Shyam Srinivasan et al.   Biotechnology Journal

Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production

(2015) Yali Wang et al.   Frontiers in Microbiology

Reconstructing Genome-Wide Protein–Protein Interaction Networks Using Multiple Strategies with Homologous Mapping

(2015) Yu-Shu Lo et al.   PLoS One

HubAlign: an accurate and efficient method for global alignment of protein–protein interaction networks

(2014) Somaye Hashemifar et al.   BIOINFORMATICS

Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis

(2014) Jesse CJ van Dam et al.   BMC Systems Biology

A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

(2014) Daniel S Weaver et al.   BMC Systems Biology

Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production

(2014) Chao Ye et al.   JOURNAL OF BIOTECHNOLOGY

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

(2014) Miguel A. Campodonico et al.   METABOLIC ENGINEERING

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

(2014) Justyna Nocon et al.   METABOLIC ENGINEERING

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

(2014) J. Carrera et al.   Molecular Systems Biology

Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

(2014) Alejandro Acevedo et al.   PLoS One

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

(2013) M. Ganter et al.   BIOINFORMATICS

A metabolite-centric view on flux distributions in genome-scale metabolic models

(2013) S Riemer et al.   BMC Systems Biology

Biotechnological potential of respiring Zymomonas mobilis: A stoichiometric analysis of its central metabolism

(2013) Agris Pentjuss et al.   JOURNAL OF BIOTECHNOLOGY

Development of a minimal chemically defined medium for Ketogulonicigenium vulgare WSH001 based on its genome-scale metabolic model

(2013) Shicun Fan et al.   JOURNAL OF BIOTECHNOLOGY

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling

(2013) J. A. H. Wodke et al.   Molecular Systems Biology

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

High-level semi-synthetic production of the potent antimalarial artemisinin

(2013) C. J. Paddon et al.   NATURE

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

(2013) Jeremy J. Minty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Genome-scale metabolic model in guiding metabolic engineering of microbial improvement

(2012) Chuan Xu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Fluxomics - connecting ‘omics analysis and phenotypes

(2012) Gal Winter et al.   ENVIRONMENTAL MICROBIOLOGY

Reconstruction and analysis of the genome-scale metabolic network of Candida glabrata

(2012) Nan Xu et al.   Molecular BioSystems

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Predictive Potential of Flux Balance Analysis of Saccharomyces cerevisiae Using as Optimization Function Combinations of Cell Compartmental Objectives

(2012) Carlos Eduardo García Sánchez 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

MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis

(2012) Leonid Chindelevitch et al.   GENOME BIOLOGY

Optimization of Biomass Composition Explains Microbial Growth-Stoichiometry Relationships

(2011) Oskar Franklin et al.   AMERICAN NATURALIST

Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol

(2011) Cong T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis

(2011) Ru-Dong Li et al.   BMC Systems Biology

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

(2011) Mohammad Tauqeer Alam et al.   FEBS LETTERS

Spatial organization of enzymes for metabolic engineering

(2011) Hanson Lee et al.   METABOLIC ENGINEERING

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

(2011) Jan Schellenberger et al.   Nature Protocols

Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity

(2011) T. Wongsurawat et al.   NUCLEIC ACIDS RESEARCH

Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins

(2010) Young-Rae Cho et al.   BMC BIOINFORMATICS

The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies

(2010) Kyung Lee et al.   Microbial Cell Factories

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

(2010) Dipak Barua et al.   PLoS Computational Biology

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

Industrial systems biology

(2009) José Manuel Otero et al.   BIOTECHNOLOGY AND BIOENGINEERING

Flux balance analysis of biological systems: applications and challenges

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

Genome-scale gene/reaction essentiality and synthetic lethality analysis

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

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

In the light of directed evolution: Pathways of adaptive protein evolution

(2009) J. D. Bloom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: application to DNA replication

(2008) J.C. Atlas et al.   IET Systems Biology

Genome shuffling to improve thermotolerance, ethanol tolerance and ethanol productivity of Saccharomyces cerevisiae

(2008) Dong-jian Shi et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery

(2008) Xiaohu Wang et al.   NUCLEIC ACIDS RESEARCH

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

(2008) R. Zhang et al.   NUCLEIC ACIDS RESEARCH