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Items: 1 to 50 of 103

1.

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism.

Weilandt DR, Hatzimanikatis V.

Biophys J. 2019 Jul 23;117(2):355-368. doi: 10.1016/j.bpj.2019.06.017. Epub 2019 Jun 25.

2.

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH).

Borer B, Ataman M, Hatzimanikatis V, Or D.

PLoS Comput Biol. 2019 Jun 19;15(6):e1007127. doi: 10.1371/journal.pcbi.1007127. eCollection 2019 Jun.

3.

Dynamic Radiolabeling of S-Palmitoylated Proteins.

Abrami L, Denhardt-Eriksson RA, Hatzimanikatis V, van der Goot FG.

Methods Mol Biol. 2019;2009:111-127. doi: 10.1007/978-1-4939-9532-5_9.

PMID:
31152399
4.

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. eCollection 2019 May.

5.

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
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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
18.

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.

19.

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
20.

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
21.

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
22.

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
23.

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
24.

Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell.

Vieira JP, Racle J, Hatzimanikatis V.

Biophys J. 2016 May 10;110(9):2120-31. doi: 10.1016/j.bpj.2016.04.004.

25.

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism.

Savoglidis G, da Silveira Dos Santos AX, Riezman I, Angelino P, Riezman H, Hatzimanikatis V.

Metab Eng. 2016 Sep;37:46-62. doi: 10.1016/j.ymben.2016.04.002. Epub 2016 Apr 23.

26.

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models.

Isakova A, Berset Y, Hatzimanikatis V, Deplancke B.

J Biol Chem. 2016 May 6;291(19):10293-306. doi: 10.1074/jbc.M115.691154. Epub 2016 Feb 24.

27.

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin.

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

PLoS Comput Biol. 2016 Feb 22;12(2):e1004774. doi: 10.1371/journal.pcbi.1004774. eCollection 2016 Feb.

28.

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models.

Andreozzi S, Chakrabarti A, Soh KC, Burgard A, Yang TH, Van Dien S, Miskovic L, Hatzimanikatis V.

Metab Eng. 2016 May;35:148-159. doi: 10.1016/j.ymben.2016.01.009. Epub 2016 Feb 5.

PMID:
26855240
29.

iSCHRUNK--In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks.

Andreozzi S, Miskovic L, Hatzimanikatis V.

Metab Eng. 2016 Jan;33:158-168. doi: 10.1016/j.ymben.2015.10.002. Epub 2015 Oct 22.

PMID:
26474788
30.

Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.

31.

Heading in the right direction: thermodynamics-based network analysis and pathway engineering.

Ataman M, Hatzimanikatis V.

Curr Opin Biotechnol. 2015 Dec;36:176-82. doi: 10.1016/j.copbio.2015.08.021. Epub 2015 Sep 16. Review.

32.

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes.

Miskovic L, Tokic M, Fengos G, Hatzimanikatis V.

Curr Opin Biotechnol. 2015 Dec;36:146-53. doi: 10.1016/j.copbio.2015.08.019. Epub 2015 Sep 2. Review.

33.

Noise analysis of genome-scale protein synthesis using a discrete computational model of translation.

Racle J, Stefaniuk AJ, Hatzimanikatis V.

J Chem Phys. 2015 Jul 28;143(4):044109. doi: 10.1063/1.4926536.

PMID:
26233109
34.

Integrative approaches for signalling and metabolic networks.

Hatzimanikatis V, Saez-Rodriguez J.

Integr Biol (Camb). 2015 Aug;7(8):844-5. doi: 10.1039/c5ib90030a. No abstract available.

PMID:
26198436
35.

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways.

Hadadi N, Hatzimanikatis V.

Curr Opin Chem Biol. 2015 Oct;28:99-104. doi: 10.1016/j.cbpa.2015.06.025. Epub 2015 Jul 11. Review.

36.

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis.

