Superessential reactions in metabolic networks (Q35935855)

11 August 2017

Superessential reactions in metabolic networks (English)

1 reference

11 August 2017

Aditya Barve

1

1 reference

11 August 2017

João Frederico Matias Rodrigues

series ordinal

2

1 reference

11 August 2017

Andreas Wagner

series ordinal

3

1 reference

11 August 2017

language of work or name

English

0 references

publication date

16 April 2012

1 reference

Proceedings of the National Academy of Sciences of the United States of America

11 August 2017

1 reference

11 August 2017

109

1 reference

11 August 2017

18

1 reference

11 August 2017

E1121-30

1 reference

Genotype networks, innovation, and robustness in sulfur metabolism

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

High-throughput generation, optimization and analysis of genome-scale metabolic models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Genotype to phenotype: a complex problem

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Abundant indispensable redundancies in cellular metabolic networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Genotype networks in metabolic reaction spaces

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Enzyme promiscuity: a mechanistic and evolutionary perspective

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Blueprint for antimicrobial hit discovery targeting metabolic networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Evolutionary plasticity and innovations in complex metabolic reaction networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Recent advances and method development for drug target identification

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Novel genomic methods for drug discovery and mechanism-based toxicological assessment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Thematic review series: Glycerolipids. Acyltransferases in bacterial glycerophospholipid synthesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Predicting synthetic rescues in metabolic networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Chorismate synthase: an attractive target for drug development against orphan diseases.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Main approaches to target discovery and validation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Drugs for bad bugs: confronting the challenges of antibacterial discovery

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Mechanisms of action of isoniazid

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Experimental and computational assessment of conditionally essential genes in Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Chance and necessity in the evolution of minimal metabolic networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Robust Salmonella metabolism limits possibilities for new antimicrobials.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Low degree metabolites explain essential reactions and enhance modularity in biological networks.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

The activity reaction core and plasticity of metabolic networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Characterization of a new pantothenate kinase isoform from Helicobacter pylori

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Large-scale identification of essential Salmonella genes by trapping lethal insertions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Flux coupling analysis of genome-scale metabolic network reconstructions.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Comprehensive transposon mutant library of Pseudomonas aeruginosa

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Genetic requirements for mycobacterial survival during infection

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Fosmidomycin for the treatment of malaria

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Genes required for mycobacterial growth defined by high density mutagenesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Analysis of optimality in natural and perturbed metabolic networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Molecular evolution of the lysine biosynthetic pathways.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

LIGAND: database of chemical compounds and reactions in biological pathways

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Nonorthologous gene displacement of phosphomevalonate kinase.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Identification, evolution, and essentiality of the mevalonate pathway for isopentenyl diphosphate biosynthesis in gram-positive cocci

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

LIGAND: chemical database of enzyme reactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

KEGG: kyoto encyclopedia of genes and genomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Analogous enzymes: independent inventions in enzyme evolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

The complete genome sequence of Escherichia coli K-12

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Characterization of the essential gene glmM encoding phosphoglucosamine mutase in Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

In silico characterization of Shikimate Kinase of Shigella flexneri: a potential drug target

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Influence of metabolic network structure and function on enzyme evolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3345022

Robustness analysis of the Escherichia coli metabolic network

11 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Synthesis and antibacterial activity of some 5-guanylhydrazone/thiocyanato-6-arylimidazo[2,1-b]-1,3, 4-thiadiazole-2-sulfonamide derivatives.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Molecular characterization of Escherichia coli NAD kinase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Molecular mechanisms involved in robustness of yeast central metabolism against null mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

A pantothenate kinase from Staphylococcus aureus refractory to feedback regulation by coenzyme A.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Impact of genome reduction on bacterial metabolism and its regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Catalytic mechanism of l,l-diaminopimelic acid with diaminopimelate epimerase by molecular docking simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Non-orthologous gene displacement

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1113065109

Non-orthologous gene displacement

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22509034

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1113065109

1 reference

11 August 2017

0 references

1 reference

11 August 2017

1 reference