Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data (Q33781701)

29 July 2017

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data (English)

1 reference

29 July 2017

0 references

Ali R Zomorrodi

1

1 reference

PubMed ID

21190580

29 July 2017

Costas D Maranas

series ordinal

2

1 reference

29 July 2017

29 December 2010

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29 July 2017

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29 July 2017

4

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29 July 2017

178

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Creative Commons Attribution 2.0 Generic

29 July 2017

start time

1 December 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

exact match

https://scigraph.springernature.com/pub.10.1186/1752-0509-4-178

0 references

cites work

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Systematizing the generation of missing metabolic knowledge

28 July 2018

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OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

28 July 2018

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A protocol for generating a high-quality genome-scale metabolic reconstruction

28 July 2018

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Genome-scale gene/reaction essentiality and synthetic lethality analysis

28 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

28 July 2018

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iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

28 July 2018

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Connecting extracellular metabolomic measurements to intracellular flux states in yeast

28 July 2018

1 reference

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GrowMatch: an automated method for reconciling in silico/in vivo growth predictions

28 July 2018

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A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189

28 July 2018

1 reference

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High-throughput, quantitative analyses of genetic interactions in E. coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Spontaneous reaction silencing in metabolic optimization

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Can single knockouts accurately single out gene functions?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Predicting synthetic rescues in metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

KEGG for linking genomes to life and the environment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Plasticity of genetic interactions in metabolic networks of yeast

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Systems approach to refining genome annotation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Experimental and computational assessment of conditionally essential genes in Escherichia coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Investigations on vitamin B(2): The sources of vitamin B(2). II. The stability of vitamin B(2). III. The chemistry of vitamin B(2).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Genome-scale thermodynamic analysis of Escherichia coli metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Metabolic functions of duplicate genes in Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Aconitase couples metabolic regulation to mitochondrial DNA maintenance

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Dihydropteroate synthase mutations in Pneumocystis jiroveci can affect sulfamethoxazole resistance in a Saccharomyces cerevisiae model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Global analysis of protein localization in budding yeast

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Biosynthesis of the purines. XVI. The synthesis of adenosine 5'-phosphate and 5-amino-4-imidazolecarboxamide ribotide by a nucleotide pyrophosphorylase.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Functional profiling of the Saccharomyces cerevisiae genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Regulation of gene expression in flux balance models of metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Concurrent knock-out of at least 20 transporter genes is required to block uptake of hexoses in Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Localization of synthesis of beta1,6-glucan in Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Genetic analysis and enzyme activity suggest the existence of more than one minimal functional unit capable of synthesizing phosphoribosyl pyrophosphate in Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Dissecting the regulatory circuitry of a eukaryotic genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

The phospholipid methyltransferases in yeast

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Hypoxanthine phosphoribosyltransferase: radiochemical assay procedures for the forward and reverse reactions.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Saccharomyces cerevisiae cho2 mutants are deficient in phospholipid methylation and cross-pathway regulation of inositol synthesis.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

The pentose phosphate pathway in the endoplasmic reticulum.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Identifying mutations in duplicated functions in Saccharomyces cerevisiae: recessive mutations in HMG-CoA reductase genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Characterization of the methyltransferases in the yeast phosphatidylethanolamine methylation pathway by selective gene disruption

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Yeast phosphatidylethanolamine methylation pathway. Cloning and characterization of two distinct methyltransferase genes.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

On the Activity and Regulation of Anaplerotic and Gluconeogenetic Enzymes during the Growth Process of Baker's Yeast. The Biphasic Growth

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Molecular characterization reveals that YMR278w encoded protein is environmental stress response homologue of Saccharomyces cerevisiae PGM2.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Optimization based automated curation of metabolic reconstructions

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

The proteome of Saccharomyces cerevisiae mitochondria

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

Systematic genetic analysis with ordered arrays of yeast deletion mutants

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

The linkage of (1-3)-beta-glucan to chitin during cell wall assembly in Saccharomyces cerevisiae.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

A Robust Toolkit for Functional Profiling of the Yeast Genome

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3023687

A new method for quantitative determination of polysaccharides in the yeast cell wall. Application to the cell wall defective mutants of Saccharomyces cerevisiae

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21190580

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structural robustness of metabolic networks with respect to multiple knockouts

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21190580

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Multiple signalling pathways trigger the exquisite sensitivity of yeast gluconeogenic mRNAs to glucose

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21190580

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1752-0509-4-178

1 reference

journals/bmcsb/ZomorrodiM10

29 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

29 July 2017

1 reference

PubMed ID

21190580