A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism

The Complete Genome Sequence and Structure of the Oleaginous Rhodococcus opacus Strain PD630 Through Nanopore Technology

(2022) Andrea Firrincieli et al.   Frontiers in Bioengineering and Biotechnology

Hot isopropanol quenching procedure for automated microtiter plate scale 13C-labeling experiments

(2022) Jochen Nießer et al.   Microbial Cell Factories

Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630

(2022) Jinjin Diao et al.   Communications Biology

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Mechanism of the oxidative stress‐mediated increase in lipid accumulation by the bacterium, R. opacus PD630: Experimental analysis and genome‐scale metabolic modeling

(2020) Archanaa Sundararaghavan et al.   BIOTECHNOLOGY AND BIOENGINEERING

Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models

(2020) Sanjeev Dahal et al.   PROTEOMICS

Engineering of an oleaginous bacterium for the production of fatty acids and fuels

(2019) Hye Mi Kim et al.   Nature Chemical Biology

A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

(2019) Garrett W. Roell et al.   METABOLIC ENGINEERING

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

(2019) Hongzhong Lu et al.   Nature Communications

Bioconversion of renewable feedstocks by Rhodococcus opacus

(2019) Anamika Chatterjee et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus

(2018) William R. Henson et al.   METABOLIC ENGINEERING

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630

(2017) Drew M. DeLorenzo et al.   ACS Synthetic Biology

Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulatingRhodococcus opacusPD630

(2016) Aki Yoneda et al.   NUCLEIC ACIDS RESEARCH

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

Rhodococcus opacus B4: a promising bacterium for production of biofuels and biobased chemicals

(2016) Ana Rita Castro et al.   AMB Express

E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data

(2016) Min Kyung Kim et al.   PLoS One

Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel 13 C-metabolite fingerprinting

(2015) Whitney D. Hollinshead et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition

(2015) Mohammad Tajparast et al.   BMC Systems Biology

Multi -omics and metabolic modelling pipelines: Challenges and tools for systems microbiology

(2015) Marco Fondi et al.   MICROBIOLOGICAL RESEARCH

Assembly: a resource for assembled genomes at NCBI

(2015) Paul A. Kitts et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Daniel Machado et al.   PLoS Computational Biology

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

Flux-coupled genes and their use in metabolic flux analysis

(2013) Hyun Uk Kim et al.   Biotechnology Journal

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

(2013) Tobias Österlund et al.   BMC Systems Biology

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Controlled vocabularies and semantics in systems biology

(2011) M. Courtot et al.   Molecular Systems Biology

Microbial degradation of aromatic compounds — from one strategy to four

(2011) Georg Fuchs et al.   NATURE REVIEWS MICROBIOLOGY

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

The biomass objective function

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

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

(2009) Rogier J P van Berlo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Advances in analysis of microbial metabolic fluxes via13C isotopic labeling

(2008) Yinjie J. Tang et al.   MASS SPECTROMETRY REVIEWS

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

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