Prof. dr. H.V. (Hans) Westerhoff
Faculty of Science
Swammerdam Institute for Life Sciences
Visiting address
- Science Park 904
Postal address
- Postbus 1212
1000 BE Amsterdam
Contact details
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Publications
2021
Verstegen, N. J. M., Ubels, V., Westerhoff, H. V., van Ham, S. M., & Barberis, M. (2021). System-Level Scenarios for the Elucidation of T Cell-Mediated Germinal Center B Cell Differentiation. Frontiers in Immunology, 12, [734282]. https://doi.org/10.3389/fimmu.2021.734282 [details]- Weglarz-Tomczak, E., Mondeel, T. D. G. A., Piebes, D. G. E., & Westerhoff, H. V. (2021). Simultaneous integration of gene expression and nutrient availability for studying the metabolism of hepatocellular carcinoma cell lines. BIOMOLECULES, 11(4), [490]. https://doi.org/10.3390/biom11040490 [details]
2020
- Abudukelimu, A., Barberis, M., Redegeld, F., Sahin, N., Sharma, R. P., & Westerhoff, H. V. (2020). Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity. Frontiers in Immunology, 10, [3091]. https://doi.org/10.3389/fimmu.2019.03091 [details]
- Kolodkin, A. N., Sharma, R. P., Colangelo, A. M., Ignatenko, A., Martorana, F., Jennen, D., Briedé, J. J., Brady, N., Barberis, M., Mondeel, T. D. G. A., Papa, M., Kumar, V., Peters, B., Skupin, A., Alberghina, L., Balling, R., & Westerhoff, H. V. (2020). ROS networks: Designs, aging, Parkinson's disease and precision therapies. Npj Systems Biology and Applications, 6, [34]. https://doi.org/10.1038/s41540-020-00150-w [details]
- Mondeel, T. D. G. A., Ivanov, O., Westerhoff, H. V., Liebermeister, W., & Barberis, M. (2020). Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs. Npj Systems Biology and Applications, 6, [8]. https://doi.org/10.1038/s41540-020-0125-0 [details]
- Sharma, R. P., Kumar, V., Schuhmacher, M., Kolodkin, A., & Westerhoff, H. V. (2020). Development and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans. Environmental Research, 182, [108948]. https://doi.org/10.1016/j.envres.2019.108948 [details]
- Westerhoff, H. V., & Kolodkin, A. N. (2020). Advice from a systems-biology model of the corona epidemics. Npj Systems Biology and Applications, 6, [18]. https://doi.org/10.1038/s41540-020-0138-8 [details]
2019
- Colangelo, A. M., Cirillo, G., Alberghina, L., Papa, M., & Westerhoff, H. V. (2019). Neural plasticity and adult neurogenesis: the deep biology perspective. Neural Regeneration Research, 14(2), 201-205. https://doi.org/10.4103/1673-5374.244775 [details]
- Damiani, C., Maspero, D., Di Filippo, M., Colombo, R., Pescini, D., Graudenzi, A., Westerhoff, H. V., Alberghina, L., Vanoni, M., & Mauri, G. (2019). Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. PLoS Computational Biology, 15(2), [e1006733]. https://doi.org/10.1371/journal.pcbi.1006733 [details]
- Hassan, Z., Sultana, M., Khan, S. I., Braster, M., Röling, W. F. M., & Westerhoff, H. V. (2019). Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation? Microorganisms, 7(8), [246]. https://doi.org/10.3390/microorganisms7080246 [details]
- Maeda, K., Westerhoff, H. V., Kurata, H., & Boogerd, F. C. (2019). Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network. Npj Systems Biology and Applications, 5, [14]. https://doi.org/10.1038/s41540-019-0091-6 [details]
2018
- Abudukelimu, A., Barberis, M., Redegeld, F. A., Sahin, N., & Westerhoff, H. V. (2018). Predictable Irreversible Switching Between Acute and Chronic Inflammation. Frontiers in Immunology, 9, [1596]. https://doi.org/10.3389/fimmu.2018.01596 [details]
- Swainston, N., Baici, A., Bakker, B. M., Cornish-Bowden, A., Fitzpatrick, P. F., Halling, P., ... Kettner, C. (2018). STRENDA DB: enabling the validation and sharing of enzyme kinetics data. The FEBS Journal, 285(12), 2193-2204. https://doi.org/10.1111/febs.14427 [details]
- Węglarz-Tomczak, E., Talma, M., Giurg, M., Westerhoff, H. V., Janowski, R., & Mucha, A. (2018). Neutral metalloaminopeptidases APN and MetAP2 as newly discovered anticancer molecular targets of actinomycin D and its simple analogs. Oncotarget, 9(50), 29365-29378. https://doi.org/10.18632/oncotarget.25532 [details]
2017
