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Hans V. Westerhoff - Publications

Affiliations: 
Vrije Universiteit Amsterdam, Amsterdam, Netherlands 
Area:
Molecular Cell Physiology
Website:
http://www.bio.vu.nl/microb/personnel/htm/westerhoff.html

214 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 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, et al. STRENDA DB: enabling the validation and sharing of enzyme kinetics data. The Febs Journal. PMID 29498804 DOI: 10.1111/febs.14427  0.32
2017 Haanstra JR, Gerding A, Dolga AM, Sorgdrager FJ, Buist-Homan M, du Toit F, Faber KN, Holzhütter HG, Szöör B, Matthews KR, Snoep JL, Westerhoff HV, Bakker BM. Targeting pathogen metabolism without collateral damage to the host. Scientific Reports. 7: 40406. PMID 28084422 DOI: 10.1038/srep40406  0.32
2015 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, et al. Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes. Scientific Data. 2: 150068. PMID 26646939 DOI: 10.1038/sdata.2015.68  0.32
2015 Snoep JL, Green K, Eicher J, Palm DC, Penkler G, du Toit F, Walters N, Burger R, Westerhoff HV, van Niekerk DD. Quantitative analysis of drug effects at the whole-body level: a case study for glucose metabolism in malaria patients. Biochemical Society Transactions. 43: 1157-63. PMID 26614654 DOI: 10.1042/BST20150145  0.32
2015 Westerhoff HV, Nakayama S, Mondeel TD, Barberis M. Systems Pharmacology: An opinion on how to turn the impossible into grand challenges. Drug Discovery Today. Technologies. 15: 23-31. PMID 26464087 DOI: 10.1016/j.ddtec.2015.06.006  0.32
2015 Westerhoff HV. Network-based pharmacology through systems biology. Drug Discovery Today. Technologies. 15: 15-6. PMID 26464085 DOI: 10.1016/j.ddtec.2015.05.001  0.32
2015 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, ... ... Westerhoff HV, et al. Silence on the relevant literature and errors in implementation. Nature Biotechnology. 33: 336-9. PMID 25850052 DOI: 10.1038/nbt.3185  0.32
2015 Lankelma J, Kooi B, Krab K, Dorsman JC, Joenje H, Westerhoff HV. A reason for intermittent fasting to suppress the awakening of dormant breast tumors. Bio Systems. 127: 1-6. PMID 25448890 DOI: 10.1016/j.biosystems.2014.11.001  0.32
2014 Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R. Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. Plos One. 9: e106453. PMID 25268481 DOI: 10.1371/journal.pone.0106453  0.32
2014 Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A. Macromolecular networks and intelligence in microorganisms. Frontiers in Microbiology. 5: 379. PMID 25101076 DOI: 10.3389/fmicb.2014.00379  0.32
2014 Ramírez-Bajo MJ, de Atauri P, Ortega F, Westerhoff HV, Gelpí JL, Centelles JJ, Cascante M. Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice. Plos One. 9: e80018. PMID 24489641 DOI: 10.1371/journal.pone.0080018  0.32
2014 Härdin HM, Zagaris A, Willms AR, Westerhoff HV. Clusters of reaction rates and concentrations in protein networks such as the phosphotransferase system. The Febs Journal. 281: 531-48. PMID 24289186 DOI: 10.1111/febs.12664  1
2013 van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiology and Molecular Biology Reviews : Mmbr. 77: 628-95. PMID 24296575 DOI: 10.1128/MMBR.00025-13  1
2013 He F, Fromion V, Westerhoff HV. (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. PMID 24261908 DOI: 10.1186/1752-0509-7-131  1
2013 Kouril T, Esser D, Kort J, Westerhoff HV, Siebers B, Snoep JL. 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: 4666-80. PMID 23865479 DOI: 10.1111/febs.12438  1