Tymoshenko S, Oppenheim RD, Agren R, Nielsen J, Soldati-Favre D, Hatzimanikatis V.

PLoS Comput Biol. 2015 May 22;11(5):e1004261. doi: 10.1371/journal.pcbi.1004261. eCollection 2015 May.

37.

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites.

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

Phys Chem Chem Phys. 2015 Apr 28;17(16):10438-53. doi: 10.1039/c4cp05825a.

PMID:
25799954
38.

Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches.

Zisaki A, Miskovic L, Hatzimanikatis V.

Curr Pharm Des. 2015;21(6):806-22. Review.

39.

Constraining the flux space using thermodynamics and integration of metabolomics data.

Soh KC, Hatzimanikatis V.

Methods Mol Biol. 2014;1191:49-63. doi: 10.1007/978-1-4939-1170-7_3.

PMID:
25178783
40.

Kinetic models in industrial biotechnology - Improving cell factory performance.

Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M.

Metab Eng. 2014 Jul;24:38-60. doi: 10.1016/j.ymben.2014.03.007. Epub 2014 Apr 16. Review.

41.

A computational framework for integration of lipidomics data into metabolic pathways.

Hadadi N, Cher Soh K, Seijo M, Zisaki A, Guan X, Wenk MR, Hatzimanikatis V.

Metab Eng. 2014 May;23:1-8. doi: 10.1016/j.ymben.2013.12.007. Epub 2014 Jan 4.

PMID:
24395008
42.

A novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor.

Fierro-Monti I, Racle J, Hernandez C, Waridel P, Hatzimanikatis V, Quadroni M.

PLoS One. 2013 Nov 27;8(11):e80423. doi: 10.1371/journal.pone.0080423. eCollection 2013.

43.

A genome-scale integration and analysis of Lactococcus lactis translation data.

Racle J, Picard F, Girbal L, Cocaign-Bousquet M, Hatzimanikatis V.

PLoS Comput Biol. 2013;9(10):e1003240. doi: 10.1371/journal.pcbi.1003240. Epub 2013 Oct 10.

44.

Editorial: metabolic modeling in biotechnology and medical research.

Mattanovich D, Hatzimanikatis V.

Biotechnol J. 2013 Sep;8(9):962-3. doi: 10.1002/biot.201300378.

PMID:
24031032
45.

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.

Chakrabarti A, Miskovic L, Soh KC, Hatzimanikatis V.

Biotechnol J. 2013 Sep;8(9):1043-57. doi: 10.1002/biot.201300091. Epub 2013 Aug 20.

PMID:
23868566
46.

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis.

Tymoshenko S, Oppenheim RD, Soldati-Favre D, Hatzimanikatis V.

Brief Funct Genomics. 2013 Jul;12(4):316-27. doi: 10.1093/bfgp/elt017. Epub 2013 Jun 22.

47.

Mechanistically consistent reduced models of synthetic gene networks.

Mier-y-Terán-Romero L, Silber M, Hatzimanikatis V.

Biophys J. 2013 May 7;104(9):2098-109. doi: 10.1016/j.bpj.2013.03.031.

48.

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters.

Merulla D, Hatzimanikatis V, van der Meer JR.

Microb Biotechnol. 2013 Sep;6(5):503-14. doi: 10.1111/1751-7915.12031. Epub 2013 Jan 15.

49.

Exploration of trade-offs between steady-state and dynamic properties in signaling cycles.

Radivojevic A, Chachuat B, Bonvin D, Hatzimanikatis V.

Phys Biol. 2012 Aug;9(4):045010. doi: 10.1088/1478-3975/9/4/045010. Epub 2012 Aug 7.

PMID:
22872041
50.

A computational framework for the design of optimal protein synthesis.

Racle J, Overney J, Hatzimanikatis V.

Biotechnol Bioeng. 2012 Aug;109(8):2127-33. doi: 10.1002/bit.24463. Epub 2012 Feb 24.

PMID:
22334333

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