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Results: 1 to 20 of 336

1.

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model.

Rybakova KN, Tomaszewska A, van Mourik S, Blom J, Westerhoff HV, Carlberg C, Bruggeman FJ.

Nucleic Acids Res. 2014 Dec 3. pii: gku1272. [Epub ahead of print]

PMID:
25477385
[PubMed - as supplied by publisher]
Free Article
2.

A reason for intermittent fasting to suppress the awakening of dormant breast tumors.

Lankelma J, Kooi B, Krab K, Dorsman JC, Joenje H, Westerhoff HV.

Biosystems. 2015 Jan;127C:1-6. doi: 10.1016/j.biosystems.2014.11.001. Epub 2014 Nov 4.

PMID:
25448890
[PubMed - as supplied by publisher]
3.

Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation.

Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R.

PLoS One. 2014 Sep 30;9(9):e106453. doi: 10.1371/journal.pone.0106453. eCollection 2014.

PMID:
25268481
[PubMed - in process]
Free PMC Article
4.

Macromolecular networks and intelligence in microorganisms.

Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A.

Front Microbiol. 2014 Jul 22;5:379. doi: 10.3389/fmicb.2014.00379. eCollection 2014.

PMID:
25101076
[PubMed]
Free PMC Article
5.

Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice.

Ramírez-Bajo MJ, de Atauri P, Ortega F, Westerhoff HV, Gelpí JL, Centelles JJ, Cascante M.

PLoS One. 2014 Jan 28;9(1):e80018. doi: 10.1371/journal.pone.0080018. eCollection 2014.

PMID:
24489641
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective.

van Heeswijk WC, Westerhoff HV, Boogerd FC.

Microbiol Mol Biol Rev. 2013 Dec;77(4):628-95. doi: 10.1128/MMBR.00025-13. Review.

PMID:
24296575
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Clusters of reaction rates and concentrations in protein networks such as the phosphotransferase system.

Härdin HM, Zagaris A, Willms AR, Westerhoff HV.

FEBS J. 2014 Jan;281(2):531-48. doi: 10.1111/febs.12664. Epub 2013 Dec 23. Review.

PMID:
24289186
[PubMed - indexed for MEDLINE]
8.

(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis.

He F, Fromion V, Westerhoff HV.

BMC Syst Biol. 2013 Nov 21;7:131. doi: 10.1186/1752-0509-7-131.

PMID:
24261908
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus.

Kouril T, Esser D, Kort J, Westerhoff HV, Siebers B, Snoep JL.

FEBS J. 2013 Sep;280(18):4666-80. doi: 10.1111/febs.12438. Epub 2013 Aug 22.

PMID:
23865479
[PubMed - indexed for MEDLINE]
10.

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae.

Mensonides FI, Bakker BM, Cremazy F, Messiha HL, Mendes P, Boogerd FC, Westerhoff HV.

FEBS Lett. 2013 Sep 2;587(17):2860-7. doi: 10.1016/j.febslet.2013.07.013. Epub 2013 Jul 12.

PMID:
23856461
[PubMed - indexed for MEDLINE]
Free Article
11.

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.

Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JE, Paton NW, Westerhoff HV, Kell DB, Mendes P.

FEBS Lett. 2013 Sep 2;587(17):2832-41. doi: 10.1016/j.febslet.2013.06.043. Epub 2013 Jul 4.

PMID:
23831062
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria.

Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T.

J Biol Chem. 2013 Jul 19;288(29):21295-306. doi: 10.1074/jbc.M113.458265. Epub 2013 May 17.

PMID:
23720742
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Optimization of stress response through the nuclear receptor-mediated cortisol signalling network.

Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant N.

Nat Commun. 2013;4:1792. doi: 10.1038/ncomms2799.

PMID:
23653204
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy.

Geenen S, du Preez FB, Snoep JL, Foster AJ, Sarda S, Kenna JG, Wilson ID, Westerhoff HV.

Biochim Biophys Acta. 2013 Oct;1830(10):4943-59. doi: 10.1016/j.bbagen.2013.04.014. Epub 2013 Apr 30.

PMID:
23643929
[PubMed - indexed for MEDLINE]
15.

Multiscale modelling approach combining a kinetic model of glutathione metabolism with PBPK models of paracetamol and the potential glutathione-depletion biomarkers ophthalmic acid and 5-oxoproline in humans and rats.

Geenen S, Yates JW, Kenna JG, Bois FY, Wilson ID, Westerhoff HV.

Integr Biol (Camb). 2013 Jun;5(6):877-88. doi: 10.1039/c3ib20245c.

PMID:
23632663
[PubMed - indexed for MEDLINE]
16.

A community-driven global reconstruction of human metabolism.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.

Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3.

PMID:
23455439
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Mathematical modelling of miRNA mediated BCR.ABL protein regulation in chronic myeloid leukaemia vis-a-vis therapeutic strategies.

Verma M, Karimiani EG, Byers RJ, Rehman S, Westerhoff HV, Day PJ.

Integr Biol (Camb). 2013 Mar;5(3):543-54. doi: 10.1039/c3ib20230e.

PMID:
23340812
[PubMed - indexed for MEDLINE]
18.

Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico.

Quinton-Tulloch MJ, Bruggeman FJ, Snoep JL, Westerhoff HV.

FEBS J. 2013 Jan;280(1):160-73. doi: 10.1111/febs.12057. Epub 2012 Dec 7.

PMID:
23121761
[PubMed - indexed for MEDLINE]
19.

Computing life: Add logos to biology and bios to physics.

Kolodkin A, Simeonidis E, Westerhoff HV.

Prog Biophys Mol Biol. 2013 Apr;111(2-3):69-74. doi: 10.1016/j.pbiomolbio.2012.10.003. Epub 2012 Oct 24.

PMID:
23103359
[PubMed - indexed for MEDLINE]
20.

'Domino' systems biology and the 'A' of ATP.

Verma M, Zakhartsev M, Reuss M, Westerhoff HV.

Biochim Biophys Acta. 2013 Jan;1827(1):19-29. doi: 10.1016/j.bbabio.2012.09.014. Epub 2012 Sep 29.

PMID:
23031542
[PubMed - indexed for MEDLINE]
Free Article
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