2013 Mensonides FI, Bakker BM, Cremazy F, Messiha HL, Mendes P, Boogerd FC, Westerhoff HV. 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: 2860-7. PMID 23856461 DOI: 10.1016/j.febslet.2013.07.013  1
2013 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, ... ... Westerhoff HV, et al. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. Febs Letters. 587: 2832-41. PMID 23831062 DOI: 10.1016/j.febslet.2013.06.043  1
2013 Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T. Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. The Journal of Biological Chemistry. 288: 21295-306. PMID 23720742 DOI: 10.1074/jbc.M113.458265  1
2013 Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant N. Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications. 4: 1792. PMID 23653204 DOI: 10.1038/ncomms2799  1
2013 Geenen S, du Preez FB, Snoep JL, Foster AJ, Sarda S, Kenna JG, Wilson ID, Westerhoff HV. Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy. Biochimica Et Biophysica Acta. 1830: 4943-59. PMID 23643929 DOI: 10.1016/j.bbagen.2013.04.014  1
2013 Geenen S, Yates JW, Kenna JG, Bois FY, Wilson ID, Westerhoff HV. 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 : Quantitative Biosciences From Nano to Macro. 5: 877-88. PMID 23632663 DOI: 10.1039/c3ib20245c  1
2013 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, ... ... Westerhoff HV, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/nbt.2488  0.32
2013 Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JE. An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology. 9: 635. PMID 23340841 DOI: 10.1038/msb.2012.73  1
2013 Verma M, Karimiani EG, Byers RJ, Rehman S, Westerhoff HV, Day PJ. Mathematical modelling of miRNA mediated BCR.ABL protein regulation in chronic myeloid leukaemia vis-a-vis therapeutic strategies. Integrative Biology : Quantitative Biosciences From Nano to Macro. 5: 543-54. PMID 23340812 DOI: 10.1039/c3ib20230e  1
2013 Quinton-Tulloch MJ, Bruggeman FJ, Snoep JL, Westerhoff HV. Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. The Febs Journal. 280: 160-73. PMID 23121761 DOI: 10.1111/febs.12057  1
2013 Kolodkin A, Simeonidis E, Westerhoff HV. Computing life: Add logos to biology and bios to physics. Progress in Biophysics and Molecular Biology. 111: 69-74. PMID 23103359 DOI: 10.1016/j.pbiomolbio.2012.10.003  1
2013 Verma M, Zakhartsev M, Reuss M, Westerhoff HV. 'Domino' systems biology and the 'A' of ATP. Biochimica Et Biophysica Acta. 1827: 19-29. PMID 23031542 DOI: 10.1016/j.bbabio.2012.09.014  1
2013 Westerhoff HV, He F, Murabito E, Crémazy F, Barberis M. Understanding Principles of the Dynamic Biochemical Networks of Life Through Systems Biology Computational Systems Biology: From Molecular Mechanisms to Disease: Second Edition. 21-44. DOI: 10.1016/B978-0-12-405926-9.00003-4  0.32
2012 García-Contreras R, Vos P, Westerhoff HV, Boogerd FC. 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: 4145-59. PMID 22978366 DOI: 10.1111/febs.12007  1
2012 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, et al. A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. Frontiers in Physiology. 3: 339. PMID 22969728 DOI: 10.3389/fphys.2012.00339  1
2012 Rehman S, Day PJ, Bayat A, Westerhoff HV. Understanding Dupuytren's Disease Using Systems Biology: A Move Away from Reductionism. Frontiers in Physiology. 3: 316. PMID 22934066 DOI: 10.3389/fphys.2012.00316  1
