Choudhury S, Narayanan B, Moret M, Hatzimanikatis V, Miskovic L
Nat Catal. 2024; 7(10):1086-1098.
PMID: 39463726
PMC: 11499278.
DOI: 10.1038/s41929-024-01220-6.
Zhao F, Mattana A, Alam R, Montgomery S, Pandya A, Manetti F
Nat Commun. 2024; 15(1):8332.
PMID: 39333478
PMC: 11436715.
DOI: 10.1038/s41467-024-52608-8.
Ortega-Arzola E, Higgins P, Cockell C
Sci Rep. 2024; 14(1):5267.
PMID: 38438463
PMC: 11306549.
DOI: 10.1038/s41598-024-54303-6.
Ebenhoh O, Ebeling J, Meyer R, Pohlkotte F, Nies T
Life (Basel). 2024; 14(2).
PMID: 38398756
PMC: 10890395.
DOI: 10.3390/life14020247.
Narayanan B, Weilandt D, Masid M, Miskovic L, Hatzimanikatis V
Nat Commun. 2024; 15(1):723.
PMID: 38267425
PMC: 10808392.
DOI: 10.1038/s41467-024-44831-0.
Metabolic control analysis enabled the improvement of the L-cysteine production process with Escherichia coli.
Caballero Cerbon D, Widmann J, Weuster-Botz D
Appl Microbiol Biotechnol. 2024; 108(1):108.
PMID: 38212968
PMC: 10784400.
DOI: 10.1007/s00253-023-12928-z.
Curating COBRA Models of Microbial Metabolism.
Navid A
Methods Mol Biol. 2021; 2349:321-338.
PMID: 34719001
DOI: 10.1007/978-1-0716-1585-0_14.
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.
Wang L, Upadhyay V, Maranas C
PLoS Comput Biol. 2021; 17(9):e1009448.
PMID: 34570771
PMC: 8496854.
DOI: 10.1371/journal.pcbi.1009448.
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics.
Oftadeh O, Salvy P, Masid M, Curvat M, Miskovic L, Hatzimanikatis V
Nat Commun. 2021; 12(1):4790.
PMID: 34373465
PMC: 8352978.
DOI: 10.1038/s41467-021-25158-6.
Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis.
Seep L, Razaghi-Moghadam Z, Nikoloski Z
Sci Rep. 2021; 11(1):8544.
PMID: 33879809
PMC: 8058346.
DOI: 10.1038/s41598-021-87643-8.
Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions.
Joshi R, McNaughton A, Thomas D, Henry C, Canon S, McCue L
ACS Omega. 2021; 6(14):9948-9959.
PMID: 33869975
PMC: 8047721.
DOI: 10.1021/acsomega.1c00997.
Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant.
Mori Y, Noda S, Shirai T, Kondo A
Nat Commun. 2021; 12(1):2195.
PMID: 33850144
PMC: 8044207.
DOI: 10.1038/s41467-021-22504-6.
Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint.
Wunsch D, Trautwein K, Scheve S, Hinrichs C, Feenders C, Blasius B
Appl Environ Microbiol. 2019; 85(24).
PMID: 31604772
PMC: 6881813.
DOI: 10.1128/AEM.02095-19.
A Mixed Quantum Chemistry/Machine Learning Approach for the Fast and Accurate Prediction of Biochemical Redox Potentials and Its Large-Scale Application to 315 000 Redox Reactions.
Jinich A, Sanchez-Lengeling B, Ren H, Harman R, Aspuru-Guzik A
ACS Cent Sci. 2019; 5(7):1199-1210.
PMID: 31404220
PMC: 6661861.
DOI: 10.1021/acscentsci.9b00297.
Development of a metabolic network dynamic model to describe distinct phenotypes occurring at different CO levels.
Mora Salguero D, Fernandez-Nino M, Serrano-Bermudez L, Paez Melo D, Winck F, Caldana C
PeerJ. 2018; 6:e5528.
PMID: 30202653
PMC: 6126472.
DOI: 10.7717/peerj.5528.
Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.
Du B, Zhang Z, Grubner S, Yurkovich J, Palsson B, Zielinski D
Biophys J. 2018; 114(11):2691-2702.
PMID: 29874618
PMC: 6129446.
DOI: 10.1016/j.bpj.2018.04.030.
A review of parameters and heuristics for guiding metabolic pathfinding.
Kim S, Pena M, Moll M, Bennett G, Kavraki L
J Cheminform. 2017; 9(1):51.
PMID: 29086092
PMC: 5602787.
DOI: 10.1186/s13321-017-0239-6.
Thermodynamic Constraints Improve Metabolic Networks.
Krumholz E, Libourel I
Biophys J. 2017; 113(3):679-689.
PMID: 28793222
PMC: 5549646.
DOI: 10.1016/j.bpj.2017.06.018.
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models.
Ataman M, Hernandez Gardiol D, Fengos G, Hatzimanikatis V
PLoS Comput Biol. 2017; 13(7):e1005444.
PMID: 28727725
PMC: 5519011.
DOI: 10.1371/journal.pcbi.1005444.
Quantification of Microbial Phenotypes.
Martinez V, Kromer J
Metabolites. 2016; 6(4).
PMID: 27941694
PMC: 5192451.
DOI: 10.3390/metabo6040045.