Expanding a dynamic flux balance model of yeast fermentation to genome-scale (Q33905999)

29 July 2017

title

Expanding a dynamic flux balance model of yeast fermentation to genome-scale (English)

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ORCID Public Data File 2021

29 July 2017

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Eduardo Agosin

series ordinal

4

object named as

Eduardo Agosin

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29 July 2017

Felipe A Vargas

1

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29 July 2017

Francisco Pizarro

series ordinal

2

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29 July 2017

J Ricardo Pérez-Correa

series ordinal

3

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29 July 2017

publication date

19 May 2011

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29 July 2017

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29 July 2017

volume

5

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29 July 2017

page(s)

75

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Further developments towards a genome-scale metabolic model of yeast

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Elimination of glycerol production in anaerobic cultures of a Saccharomyces cerevisiae strain engineered to use acetic acid as an electron acceptor.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Industrial systems biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Engineering of 2,3-butanediol dehydrogenase to reduce acetoin formation by glycerol-overproducing, low-alcohol Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: a systems biological analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Progress in metabolic engineering of Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Dynamic analysis of integrated signaling, metabolic, and regulatory networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

New insights into the Saccharomyces cerevisiae fermentation switch: dynamic transcriptional response to anaerobicity and glucose-excess.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Systems metabolic engineering of Escherichia coli for L-threonine production

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

A systems biology perspective of wine fermentations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Towards industrial pentose-fermenting yeast strains

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Effect of FPS1 deletion on the fermentation properties of Saccharomyces cerevisiae.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Effects of GPD1 overexpression in Saccharomyces cerevisiae commercial wine yeast strains lacking ALD6 genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Evolutionary programming as a platform for in silico metabolic engineering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Metabolic functions of duplicate genes in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Functional analysis of the ALD gene family of Saccharomyces cerevisiae during anaerobic growth on glucose: the NADP+-dependent Ald6p and Ald5p isoforms play a major role in acetate formation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Biomass content governs fermentation rate in nitrogen-deficient wine musts.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Advances in flux balance analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Anaerobic nutrition of Saccharomyces cerevisiae. I. Ergosterol requirement for growth in a defined medium

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Genome-scale microbial in silico models: the constraints-based approach.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Analysis of optimality in natural and perturbed metabolic networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Dynamic flux balance analysis of diauxic growth in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

The genomics of yeast responses to environmental stress and starvation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Decreasing acetic acid accumulation by a glycerol overproducing strain of Saccharomyces cerevisiae by deleting the ALD6 aldehyde dehydrogenase gene

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Stoichiometry and compartmentation of NADH metabolism in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae: role of the cytosolic Mg(2+) and mitochondrial K(+) acetaldehyde dehydrogenases Ald6p and Ald4p in acetate formation during alcoholic fermentation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Glycerol overproduction by engineered saccharomyces cerevisiae wine yeast strains leads to substantial changes in By-product formation and to a stimulation of fermentation rate in stationary phase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Succinic acid production by yeasts grown under different hypoxic conditions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Overexpressing GLT1 in gpd1Delta mutant to improve the production of ethanol of Saccharomyces cerevisiae.

5 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Improved production of ethanol by deleting FPS1 and over-expressing GLT1 in Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Coupling kinetic expressions and metabolic networks for predicting wine fermentations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Dynamic metabolic engineering for increasing bioprocess productivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Modeling of yeast metabolism and process dynamics in batch fermentation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Stoichiometry and compartmentation of NADH metabolism inSaccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Investigation by 13C-NMR and tricarboxylic acid (TCA) deletion mutant analysis of pathways for succinate formation in Saccharomyces cerevisiae during anaerobic fermentation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Oxygen addition and sterol synthesis in Saccharomyces cerevisiae during enological fermentation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Analysis of Saccharomyces cerevisiae hexose carrier expression during wine fermentation: both low- and high-affinity Hxt transporters are expressed

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

The hexose transporters of Saccharomyces cerevisiae play different roles during enological fermentation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Comparing the transcriptomes of wine yeast strains: toward understanding the interaction between environment and transcriptome during fermentation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Interruption of glycerol pathway in industrial alcoholic yeasts to improve the ethanol production

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Constraints-based models: regulation of gene expression reduces the steady-state solution space

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-75

Dynamic metabolic flux analysis demonstrated on cultures where the limiting substrate is changed from carbon to nitrogen and vice versa

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Genome‐scale metabolic modeling of a clostridial co‐culture for consolidated bioprocessing

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3118138

Improved ethanol production by glycerol-3-phosphate dehydrogenase mutants of Saccharomyces cerevisiae

29 October 2018

1 reference

12 December 2020

Anaerobic nutrition of Saccharomyces cerevisiae. II. Unsaturated fatty acid requirement for growth in a defined medium

1 reference

12 December 2020

A theoretical evaluation of growth yields of yeasts

1 reference

12 December 2020

Induction of major heat-shock proteins of Saccharomyces cerevisiae, including plasma membrane Hsp30, by ethanol levels above a critical threshold

1 reference

12 December 2020

Physiology of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures

1 reference

12 December 2020

Kinetic characterization of individual hexose transporters of Saccharomyces cerevisiae and their relation to the triggering mechanisms of glucose repression

1 reference

12 December 2020

Identifiers

DOI

10.1186/1752-0509-5-75

1 reference

journals/bmcsb/VargasPPA11

29 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

29 July 2017

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