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

por Haraldsdóttir, Hulda S., Fleming, Ronan M. T.
Publicado 2016

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

por Thiele, Ines, Fleming, Ronan M.T.
Publicado 2022

fastGapFill: efficient gap filling in metabolic networks

por Thiele, Ines, Vlassis, Nikos, Fleming, Ronan M. T.
Publicado 2014

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

por Heirendt, Laurent, Thiele, Ines, Fleming, Ronan M T
Publicado 2017

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions

por Thiele, Ines, Preciat, German, Fleming, Ronan M T
Publicado 2022

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

por Aurich, Maike K., Fleming, Ronan M. T., Thiele, Ines
Publicado 2016

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

por Aurich, Maike K., Fleming, Ronan M. T., Thiele, Ines
Publicado 2017

A Systems Biology Approach to Drug Targets in Pseudomonas aeruginosa Biofilm

por Sigurdsson, Gunnar, Fleming, Ronan M. T., Heinken, Almut, Thiele, Ines
Publicado 2012

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

por Heinken, Almut, Sahoo, Swagatika, Fleming, Ronan M. T., Thiele, Ines
Publicado 2013

Consistent Estimation of Gibbs Energy Using Component Contributions

por Noor, Elad, Haraldsdóttir, Hulda S., Milo, Ron, Fleming, Ronan M. T.
Publicado 2013

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

por Heinken, Almut, Magnúsdóttir, Stefanía, Fleming, Ronan M T, Thiele, Ines
Publicado 2021

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

por Thiele, Ines, Jamshidi, Neema, Fleming, Ronan M. T., Palsson, Bernhard Ø.
Publicado 2009

Quantitative systems pharmacology and the personalized drug–microbiota–diet axis

por Thiele, Ines, Clancy, Catherine M., Heinken, Almut, Fleming, Ronan M.T.
Publicado 2017

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

por Haraldsdóttir, Hulda S, Cousins, Ben, Thiele, Ines, Fleming, Ronan M.T, Vempala, Santosh
Publicado 2017

Embryonic development of selectively vulnerable neurons in Parkinson’s disease

por Oliveira, Miguel A. P., Balling, Rudi, Smidt, Marten P., Fleming, Ronan M. T.
Publicado 2017

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

por Sompairac, Nicolas, Modamio, Jennifer, Barillot, Emmanuel, Fleming, Ronan M. T., Zinovyev, Andrei, Kuperstein, Inna
Publicado 2019

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

por Baldini, Federico, Heinken, Almut, Heirendt, Laurent, Magnusdottir, Stefania, Fleming, Ronan M T, Thiele, Ines
Publicado 2019

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

por Thiele, Ines, Fleming, Ronan M. T., Que, Richard, Bordbar, Aarash, Diep, Dinh, Palsson, Bernhard O.
Publicado 2012

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

por Heinken, Almut, Ravcheev, Dmitry A., Baldini, Federico, Heirendt, Laurent, Fleming, Ronan M. T., Thiele, Ines
Publicado 2019

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

por Fleming, Ronan M T, Haraldsdottir, Hulda S, Minh, Le Hoai, Vuong, Phan Tu, Hankemeier, Thomas, Thiele, Ines
Publicado 2023