Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa

(2019) Laura J. Dunphy et al.   Cell Systems

Reconciling high-throughput gene essentiality data with metabolic network reconstructions

(2019) Anna S. Blazier et al.   PLoS Computational Biology

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization

(2018) Matthew L. Jenior et al.   mSphere

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

(2017) Edik M. Blais et al.   Nature Communications

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

Composition of the outgrowth medium modulates wake-up kinetics and ampicillin sensitivity of stringent and relaxed Escherichia coli

(2016) Vallo Varik et al.   Scientific Reports

The Cost of Protein Production

(2016) Moshe Kafri et al.   Cell Reports

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

(2016) Jonathan M. Monk et al.   Cell Systems

Evolutionary pressures on microbial metabolic strategies in the chemostat

(2016) Meike T. Wortel et al.   Scientific Reports

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

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

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

(2015) Semidán Robaina Estévez et al.   PLoS One

E1 of α-ketoglutarate dehydrogenase defendsMycobacterium tuberculosisagainst glutamate anaplerosis and nitroxidative stress

(2015) Christina Maksymiuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transhydrogenase Promotes the Robustness and Evolvability of E. coli Deficient in NADPH Production

(2015) Hsin-Hung Chou et al.   PLoS Genetics

Escherichia coli pyruvate:flavodoxin oxidoreductase, YdbK - regulation of expression and biological roles in protection against oxidative stress

(2015) Takayuki Nakayama et al.   GENES & GENETIC SYSTEMS

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

(2014) Joao C. Guimaraes et al.   NUCLEIC ACIDS RESEARCH

The double-stranded transcriptome of Escherichia coli

(2014) M. Lybecker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Daniel Machado et al.   PLoS Computational Biology

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis

(2014) Oriol Güell et al.   PLoS Computational Biology

Flux-coupled genes and their use in metabolic flux analysis

(2013) Hyun Uk Kim et al.   Biotechnology Journal

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume

(2013) Meng Li et al.   ENVIRONMENTAL MICROBIOLOGY

Links between metabolic plasticity and functional redundancy in freshwater bacterioplankton communities

(2013) Jérôme Comte et al.   Frontiers in Microbiology

Amino acid fermentation at the origin of the genetic code

(2012) Harold P de Vladar   Biology Direct

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

(2012) Nadine Töpfer et al.   BMC Systems Biology

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

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

(2012) Ali Navid et al.   BMC Systems Biology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Mechanism for Regulation of the Putrescine Utilization Pathway by the Transcription Factor PuuR in Escherichia coli K-12

(2012) N. Nemoto et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments

(2012) Zhide Fang et al.   Cell and Bioscience

Temporal Expression-based Analysis of Metabolism

(2012) Sara B. Collins et al.   PLoS Computational Biology

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

AUC-RF: A New Strategy for Genomic Profiling with Random Forest

(2011) M. Luz Calle et al.   HUMAN HEREDITY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

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

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

Applications of genome-scale metabolic reconstructions

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

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

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