Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. (Q91763183)

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24 April 2020

title

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. (English)

1 reference

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3

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Sebastián Mendoza

4

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Almut Heinken

6

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Siu Hung Joshua Chan

15

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Luis Vitores Valcarcel

24

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Iñigo Apaolaza

25

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James T Yurkovich

35

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Miguel A P Oliveira

36

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Inna Kuperstein

39

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Francisco J Aragón Artacho

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43

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Egils Stalidzans

45

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Nathan E. Lewis

51

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Ines Thiele

54

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Ronan Mt Fleming

55

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53

Bernhard Ø Palsson

1 reference

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8

Jacek Wachowiak

1 reference

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40

Andrei Zinovyev

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9

Sarah M Keating

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author name string

Laurent Heirendt

1

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Sylvain Arreckx

2

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Anne Richelle

5

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Hulda S Haraldsdóttir

7

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Vanja Vlasov

10

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Stefania Magnusdóttir

11

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Chiam Yu Ng

12

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German Preciat

13

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Alise Žagare

14

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Maike K Aurich

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Catherine M Clancy

17

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Jennifer Modamio

18

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John T Sauls

19

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Alberto Noronha

20

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Aarash Bordbar

21

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Benjamin Cousins

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Diana C El Assal

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Susan Ghaderi

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Masoud Ahookhosh

27

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Marouen Ben Guebila

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Ding Ma

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Yuekai Sun

33

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Lin Wang

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Phan T Vuong

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Lemmer P El Assal

38

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H Scott Hinton

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William A Bryant

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Francisco J Planes

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Santosh Vempala

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Michael Hucka

48

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Michael A Saunders

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Costas D Maranas

50

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Thomas Sauter

52

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publication date

1 March 2019

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24 April 2020

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24 April 2020

volume

14

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24 April 2020

issue

3

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24 April 2020

page(s)

639-702

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describes a project that uses

24 April 2020

Jupyter notebook file

1 reference

1 reference

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635304/

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23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

sybil – Efficient constraint-based modelling in R

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Ten simple rules for reproducible computational research

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

To supplement or not to supplement: a metabolic network framework for human nutritional supplements

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Robust flux balance analysis of multiscale biochemical reaction networks.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Consistent estimation of Gibbs energy using component contributions

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Integrating pathways of Parkinson's disease in a molecular interaction map.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Simple topological properties predict functional misannotations in a metabolic network

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

A community-driven global reconstruction of human metabolism.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Software applications for flux balance analysis

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Integration of expression data in genome-scale metabolic network reconstructions

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

A compendium of inborn errors of metabolism mapped onto the human metabolic network

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

The case for open computer programs

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

FAME, the Flux Analysis and Modeling Environment

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Construction and completion of flux balance models from pathway databases

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Minimal cut sets in a metabolic network are elementary modes in a dual network

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Social engineering for virtual 'big science' in systems biology

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

An application programming interface for CellNetAnalyzer

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Elimination of thermodynamically infeasible loops in steady-state metabolic models

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

FASIMU: flexible software for flux-balance computation series in large metabolic networks

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

iMAT: an integrative metabolic analysis tool

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Drug off-target effects predicted using structural analysis in the context of a metabolic network model

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Computationally efficient flux variability analysis

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Systematizing the generation of missing metabolic knowledge

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

The biomass objective function

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

OptFlux: an open-source software platform for in silico metabolic engineering

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Network thermodynamics in the post-genomic era.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

What is flux balance analysis?

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Large-scale identification of genetic design strategies using local search

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

FBA-SimVis: interactive visualization of constraint-based metabolic models

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Hypergraphs and cellular networks

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Generalized reaction patterns for prediction of unknown enzymatic reactions

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Predicting metabolic biomarkers of human inborn errors of metabolism

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

On the use of protein turnover and half-lives

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Detection of stoichiometric inconsistencies in biomolecular models.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Context-specific metabolic networks are consistent with experiments

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

LibSBML: an API library for SBML.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Optimization based automated curation of metabolic reconstructions

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Structural and functional analysis of cellular networks with CellNetAnalyzer

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

HMDB: the Human Metabolome Database

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Systems biology, metabolic modelling and metabolomics in drug discovery and development

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

LMSD: LIPID MAPS structure database

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Systems approach to refining genome annotation

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

ScrumPy: metabolic modelling with Python

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Systems biology of the human red blood cell

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Evolutionary programming as a platform for in silico metabolic engineering

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Modelling cellular systems with PySCeS.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Cytoscape: a software environment for integrated models of biomolecular interaction networks

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

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

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

The system architecture of the BioPath system

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Energy balance for analysis of complex metabolic networks

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

KEGG: kyoto encyclopedia of genes and genomes

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

The game of the pentose phosphate cycle

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6635304

ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE

23 February 2021

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41596-018-0098-2

inferred from DOI database lookup

7 January 2021

based on heuristic

Accelerating the DC algorithm for smooth functions

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41596-018-0098-2

inferred from DOI database lookup

7 January 2021

based on heuristic

ChemSpider - building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1186/1758-2946-2-S1-O16

10.1038/S41596-018-0098-2

2 January 2022

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30787451%20AND%20SRC:MED&resulttype=core&format=json

24 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30787451%20AND%20SRC:MED&resulttype=core&format=json

24 April 2020

1 reference