(Q34987962)

5 August 2017

title

Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum (English)

1 reference

5 August 2017

main subject

Mycoplasma gallisepticum

object named as

Mycoplasma gallisepticum

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Ranjan Srivastava

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

author name string

Joseph Zinski

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Steven M Szczepanek

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Erik L Johnson

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Edan R Tulman

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Wei-Mei Ching

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Steven J Geary

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

publication date

5 September 2013

1 reference

PLOS Computational Biology

5 August 2017

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

issue

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

page(s)

e1003208

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons CC0 License

13 June 2020

copyright license

start time

5 September 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

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8 July 2018

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8 July 2018

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Metabolic flux analysis and pharmaceutical production

8 July 2018

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System-level analysis of Salmonella metabolism during infection

8 July 2018

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Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain

8 July 2018

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8 July 2018

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A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189

8 July 2018

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Reconstruction of biochemical networks in microorganisms

8 July 2018

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Genome-scale models of bacterial metabolism: reconstruction and applications

8 July 2018

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Metabolic network model of a human oral pathogen.

8 July 2018

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The Mycobacterium tuberculosis MEP (2C-methyl-d-erythritol 4-phosphate) pathway as a new drug target

8 July 2018

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Human metabolic network reconstruction and its impact on drug discovery and development

8 July 2018

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8 July 2018

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Metabolic reconstruction and analysis for parasite genomes

8 July 2018

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A processive lipid glycosyltransferase in the small human pathogen Mycoplasma pneumoniae: involvement in host immune response

8 July 2018

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8 July 2018

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Targeting the methyl erythritol phosphate (MEP) pathway for novel antimalarial, antibacterial and herbicidal drug discovery: inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) enzyme.

8 July 2018

1 reference

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8 July 2018

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8 July 2018

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Localization of Enzymes in Mycoplasma

8 July 2018

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Identification of a virulence-associated determinant, dihydrolipoamide dehydrogenase (lpd), in Mycoplasma gallisepticum through in vivo screening of transposon mutants

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

MetaCyc: a multiorganism database of metabolic pathways and enzymes

8 July 2018

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From genomics to chemical genomics: new developments in KEGG

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Protein database searches using compositionally adjusted substitution matrices

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Reconstructing the metabolic network of a bacterium from its genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Mycoplasma penetrans is capable of activating V gamma 9/V delta 2 T cells while other human pathogenic mycoplasmas fail to do so

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Biosynthesis of isoprenoids via the non-mevalonate pathway

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

The Methylerythritol Phosphate Pathway and its Significance as a Novel Drug Target

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

COMPARATIVE BIOSYNTHESIS OF MEVALONIC ACID BY MYCOPLASMA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

DEFINED MEDIUM FOR MYCOPLASMA LAIDLAWII

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

LIPID COMPOSITION AND SYNTHESIS IN THE PLEUROPNEUMONIA-LIKE ORGANISM MYCOPLASMA GALLISEPTICUM.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Culture and metabolism of Mycoplasma gallisepticum.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain Rlow

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Fosmidomycin for the treatment of malaria

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Microbial isoprenoid biosynthesis and human gammadelta T cell activation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Missing genes in metabolic pathways: a comparative genomics approach

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms

8 July 2018

1 reference

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Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. A metabolic milestone achieved through genomics.

8 July 2018

1 reference

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The Pathway Tools software

8 July 2018

1 reference

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Genome-scale metabolic model of Helicobacter pylori 26695.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Metabolic modelling of microbes: the flux-balance approach

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Metabolic modeling of microbial strains in silico.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Deoxyxylulose phosphate pathway to terpenoids

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Evidence of a role for LytB in the nonmevalonate pathway of isoprenoid biosynthesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Avian mycoplasmosis (Mycoplasma gallisepticum).

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

The underlying pathway structure of biochemical reaction networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

The comparative metabolism of the mollicutes (Mycoplasmas): the utility for taxonomic classification and the relationship of putative gene annotation and phylogeny to enzymatic function in the smallest free-living cells.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

The Minimal Gene Complement of Mycoplasma genitalium

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Control of membrane lipids in Mycoplasma gallisepticum: effect on lipid order

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Lipid tracers of mycoplasma phylogeny

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Electrophysiology of mycoplasma membranes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Immunochemical Analysis of Serologically Active Lipids of Mycoplasma pneumoniae

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Studies with lectins on the surface carbohydrate structures of mycoplasma membranes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Sodium and proton transport in Mycoplasma gallisepticum

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Cell volume regulation in Mycoplasma gallisepticum

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Interaction of albumin and phospholipid:cholesterol liposomes in growth of Mycoplasma spp

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Characterization and solubilization of the membrane-bound ATPase of Mycoplasma gallisepticum

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Synthesis of deoxyribomononucleotides in Mollicutes: dependence on deoxyribose-1-phosphate and PPi.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Role of Na+ cycle in cell volume regulation of Mycoplasma gallisepticum

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Volume regulation in Mycoplasma gallisepticum: evidence that Na+ is extruded via a primary Na+ pump

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Antiphospholipid antibodies and Mycoplasma pneumoniae infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Serine hydroxymethyltransferase catalyzes the hydrolysis of 5,10-methenyltetrahydrofolate to 5-formyltetrahydrofolate

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Differences in incorporation of nucleic acid bases and nucleosides by various Mycoplasma and Acholeplasma species

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Lipid distribution in Acholeplasma laidlawii membrane. A study using the lactoperoxidase-mediated iodination

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Membrane lipids of Mycoplasma gallisepticum: a disaturated phosphatidylcholine and a phosphatidylglycerol with an unusual positional distribution of fatty acids

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

Antibiotic overproduction in Streptomyces coelicolor A3 2 mediated by phosphofructokinase deletion

8 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Design and application of genome-scale reconstructed metabolic models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Optimization based automated curation of metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Filling gaps in a metabolic network using expression information

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Impact of genome reduction on bacterial metabolism and its regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Accumulation of a potent gammadelta T-cell stimulator after deletion of the lytB gene in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

The herbicide ketoclomazone inhibits 1-deoxy-D-xylulose 5-phosphate synthase in the 2-C-methyl-D-erythritol 4-phosphate pathway and shows antibacterial activity against Haemophilus influenzae

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Phylogenetic relationships among mycoplasmas based on the whole genomic information.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Pyrimidine Deoxyribonucleotide Metabolism in Members of the Class Mollicutes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Distinctions in Mollicutes Purine Metabolism: Pyrophosphate-Dependent Nucleoside Kinase and Dependence on Guanylate Salvage

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing "household" nucleoside diphosphate kinase gene and activity by glycolytic kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003208

Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764002

CHEMICAL COMPOSITION OF MYCOPLASMA CELLS AND MEMBRANES

26 October 2018

1 reference

12 December 2020

Malate/lactate dehydrogenase in mollicutes: evidence for a multienzyme protein

1 reference

12 December 2020

The cell membrane of mycoplasma

1 reference

12 December 2020

STUDIES ON THE NUTRITION AND GROWTH REQUIREMENTS OF MYCOPLASMA GALLISEPTICUM

1 reference

12 December 2020

Presence of anaplerotic reactions and transamination, and the absence of the tricarboxylic acid cycle in mollicutes

1 reference

12 December 2020

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE

1 reference

12 December 2020

Diversity of energy-yielding substrates and metabolism in avian mycoplasmas

1 reference

12 December 2020

Tissue cultures and mycoplasmas

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1003208

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/BautistaZSJTCGS13

13 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24039564%20AND%20SRC:MED&resulttype=core&format=json