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Development and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans.

Sharma RP, Kumar V, Schuhmacher M, Kolodkin A, Westerhoff HV.

Environ Res. 2020 Mar;182:108948. doi: 10.1016/j.envres.2019.108948. Epub 2019 Nov 26.


Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

Hassan Z, Sultana M, Khan SI, Braster M, Röling WFM, Westerhoff HV.

Microorganisms. 2019 Aug 8;7(8). pii: E246. doi: 10.3390/microorganisms7080246.


Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network.

Maeda K, Westerhoff HV, Kurata H, Boogerd FC.

NPJ Syst Biol Appl. 2019 Apr 12;5:14. doi: 10.1038/s41540-019-0091-6. eCollection 2019.


Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.

Damiani C, Maspero D, Di Filippo M, Colombo R, Pescini D, Graudenzi A, Westerhoff HV, Alberghina L, Vanoni M, Mauri G.

PLoS Comput Biol. 2019 Feb 28;15(2):e1006733. doi: 10.1371/journal.pcbi.1006733. eCollection 2019 Feb.


Neural plasticity and adult neurogenesis: the deep biology perspective.

Colangelo AM, Cirillo G, Alberghina L, Papa M, Westerhoff HV.

Neural Regen Res. 2019 Feb;14(2):201-205. doi: 10.4103/1673-5374.244775. Review.


Predictable Irreversible Switching Between Acute and Chronic Inflammation.

Abudukelimu A, Barberis M, Redegeld FA, Sahin N, Westerhoff HV.

Front Immunol. 2018 Aug 7;9:1596. doi: 10.3389/fimmu.2018.01596. eCollection 2018.


Neutral metalloaminopeptidases APN and MetAP2 as newly discovered anticancer molecular targets of actinomycin D and its simple analogs.

Węglarz-Tomczak E, Talma M, Giurg M, Westerhoff HV, Janowski R, Mucha A.

Oncotarget. 2018 Jun 29;9(50):29365-29378. doi: 10.18632/oncotarget.25532. eCollection 2018 Jun 29.


Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats.

Marozava S, Vargas-López R, Tian Y, Merl-Pham J, Braster M, Meckenstock RU, Smidt H, Röling WFM, Westerhoff HV.

Environ Microbiol. 2018 Jul;20(7):2652-2669. doi: 10.1111/1462-2920.14295.


STRENDA DB: enabling the validation and sharing of enzyme kinetics data.

Swainston N, Baici A, Bakker BM, Cornish-Bowden A, Fitzpatrick PF, Halling P, Leyh TS, O'Donovan C, Raushel FM, Reschel U, Rohwer JM, Schnell S, Schomburg D, Tipton KF, Tsai MD, Westerhoff HV, Wittig U, Wohlgemuth R, Kettner C.

FEBS J. 2018 Jun;285(12):2193-2204. doi: 10.1111/febs.14427. Epub 2018 Mar 23.


Rational cell culture optimization enhances experimental reproducibility in cancer cells.

Wright Muelas M, Ortega F, Breitling R, Bendtsen C, Westerhoff HV.

Sci Rep. 2018 Feb 14;8(1):3029. doi: 10.1038/s41598-018-21050-4.


A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect.

Damiani C, Colombo R, Gaglio D, Mastroianni F, Pescini D, Westerhoff HV, Mauri G, Vanoni M, Alberghina L.

PLoS Comput Biol. 2017 Sep 28;13(9):e1005758. doi: 10.1371/journal.pcbi.1005758. eCollection 2017 Sep.


MUFINS: multi-formalism interaction network simulator.

Wu H, von Kamp A, Leoncikas V, Mori W, Sahin N, Gevorgyan A, Linley C, Grabowski M, Mannan AA, Stoy N, Stewart GR, Ward LT, Lewis DJM, Sroka J, Matsuno H, Klamt S, Westerhoff HV, McFadden J, Plant NJ, Kierzek AM.

NPJ Syst Biol Appl. 2016 Nov 17;2:16032. doi: 10.1038/npjsba.2016.32. eCollection 2016.


Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters.

Abudukelimu A, Mondeel TDGA, Barberis M, Westerhoff HV.

Biochem Soc Trans. 2017 Jun 15;45(3):635-652. doi: 10.1042/BST20160281. Review.


The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico.

Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV.

Int J Mol Sci. 2017 Apr 20;18(4). pii: E876. doi: 10.3390/ijms18040876.


Targeting pathogen metabolism without collateral damage to the host.

Haanstra JR, Gerding A, Dolga AM, Sorgdrager FJH, Buist-Homan M, du Toit F, Faber KN, Holzhütter HG, Szöör B, Matthews KR, Snoep JL, Westerhoff HV, Bakker BM.

Sci Rep. 2017 Jan 13;7:40406. doi: 10.1038/srep40406.


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;16:180. 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.


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.


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.


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.


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.


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.


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.


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.


'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.


Why in vivo may not equal in vitro - new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions.

García-Contreras R, Vos P, Westerhoff HV, Boogerd FC.

FEBS J. 2012 Nov;279(22):4145-59. doi: 10.1111/febs.12007. Epub 2012 Oct 12.


A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells.

Jozefczuk J, Kashofer K, Ummanni R, Henjes F, Rehman S, Geenen S, Wruck W, Regenbrecht C, Daskalaki A, Wierling C, Turano P, Bertini I, Korf U, Zatloukal K, Westerhoff HV, Lehrach H, Adjaye J.

Front Physiol. 2012 Sep 3;3:339. doi: 10.3389/fphys.2012.00339. eCollection 2012.


Understanding Dupuytren's Disease Using Systems Biology: A Move Away from Reductionism.

Rehman S, Day PJ, Bayat A, Westerhoff HV.

Front Physiol. 2012 Aug 9;3:316. doi: 10.3389/fphys.2012.00316. eCollection 2012. No abstract available.


Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence.

Kolodkin A, Simeonidis E, Balling R, Westerhoff HV.

Front Physiol. 2012 Jul 23;3:291. doi: 10.3389/fphys.2012.00291. eCollection 2012.


Dupuytren's disease metabolite analyses reveals alterations following initial short-term fibroblast culturing.

Rehman S, Xu Y, Dunn WB, Day PJ, Westerhoff HV, Goodacre R, Bayat A.

Mol Biosyst. 2012 Sep;8(9):2274-88. Epub 2012 Jul 6.


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