- Abudukelimu, A., Mondeel, T. D. G. A., Barberis, M., & Westerhoff, H. V. (2017). Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters. Biochemical Society Transactions, 45(3), 635-652. https://doi.org/10.1042/BST20160281 [details]
- Damiani, C., Colombo, R., Gaglio, D., Mastroianni, F., Pescini, D., Westerhoff, H. W., ... Alberghina, L. (2017). 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. PLoS Computational Biology, 13(9), [e1005758]. https://doi.org/10.1371/journal.pcbi.1005758 [details]
- Haanstra, J. R., Gerding, A., Dolga, A. M., Sorgdrager, F. J. H., Buist-Homan, M., du Toit, F., ... Bakker, B. M. (2017). Targeting pathogen metabolism without collateral damage to the host. Scientific Reports, 7, [40406]. https://doi.org/10.1038/srep40406 [details]
- Zhang, Y., Kouril, T., Snoep, J. L., Siebers, B., Barberis, M., & Westerhoff, H. V. (2017). The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico. International Journal of Molecular Sciences, 18(4), [876]. https://doi.org/10.3390/ijms18040876 [details]
- van de Peppel, J., Strini, T., Tilburg, J., Westerhoff, H., van Wijnen, A. J., & van Leeuwen, J. P. (2017). Identification of Three Early Phases of Cell-Fate Determination during Osteogenic and Adipogenic Differentiation by Transcription Factor Dynamics. Stem Cell Reports, 8(4), 947-960. https://doi.org/10.1016/j.stemcr.2017.02.018 [details]
2016
- Dols, J. A. M., Molenaar, D., van der Helm, J. J., Caspers, M. P. M., de Kat Angelino-Bart, A., Schuren, F. H. J., Speksnijder, A. G. C. L., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de Vries, H. J. C., & Kort, R. (2016). Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity. BMC Infectious Diseases, 16, [180]. https://doi.org/10.1186/s12879-016-1513-3 [details]
- He, F., Murabito, E., & Westerhoff, H. V. (2016). Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering. Journal of the Royal Society Interface, 13(117), [1046]. https://doi.org/10.1098/rsif.2015.1046 [details]
- Wu, H., von Kamp, A., Leoncikas, V., Mori, W., Sahin, N., Gevorgyan, A., ... Kierzek, A. M. (2016). MUFINS: multi-formalism interaction network simulator. Npj Systems Biology and Applications, 2, [16032]. https://doi.org/10.1038/npjsba.2016.32 [details]
2015
- Lankelma, J., Kooi, B., Krab, K., Dorsman, J. C., Joenje, H., & Westerhoff, H. V. (2015). A reason for intermittent fasting to suppress the awakening of dormant breast tumors. Biosystems, 127, 1-6. https://doi.org/10.1016/j.biosystems.2014.11.001 [details]
- Rybakova, K. N., Bruggeman, F. J., Tomaszewska, A., Moné, M. J., Carlberg, C., & Westerhoff, H. V. (2015). Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism. PLoS Computational Biology, 11(4), e1004236. https://doi.org/10.1371/journal.pcbi.1004236 [details]
- Rybakova, K. N., Tomaszewska, A., van Mourik, S., Blom, J., Westerhoff, H. V., Carlberg, C., & Bruggeman, F. J. (2015). Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model. Nucleic Acids Research, 43(1), 153-161. https://doi.org/10.1093/nar/gku1272 [details]
- Sellick, C. A., Croxford, A. S., Maqsood, A. R., Stephens, G. M., Westerhoff, H. V., Goodacre, R., & Dickson, A. J. (2015). Metabolite profiling of CHO cells: Molecular reflections of bioprocessing effectiveness. Biotechnology Journal, 10(9), 1434-1445. https://doi.org/10.1002/biot.201400664 [details]
- Snoep, J. L., Green, K., Eicher, J., Palm, D. C., Penkler, G., du Toit, F., ... van Niekerk, D. D. (2015). Quantitative analysis of drug effects at the whole-body level: a case study for glucose metabolism in malaria patients. Biochemical Society Transactions, 43(6), 1157-1163. https://doi.org/10.1042/BST20150145 [details]
- Westerhoff, H. V. (2015). Network-based pharmacology through systems biology. Drug Discovery Today. Technologies, 15, 15-16. https://doi.org/10.1016/j.ddtec.2015.05.001 [details]
- Westerhoff, H. V., Nakayama, S., Mondeel, T. D. G. A., & Barberis, M. (2015). Systems Pharmacology: An opinion on how to turn the impossible into grand challenges. Drug Discovery Today. Technologies, 15, 23-31. https://doi.org/10.1016/j.ddtec.2015.06.006 [details]
