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- Ines Thiele, Neil Swainston, +43 authors Bernhard Ø Palsson
- Nature biotechnology
- 2013

Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the… (More)

- Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming
- PLoS Computational Biology
- 2013

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the… (More)

- Naama Tepper, Elad Noor, +5 authors Tomer Shlomi
- PloS one
- 2013

Steady-state metabolite concentrations in a microorganism typically span several orders of magnitude. The underlying principles governing these concentrations remain poorly understood. Here, we hypothesize that observed variation can be explained in terms of a compromise between factors that favor minimizing metabolite pool sizes (e.g. limited solvent… (More)

- Swagatika Sahoo, Hulda S Haraldsdóttir, Ronan M T Fleming, Ines Thiele
- The FEBS journal
- 2015

Metabolism contributes significantly to the pharmacokinetics and pharmacodynamics of a drug. In addition, diet and genetics have a profound effect on cellular metabolism with respect to both health and disease. In the present study, we assembled a comprehensive, literature-based drug metabolic reconstruction of the 18 most highly prescribed drug groups,… (More)

- Hulda S. Haraldsdóttir, Ines Thiele, Ronan M. T. Fleming
- J. Cheminformatics
- 2014

BACKGROUND
An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated with various database or structure based identifiers. Metabolite annotations in metabolic reconstructions may be incorrect or incomplete and thus need to be updated prior to their use. Genome-scale metabolic… (More)

- Hulda S. Haraldsdóttir, Ronan M. T. Fleming
- PLoS computational biology
- 2016

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the… (More)

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- German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming
- J. Cheminformatics
- 2017

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

Summary
In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to… (More)

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