Structural conserved moiety splitting of a stoichiometric matrix
- Susan Ghaderi, Hulda S Haraldsdóttir, Masoud Ahookhosh, Sylvain Arreckx, Ronan M T Fleming
- J Theor Biol, 10.1016/j.jtbi.2020.110276
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
- Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, …, Bernhard Ø Palsson, Ines Thiele, Ronan M T Fleming
- Nat Protoc, 10.1038/s41596-018-0098-2
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
- Alberto Noronha, Jennifer Modamio, Yohan Jarosz, …, Reinhard Schneider, Ronan M T Fleming, Ines Thiele
- Nucleic Acids Res, 10.1093/nar/gky992
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
- German A Preciat Gonzalez, Lemmer R P El Assal, Alberto Noronha, Ines Thiele, Hulda S Haraldsdóttir, Ronan M T Fleming
- None, 10.1186/s13321-017-0223-1
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
- Hulda S Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M T Fleming, Santosh Vempala
- Bioinformatics, 10.1093/bioinformatics/btx052
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks
- Hulda S Haraldsdóttir, Ronan M T Fleming
- PLoS Comput Biol, 10.1371/journal.pcbi.1004999
Modeling the effects of commonly used drugs on human metabolism
- Swagatika Sahoo, Hulda S Haraldsdóttir, Ronan M T Fleming, Ines Thiele
- FEBS J, 10.1111/febs.13128
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
- Hulda S Haraldsdóttir, Ines Thiele, Ronan Mt Fleming
- None, 10.1186/1758-2946-6-2
Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load
- Naama Tepper, Elad Noor, Daniel Amador-Noguez, …, Josh Rabinowitz, Wolfram Liebermeister, Tomer Shlomi
- PLoS One, 10.1371/journal.pone.0075370
Consistent estimation of Gibbs energy using component contributions
- Elad Noor, Hulda S Haraldsdóttir, Ron Milo, Ronan M T Fleming
- PLoS Comput Biol, 10.1371/journal.pcbi.1003098
A community-driven global reconstruction of human metabolism
- Ines Thiele, Neil Swainston, Ronan M T Fleming, …, Douglas B Kell, Pedro Mendes, Bernhard Ø Palsson
- Nat Biotechnol, 10.1038/nbt.2488
Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction
- H S Haraldsdóttir, I Thiele, R M T Fleming
- Biophys J, 10.1016/j.bpj.2012.02.032