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List of works by Ronan Mt Fleming

3D Cultures of Parkinson's Disease-Specific Dopaminergic Neurons for High Content Phenotyping and Drug Testing

scientific article published on 20 November 2018

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

scientific article

A community-driven global reconstruction of human metabolism. ⬇️

scientific article

A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease

scientific article

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

scientific article published on 14 August 2017

A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm

scientific article

A systems biology approach to studying the role of microbes in human health.

scientific article published on 25 October 2012

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

scientific article published on 5 October 2011

Automated microfluidic cell culture of stem cell derived dopaminergic neurons

scientific article published in Scientific Reports

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

scientific article

Cardinality optimization in constraint-based modelling: application to human metabolism

scientific article published in September 2023

Community-driven roadmap for integrated disease maps

scientific article published on 23 April 2018

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

scientific article published on 14 June 2017

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

scientific article

Conditions for duality between fluxes and concentrations in biochemical networks

scientific article published on 23 June 2016

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

scientific article published on 01 March 2019

Derivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells

scientific article

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.

scientific article

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Embryonic development of selectively vulnerable neurons in Parkinson's disease.

scientific article

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

scientific article

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

scientific article

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks ⬇️

scientific article

Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease

scientific article published on 01 November 2019

LC-MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide

scientific article published on 31 July 2019

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

scientific article published on 03 August 2016

Modeling the effects of commonly used drugs on human metabolism

scientific article published on 21 November 2014

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).

scientific article

Personalized whole-body models integrate metabolism, physiology, and the gut microbiome

scientific article published on 01 May 2020

Prediction of intracellular metabolic states from extracellular metabolomic data

scientific article

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

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

scientific article published in April 2012

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

scientific article

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

scientific article (publication date: 4 August 2011)

Recon3D enables a three-dimensional view of gene variation in human metabolism.

scientific article published on 19 February 2018

ReconMap: an interactive visualization of human metabolism

scientific article

Reply to "Challenges in modeling the human gut microbiome"

scientific article published on 01 August 2018

Robust flux balance analysis of multiscale biochemical reaction networks.

scientific article

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

article

Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication

scientific article published in 2022

fastGapFill: efficient gap filling in metabolic networks

scientific article

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

scientific article

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