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Items: 1 to 20 of 101

1.

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models.

Pandey V, Hadadi N, Hatzimanikatis V.

PLoS Comput Biol. 2019 May 13;15(5):e1007036. doi: 10.1371/journal.pcbi.1007036. [Epub ahead of print]

2.

Impact of iron reduction on the metabolism of Clostridium acetobutylicum.

List C, Hosseini Z, Lederballe Meibom K, Hatzimanikatis V, Bernier-Latmani R.

Environ Microbiol. 2019 Apr 25. doi: 10.1111/1462-2920.14640. [Epub ahead of print]

PMID:
31020759
3.

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data.

Pandey V, Hatzimanikatis V.

PLoS Comput Biol. 2019 Apr 19;15(4):e1006760. doi: 10.1371/journal.pcbi.1006760. eCollection 2019 Apr.

4.

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites.

Hadadi N, MohammadiPeyhani H, Miskovic L, Seijo M, Hatzimanikatis V.

Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7298-7307. doi: 10.1073/pnas.1818877116. Epub 2019 Mar 25.

5.

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis.

Salvy P, Fengos G, Ataman M, Pathier T, Soh KC, Hatzimanikatis V.

Bioinformatics. 2019 Jan 1;35(1):167-169. doi: 10.1093/bioinformatics/bty499.

6.

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations.

Hameri T, Fengos G, Ataman M, Miskovic L, Hatzimanikatis V.

Metab Eng. 2019 Mar;52:29-41. doi: 10.1016/j.ymben.2018.10.005. Epub 2018 Oct 26.

7.

Efficient cleavage of aryl ether C-O linkages by Rh-Ni and Ru-Ni nanoscale catalysts operating in water.

Bulut S, Siankevich S, van Muyden AP, Alexander DTL, Savoglidis G, Zhang J, Hatzimanikatis V, Yan N, Dyson PJ.

Chem Sci. 2018 Jun 6;9(25):5530-5535. doi: 10.1039/c8sc00742j. eCollection 2018 Jul 7.

8.

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors.

Tokic M, Hadadi N, Ataman M, Neves D, Ebert BE, Blank LM, Miskovic L, Hatzimanikatis V.

ACS Synth Biol. 2018 Aug 17;7(8):1858-1873. doi: 10.1021/acssynbio.8b00049. Epub 2018 Aug 7.

PMID:
30021444
9.

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions.

Bryan LC, Weilandt DR, Bachmann AL, Kilic S, Lechner CC, Odermatt PD, Fantner GE, Georgeon S, Hantschel O, Hatzimanikatis V, Fierz B.

Nucleic Acids Res. 2017 Oct 13;45(18):10504-10517. doi: 10.1093/nar/gkx697.

10.

Identification and dynamics of the human ZDHHC16-ZDHHC6 palmitoylation cascade.

Abrami L, Dallavilla T, Sandoz PA, Demir M, Kunz B, Savoglidis G, Hatzimanikatis V, van der Goot FG.

Elife. 2017 Aug 15;6. pii: e27826. doi: 10.7554/eLife.27826.

11.

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites.

Ataman M, Hatzimanikatis V.

PLoS Comput Biol. 2017 Jul 20;13(7):e1005513. doi: 10.1371/journal.pcbi.1005513. eCollection 2017 Jul. Erratum in: PLoS Comput Biol. 2017 Sep 19;13(9):e1005764.

12.

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models.

Ataman M, Hernandez Gardiol DF, Fengos G, Hatzimanikatis V.

PLoS Comput Biol. 2017 Jul 20;13(7):e1005444. doi: 10.1371/journal.pcbi.1005444. eCollection 2017 Jul.

13.

A design-build-test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models.

Miskovic L, Alff-Tuomala S, Soh KC, Barth D, Salusjärvi L, Pitkänen JP, Ruohonen L, Penttilä M, Hatzimanikatis V.

Biotechnol Biofuels. 2017 Jun 26;10:166. doi: 10.1186/s13068-017-0838-5. eCollection 2017.

14.

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas.

Islam MA, Hadadi N, Ataman M, Hatzimanikatis V, Stephanopoulos G.

Metab Eng. 2017 May;41:173-181. doi: 10.1016/j.ymben.2017.04.005. Epub 2017 Apr 19.

PMID:
28433737
15.

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks.

Chiappino-Pepe A, Tymoshenko S, Ataman M, Soldati-Favre D, Hatzimanikatis V.

PLoS Comput Biol. 2017 Mar 23;13(3):e1005397. doi: 10.1371/journal.pcbi.1005397. eCollection 2017 Mar.

16.

Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation.

Berset Y, Merulla D, Joublin A, Hatzimanikatis V, van der Meer JR.

ACS Synth Biol. 2017 May 19;6(5):862-874. doi: 10.1021/acssynbio.6b00364. Epub 2017 Feb 24.

PMID:
28215088
17.

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites.

Hadadi N, Hafner J, Soh KC, Hatzimanikatis V.

Biotechnol J. 2017 Jan;12(1). doi: 10.1002/biot.201600464.

PMID:
27897385
18.

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach.

Panayiotou C, Mastrogeorgopoulos S, Ataman M, Hadadi N, Hatzimanikatis V.

Phys Chem Chem Phys. 2016 Nov 30;18(47):32570-32592.

PMID:
27874110
19.

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks.

Kiparissides A, Hatzimanikatis V.

Metab Eng. 2017 Jan;39:117-127. doi: 10.1016/j.ymben.2016.11.006. Epub 2016 Nov 12.

PMID:
27845184
20.

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies.

Hadadi N, Hafner J, Shajkofci A, Zisaki A, Hatzimanikatis V.

ACS Synth Biol. 2016 Oct 21;5(10):1155-1166. Epub 2016 Jul 28.

PMID:
27404214

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