Reconstruction of biochemical networks in microorganisms (Q29616018)

Europe PubMed Central

title

Reconstruction of biochemical networks in microorganisms (English)

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author name string

Feist AM

1

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Herrgård MJ

2

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Thiele I

3

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Reed JL

4

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30 April 2017

Palsson BØ

5

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language of work or name

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30 April 2017

publication date

February 2009

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Nature Reviews Microbiology

30 April 2017

published in

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volume

7

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30 April 2017

issue

2

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30 April 2017

page(s)

129-43

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Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

30 April 2017

cites work

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The RAST Server: rapid annotations using subsystems technology

30 April 2017

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Database resources of the National Center for Biotechnology Information

30 April 2017

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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

30 April 2017

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Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

30 April 2017

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Structural and functional analysis of cellular networks with CellNetAnalyzer

30 April 2017

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

30 April 2017

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

30 April 2017

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Entrez Gene: gene-centered information at NCBI

30 April 2017

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Matrix formalism to describe functional states of transcriptional regulatory systems

30 April 2017

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Identifying transcription factor functions and targets by phenotypic activation

30 April 2017

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RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

30 April 2017

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The integrated microbial genomes (IMG) system

30 April 2017

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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

30 April 2017

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The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

30 April 2017

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Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis

30 April 2017

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Automation of gene assignments to metabolic pathways using high-throughput expression data

30 April 2017

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Regulatory on/off minimization of metabolic flux changes after genetic perturbations

30 April 2017

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metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella

30 April 2017

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CYGD: the Comprehensive Yeast Genome Database

30 April 2017

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PSORTdb: a protein subcellular localization database for bacteria

30 April 2017

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Compilation of tRNA sequences and sequences of tRNA genes

30 April 2017

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Genome-scale models of microbial cells: evaluating the consequences of constraints

30 April 2017

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Transcriptional regulatory code of a eukaryotic genome

30 April 2017

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A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

30 April 2017

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Global organization of metabolic fluxes in the bacterium Escherichia coli

30 April 2017

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Network biology: understanding the cell's functional organization

30 April 2017

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BRENDA, the enzyme database: updates and major new developments

30 April 2017

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30 April 2017

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Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

3 June 2018

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UniProt: the Universal Protein knowledgebase

30 April 2017

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The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

30 April 2017

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Global analysis of protein localization in budding yeast

30 April 2017

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Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

30 April 2017

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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

30 April 2017

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Analysis of optimality in natural and perturbed metabolic networks

30 April 2017

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The Pathway Tools software

30 April 2017

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Genome-wide location and function of DNA binding proteins

30 April 2017

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KEGG: kyoto encyclopedia of genes and genomes

30 April 2017

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SGD: Saccharomyces Genome Database

30 April 2017

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

30 April 2017

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Dynamic analysis of integrated signaling, metabolic, and regulatory networks

3 June 2018

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Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

3 June 2018

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New surveyor tools for charting microbial metabolic maps.

3 June 2018

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Metabolic reconstruction and analysis for parasite genomes

3 June 2018

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Multidimensional annotation of the Escherichia coli K-12 genome

3 June 2018

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Systematic condition-dependent annotation of metabolic genes

3 June 2018

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Regulation of gene expression by small non-coding RNAs: a quantitative view

3 June 2018

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Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli.

3 June 2018

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Orthologous transcription factors in bacteria have different functions and regulate different genes

3 June 2018

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Mechanisms of gene regulation in Plasmodium.

3 June 2018

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Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

3 June 2018

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A survey of orphan enzyme activities

3 June 2018

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Target identification of small noncoding RNAs in bacteria

3 June 2018

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Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy

3 June 2018

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Identification of bacterial small non-coding RNAs: experimental approaches

3 June 2018

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Toward the automated generation of genome-scale metabolic networks in the SEED.

3 June 2018

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Genetic reconstruction of a functional transcriptional regulatory network

3 June 2018

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Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains

3 June 2018

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Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate.

3 June 2018

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Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae

3 June 2018

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Plasticity of genetic interactions in metabolic networks of yeast

3 June 2018

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Targeting nutrient uptake mechanisms in Plasmodium

3 June 2018

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A systems approach to measuring the binding energy landscapes of transcription factors

3 June 2018

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TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels

3 June 2018

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Systematic assignment of thermodynamic constraints in metabolic network models

3 June 2018

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Advancements in transfection technologies for Plasmodium.

3 June 2018

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A chromatin-mediated mechanism for specification of conditional transcription factor targets

3 June 2018

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Systems approach to refining genome annotation

3 June 2018

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Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

3 June 2018

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An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling

3 June 2018

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Experimental and computational assessment of conditionally essential genes in Escherichia coli

3 June 2018

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Transcriptional regulatory networks in bacteria: from input signals to output responses.

3 June 2018

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Accelerating the reconstruction of genome-scale metabolic networks

3 June 2018

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Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

3 June 2018

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A systems approach to mapping DNA damage response pathways

3 June 2018

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Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

3 June 2018

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GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

3 June 2018

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The role of RNAs in the regulation of virulence-gene expression.

3 June 2018

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Towards multidimensional genome annotation

3 June 2018

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How to find small non-coding RNAs in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

An algorithmic framework for genome-wide modeling and analysis of translation networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Genome-scale thermodynamic analysis of Escherichia coli metabolism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

The MicrobesOnline Web site for comparative genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

From genomes to in silico cells via metabolic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Identification of the Escherichia coli K-12 ybhE gene as pgl, encoding 6-phosphogluconolactonase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

OptStrain: a computational framework for redesign of microbial production systems.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Integrating high-throughput and computational data elucidates bacterial networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Thirteen years of building constraint-based in silico models of Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

PathFinder: reconstruction and dynamic visualization of metabolic pathways

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Genomes OnLine Database (GOLD): a monitor of genome projects world-wide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Biochemical production capabilities of Escherichia coli.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Simple constrained-optimization view of acetate overflow in E. coli.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Fermentation equations for propionic-acid bacteria and production of assorted oxychemicals from various sugars.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Equations and calculations for fermentations of butyric acid bacteria.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

A predictive model for transcriptional control of physiology in a free living cell.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Distinct physiological states of Plasmodium falciparum in malaria-infected patients

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Optimization based automated curation of metabolic reconstructions

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Bayesian-based selection of metabolic objective functions

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Stochastic kinetics description of a simple transcription model.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Metabolomics approach for enzyme discovery.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Simulating cellular dynamics through a coupled transcription, translation, metabolic model

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

A mathematical model for prokaryotic protein synthesis.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

The Comprehensive Microbial Resource.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

The EMBL Nucleotide Sequence Database

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3119670

Systems-level analysis of genome-scalein silico metabolic models using MetaFluxNet

26 November 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNRMICRO1949

Two-dimensional annotation of genomes

31 March 2020

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNRMICRO1949

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=19116616

31 March 2020

Identifiers

2 references

30 April 2017

Dimensions Publication ID

1030033285

0 references

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=19116616

2 references

30 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=19116616

PubMed publication ID

2 references

30 April 2017