- 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, H. V., & Adjaye, J. (2015). Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes. Scientific Data, 2, [150068]. https://doi.org/10.1038/sdata.2015.68 [details]
2014
- Härdin, H. M., Zagaris, A., Willms, A. R., & Westerhoff, H. V. (2014). Clusters of reaction rates and concentrations in protein networks such as the phosphotransferase system. The FEBS Journal, 281(2), 531-548. https://doi.org/10.1111/febs.12664 [details]
- Murabito, E., Verma, M., Bekker, M., Bellomo, D., Westerhoff, H. V., Teusink, B., & Steuer, R. (2014). Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS ONE, 9(9), [e106453]. https://doi.org/10.1371/journal.pone.0106453 [details]
- Ramírez-Bajo, M. J., de Atauri, P., Ortega, F., Westerhoff, H. V., Gelpí, J. L., Centelles, J. J., & Cascante, M. (2014). Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice. PLoS ONE, 9(1), [e80018]. https://doi.org/10.1371/journal.pone.0080018 [details]
- Westerhoff, H. V., Brooks, A. N., Simeonidis, E., García-Contreras, R., He, F., Boogerd, F. C., ... Kolodkin, A. (2014). Macromolecular networks and intelligence in microorganisms. Frontiers in Microbiology, 5, [379]. https://doi.org/10.3389/fmicb.2014.00379 [details]
2013
- Feldman-Salit, A., Hering, S., Messiha, H. L., Veith, N., Cojocaru, V., Sieg, A., ... Fiedler, T. (2013). Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. The Journal of Biological Chemistry, 288(29), 21295-21306. https://doi.org/10.1074/jbc.M113.458265 [details]
- Geenen, S., Yates, J. W. T., Kenna, J. G., Bois, F. Y., Wilson, I. D., & Westerhoff, H. V. (2013). 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. Integrative Biology, 5(6), 877-888. https://doi.org/10.1039/c3ib20245c [details]
- Geenen, S., du Preez, F. B., Snoep, J. L., Foster, A. J., Sarda, S., Kenna, J. G., ... Westerhoff, H. V. (2013). Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy. Biochimica et Biophysica Acta G General Subjects, 1830(10), 4943-59. https://doi.org/10.1016/j.bbagen.2013.04.014 [details]
- He, F., Fromion, V., & Westerhoff, H. V. (2013). (Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis. BMC Systems Biology, 7, [131]. https://doi.org/10.1186/1752-0509-7-131 [details]
- Kolodkin, A., Sahin, N., Phillips, A., Hood, S. R., Bruggeman, F. J., Westerhoff, H. V., & Plant, N. (2013). Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications, 4, 1792. https://doi.org/10.1038/ncomms2799 [details]
- Kolodkin, A., Simeonidis, E., & Westerhoff, H. V. (2013). Computing life: add logos to biology and bios to physics. Progress in Biophysics & Molecular Biology, 111(2-3), 69-74. https://doi.org/10.1016/j.pbiomolbio.2012.10.003 [details]
- Kouril, T., Esser, D., Kort, J., Westerhoff, H. V., Siebers, B., & Snoep, J. L. (2013). Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus. The FEBS Journal, 280(18), 4666-4680. https://doi.org/10.1111/febs.12438 [details]
- Mensonides, F. I., Bakker, B. M., Cremazy, F., Messiha, H. L., Mendes, P., Boogerd, F. C., & Westerhoff, H. V. (2013). A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae. FEBS Letters, 587(17), 2860-2867. https://doi.org/10.1016/j.febslet.2013.07.013 [details]
- Quinton-Tulloch, M. J., Bruggeman, F. J., Snoep, J. L., & Westerhoff, H. V. (2013). Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. The FEBS Journal, 280(1), 160-173. https://doi.org/10.1111/febs.12057 [details]
- Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., ... Mendes, P. (2013). A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Letters, 587(17), 2832-2841. https://doi.org/10.1016/j.febslet.2013.06.043 [details]
- Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., ... Palsson, B. Ø. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31(5), 419-25. https://doi.org/10.1038/nbt.2488 [details]
- Verma, M., Karimiani, E. G., Byers, R. J., Rehman, S., Westerhoff, H. V., & Day, P. J. (2013). 555 mediated BCR.ABL protein regulation in chronic myeloid leukaemia vis-a-vis therapeutic strategies. Integrative Biology, 5(3), 543-554. https://doi.org/10.1039/c3ib20230e [details]
- Verma, M., Zakhartsev, M., Reuss, M., & Westerhoff, H. V. (2013). 'Domino' systems biology and the 'A' of ATP. Biochimica et Biophysica Acta - Bioenergetics, 1827(1), 19-29. https://doi.org/10.1016/j.bbabio.2012.09.014 [details]
