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1.
Cardinality optimization in constraint-based modelling: application to human metabolism.
Bioinformatics
; 39(9)2023 09 02.
Article
in English
| MEDLINE | ID: mdl-37697651
2.
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.
Nucleic Acids Res
; 47(D1): D614-D624, 2019 01 08.
Article
in English
| MEDLINE | ID: mdl-30371894
3.
Structural conserved moiety splitting of a stoichiometric matrix.
J Theor Biol
; 499: 110276, 2020 08 21.
Article
in English
| MEDLINE | ID: mdl-32333975
4.
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.
Bioinformatics
; 33(11): 1741-1743, 2017 Jun 01.
Article
in English
| MEDLINE | ID: mdl-28158334
5.
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks.
PLoS Comput Biol
; 12(11): e1004999, 2016 Nov.
Article
in English
| MEDLINE | ID: mdl-27870845
6.
Consistent estimation of Gibbs energy using component contributions.
PLoS Comput Biol
; 9(7): e1003098, 2013.
Article
in English
| MEDLINE | ID: mdl-23874165
7.
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Nat Protoc
; 14(3): 639-702, 2019 03.
Article
in English
| MEDLINE | ID: mdl-30787451
8.
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.
J Cheminform
; 9(1): 39, 2017 Jun 14.
Article
in English
| MEDLINE | ID: mdl-29086112
9.
Modeling the effects of commonly used drugs on human metabolism.
FEBS J
; 282(2): 297-317, 2015 Jan.
Article
in English
| MEDLINE | ID: mdl-25345908
10.
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2.
J Cheminform
; 6(1): 2, 2014 Jan 27.
Article
in English
| MEDLINE | ID: mdl-24468196
11.
Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load.
PLoS One
; 8(9): e75370, 2013.
Article
in English
| MEDLINE | ID: mdl-24086517
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