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Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity.

Dols JA, Molenaar D, van der Helm JJ, Caspers MP, de Kat Angelino-Bart A, Schuren FH, Speksnijder AG, Westerhoff HV, Richardus JH, Boon ME, Reid G, de Vries HJ, Kort R.

BMC Infect Dis. 2016 Apr 23;16(1):180. doi: 10.1186/s12879-016-1513-3.


Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

He F, Murabito E, Westerhoff HV.

J R Soc Interface. 2016 Apr;13(117). pii: 20151046. doi: 10.1098/rsif.2015.1046. Epub 2016 Apr 13. Review.


Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes.

Wruck W, Kashofer K, Rehman S, Daskalaki A, Berg D, Gralka E, Jozefczuk J, Drews K, Pandey V, Regenbrecht C, Wierling C, Turano P, Korf U, Zatloukal K, Lehrach H, Westerhoff HV, Adjaye J.

Sci Data. 2015 Dec 8;2:150068. doi: 10.1038/sdata.2015.68.


Quantitative analysis of drug effects at the whole-body level: a case study for glucose metabolism in malaria patients.

Snoep JL, Green K, Eicher J, Palm DC, Penkler G, du Toit F, Walters N, Burger R, Westerhoff HV, van Niekerk DD.

Biochem Soc Trans. 2015 Dec;43(6):1157-63. doi: 10.1042/BST20150145. Review.


Systems Pharmacology: An opinion on how to turn the impossible into grand challenges.

Westerhoff HV, Nakayama S, Mondeel TD, Barberis M.

Drug Discov Today Technol. 2015 Aug;15:23-31. doi: 10.1016/j.ddtec.2015.06.006. Epub 2015 Jul 25. Review.


Network-based pharmacology through systems biology.

Westerhoff HV.

Drug Discov Today Technol. 2015 Aug;15:15-6. doi: 10.1016/j.ddtec.2015.05.001. Epub 2015 Jul 17. No abstract available.


Metabolite profiling of CHO cells: Molecular reflections of bioprocessing effectiveness.

Sellick CA, Croxford AS, Maqsood AR, Stephens GM, Westerhoff HV, Goodacre R, Dickson AJ.

Biotechnol J. 2015 Sep;10(9):1434-45. doi: 10.1002/biot.201400664.


Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism.

Rybakova KN, Bruggeman FJ, Tomaszewska A, Moné MJ, Carlberg C, Westerhoff HV.

PLoS Comput Biol. 2015 Apr 24;11(4):e1004236. doi: 10.1371/journal.pcbi.1004236. eCollection 2015 Apr.


Silence on the relevant literature and errors in implementation.

Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN.

Nat Biotechnol. 2015 Apr;33(4):336-9. doi: 10.1038/nbt.3185. No abstract available.


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. 2015 Jan;43(1):153-61. doi: 10.1093/nar/gku1272. Epub 2014 Dec 3.


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


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. Erratum in: PLoS One. 2014;9(10):e112204. PLoS One. 2014;9(12):e116129.


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.


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.


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.


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.


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.


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.


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.

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