- van Heeswijk, W. C., Westerhoff, H. V., & Boogerd, F. C. (2013). Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective. Microbiology and Molecular Biology Reviews, 77(4), 628-695. https://doi.org/10.1128/MMBR.00025-13 [details]
2012
- Adamczyk, M., & Westerhoff, H. V. (2012). Engineering of self-sustaining systems: substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnology Journal, 7(7), 877-883. https://doi.org/10.1002/biot.201100314 [details]
- García-Contreras, R., Vos, P., Westerhoff, H. V., & Boogerd, F. C. (2012). Why in vivo may not equal in vitro - new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions. The FEBS Journal, 279(22), 4145-4159. https://doi.org/10.1111/febs.12007 [details]
- Geenen, S., Taylor, P. N., Snoep, J. L., Wilson, I. D., Kenna, J. G., & Westerhoff, H. V. (2012). Systems biology tools for toxicology. Archives of toxicology = Archiv für Toxikologie, 86(8), 1251-1271. https://doi.org/10.1007/s00204-012-0857-8 [details]
- Jozefczuk, J., Kashofer, K., Ummanni, R., Henjes, F., Rehman, S., Geenen, S., ... Adjaye, J. (2012). A systems biology approach to deciphering the etiology of steatosis employing patient-derived dermal fibroblasts and iPS cells. Frontiers in Physiology, 3, 339. https://doi.org/10.3389/fphys.2012.00339 [details]
- Kolodkin, A., Simeonidis, E., Balling, R., & Westerhoff, H. V. (2012). Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence. Frontiers in Physiology, 3, 291. https://doi.org/10.3389/fphys.2012.00291 [details]
- Rehman, S., Day, P. J. R., Bayat, A., & Westerhoff, H. V. (2012). Understanding Dupuytren's disease using systems biology: a move away from reductionism. Frontiers in Physiology, 3, 316. https://doi.org/10.3389/fphys.2012.00316 [details]
- van Eunen, K., Kiewiet, J. A. L., Westerhoff, H. V., & Bakker, B. M. (2012). Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics. PLoS Computational Biology, 8(4), e1002483. https://doi.org/10.1371/journal.pcbi.1002483 [details]
2011
- Geenen, S., du Preez, F. B., Reed, M., Nijhout, H. F., Kenna, J. G., Wilson, I. D., ... Snoep, J. L. (2011). A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism. European Journal of Pharmaceutical Sciences, 46(4), 233-243. https://doi.org/10.1016/j.ejps.2011.08.017 [details]
- Sellick, C. A., Croxford, A. S., Maqsood, A. R., Stephens, G., Westerhoff, H. V., Goodacre, R., & Dickson, A. J. (2011). Metabolite profiling of recombinant CHO cells: designing tailored feeding regimes that enhance recombinant antibody production. Biotechnology and Bioengineering, 108(12), 3025-3031. https://doi.org/10.1002/bit.23269 [details]
2010
- van Eunen, K., Bouwman, J., Daran-Lapujade, P., Postmus, J., Canelas, A. B., Mensonides, F. I. C., ... Bakker, B. M. (2010). Measuring enzyme activities under standardized in vivo-like conditions for systems biology. The FEBS Journal, 277(3), 749-760. https://doi.org/10.1111/j.1742-4658.2009.07524.x [details]
2009
- Härdin, H. M., Zagaris, A., Krab, K., & Westerhoff, H. V. (2009). Simplified yet highly accurate enzyme kinetics for cases of low substrate concentrations. The FEBS Journal, 276(19), 5491-5506. https://doi.org/10.1111/j.1742-4658.2009.07233.x [details]
2015
- Bastiaens, P., Birtwistle, M. R., Blüthgen, N., Bruggeman, F. J., Cho, K. H., Cosentino, C., de la Fuente, A., Hoek, J. B., Kiyatkin, A., Klamt, S., Kolch, W., Legewie, S., Mendes, P., Naka, T., Santra, T., Sontag, E., Westerhoff, H. V., & Kholodenko, B. N. (2015). Silence on the relevant literature and errors in implementation. Nature Biotechnology, 33(4), 336-339. https://doi.org/10.1038/nbt.3185 [details]
This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list. -
Ancillary activities
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University of Manchester, SCEAS
Hoogleraar
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University of Manchester, SCEAS
Verstegen, N. J. M., Ubels, V., Westerhoff, H. V., van Ham, S. M., & Barberis, M. (2021). System-Level Scenarios for the Elucidation of T Cell-Mediated Germinal Center B Cell Differentiation. Frontiers in Immunology, 12, [734282].