A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models (Q38715815)

24 June 2018

title

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models (English)

1 reference

24 June 2018

1 reference

PubMed publication ID

5 September 2017

Sjoerd Opdam

1 reference

24 June 2018

Anne Richelle

1 reference

24 June 2018

Benjamin Kellman

1 reference

24 June 2018

Shanzhong Li

1 reference

24 June 2018

Daniel C Zielinski

1 reference

24 June 2018

publication date

15 February 2017

1 reference

24 June 2018

published in

Cell Systems

1 reference

24 June 2018

volume

1 reference

24 June 2018

issue

1 reference

24 June 2018

page(s)

318-329.e6

1 reference

24 June 2018

Recon 2.2: from reconstruction to model of human metabolism

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Identification and characterization of essential genes in the human genome.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Modeling cancer metabolism on a genome scale

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Proteomics. Tissue-based map of the human proteome

30 June 2018

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

30 June 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

3 December 2018

12 December 2020

Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Generalized framework for context-specific metabolic model extraction methods

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Trimmomatic: a flexible trimmer for Illumina sequence data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Fast reconstruction of compact context-specific metabolic network models

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Constraint-based models predict metabolic and associated cellular functions.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Genome-scale CRISPR-Cas9 knockout screening in human cells

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Genetic screens in human cells using the CRISPR-Cas9 system

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

The metabolic demands of cancer cells are coupled to their size and protein synthesis rates

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

A reversible gene trap collection empowers haploid genetics in human cells

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

DNMT1-interacting RNAs block gene-specific DNA methylation

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Wnt signaling potentiates nevogenesis

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

The evolution of genome-scale models of cancer metabolism

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Intracellular water exchange for measuring the dry mass, water mass and changes in chemical composition of living cells

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Human housekeeping genes, revisited

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

A community-driven global reconstruction of human metabolism.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Analysis of omics data with genome-scale models of metabolism

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

A proof for loop-law constraints in stoichiometric metabolic networks.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

STAR: ultrafast universal RNA-seq aligner

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Predicting selective drug targets in cancer through metabolic networks.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Blueprint for antimicrobial hit discovery targeting metabolic networks

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

bioDBnet: the biological database network

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Context-specific metabolic networks are consistent with experiments

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Global reconstruction of the human metabolic network based on genomic and bibliomic data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Integrating high-throughput and computational data elucidates bacterial networks

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Karyotypic complexity of the NCI-60 drug-screening panel.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

The phosphatidylinositol 3-Kinase AKT pathway in human cancer

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Cancer: Why tumours eat tryptophan

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Metabolic flux analysis of hybridoma cells in different culture media using mass balances

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

Analysis of CHO cells metabolic redistribution in a glutamate-based defined medium in continuous culture.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

In human hepatocellular carcinoma cells the total membrane surface area of each major organelle is a particular allometric function of the cytoplasmic volume. A morphometric study.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5526624

The energetics of mammalian cell growth

31 August 2018

1 reference

12 December 2020

iMAT: an integrative metabolic analysis tool

1 reference

12 December 2020

Increased cystine uptake capability associated with malignant progression of Nb2 lymphoma cells

1 reference

12 December 2020

Network-based prediction of human tissue-specific metabolism

1 reference

12 December 2020

Metabolism and enzyme content of diploid and tetraploid lympnomas and carcinomas

1 reference

12 December 2020

Reducing Recon 2 for steady-state flux analysis of HEK cell culture

1 reference

12 December 2020

10.1016/J.CELS.2017.01.010

Identifiers

DOI

1 reference

24 June 2018

PMC publication ID

5526624

1 reference

24 June 2018

PubMed publication ID

28215528

1 reference

24 June 2018