2012 Kolodkin A, Simeonidis E, Balling R, Westerhoff HV. Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence. Frontiers in Physiology. 3: 291. PMID 22934043 DOI: 10.3389/fphys.2012.00291  1
2012 Rehman S, Xu Y, Dunn WB, Day PJ, Westerhoff HV, Goodacre R, Bayat A. Dupuytren's disease metabolite analyses reveals alterations following initial short-term fibroblast culturing. Molecular Biosystems. 8: 2274-88. PMID 22772395 DOI: 10.1039/c2mb25173f  1
2012 Adamczyk M, Westerhoff HV. 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: 877-83. PMID 22700394 DOI: 10.1002/biot.201100314  1
2012 van Eunen K, Kiewiet JA, Westerhoff HV, Bakker BM. Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics. Plos Computational Biology. 8: e1002483. PMID 22570597 DOI: 10.1371/journal.pcbi.1002483  1
2012 Geenen S, Taylor PN, Snoep JL, Wilson ID, Kenna JG, Westerhoff HV. Systems biology tools for toxicology. Archives of Toxicology. 86: 1251-71. PMID 22569772 DOI: 10.1007/s00204-012-0857-8  1
2012 Geenen S, du Preez FB, Reed M, Nijhout HF, Kenna JG, Wilson ID, Westerhoff HV, Snoep JL. A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 46: 233-43. PMID 21888969 DOI: 10.1016/j.ejps.2011.08.017  1
2012 Kolodkin A, Boogerd FC, Plant N, Bruggeman FJ, Goncharuk V, Lunshof J, Moreno-Sanchez R, Yilmaz N, Bakker BM, Snoep JL, Balling R, Westerhoff HV. Emergence of the silicon human and network targeting drugs. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 46: 190-7. PMID 21704158 DOI: 10.1016/j.ejps.2011.06.006  1
2011 Swat M, Kie?basa SM, Polak S, Olivier B, Bruggeman FJ, Tulloch MQ, Snoep JL, Verhoeven AJ, Westerhoff HV. What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform. Interface Focus. 1: 16-23. PMID 22419971 DOI: 10.1098/rsfs.2010.0011  1
2011 De Vos D, Bruggeman FJ, Westerhoff HV, Bakker BM. How molecular competition influences fluxes in gene expression networks. Plos One. 6: e28494. PMID 22163025 DOI: 10.1371/journal.pone.0028494  1
2011 Jameson D, Verma M, Westerhoff HV. Methods in systems biology. Preface. Methods in Enzymology. 500: xxiii-xxiv. PMID 21943919 DOI: 10.1016/B978-0-12-385118-5.00031-1  1
2011 van Eunen K, Rossell S, Bouwman J, Westerhoff HV, Bakker BM. Quantitative analysis of flux regulation through hierarchical regulation analysis. Methods in Enzymology. 500: 571-95. PMID 21943915 DOI: 10.1016/B978-0-12-385118-5.00027-X  1
2011 Adamczyk M, van Eunen K, Bakker BM, Westerhoff HV. Enzyme kinetics for systems biology when, why and how. Methods in Enzymology. 500: 233-57. PMID 21943901 DOI: 10.1016/B978-0-12-385118-5.00013-X  1
2011 Nilapwar SM, Nardelli M, Westerhoff HV, Verma M. Absorption spectroscopy. Methods in Enzymology. 500: 59-75. PMID 21943892 DOI: 10.1016/B978-0-12-385118-5.00004-9  1
2011 Westerhoff HV. Systems biology left and right. Methods in Enzymology. 500: 3-11. PMID 21943889 DOI: 10.1016/B978-0-12-385118-5.00001-3  1
2011 Rehman S, Goodacre R, Day PJ, Bayat A, Westerhoff HV. Dupuytren's: a systems biology disease. Arthritis Research & Therapy. 13: 238. PMID 21943049 DOI: 10.1186/ar3438  1
2011 Sellick CA, Croxford AS, Maqsood AR, Stephens G, Westerhoff HV, Goodacre R, Dickson AJ. Metabolite profiling of recombinant CHO cells: designing tailored feeding regimes that enhance recombinant antibody production. Biotechnology and Bioengineering. 108: 3025-31. PMID 21769861 DOI: 10.1002/bit.23269  1
2011 Geenen S, Guallar-Hoyas C, Michopoulos F, Kenna JG, Kolaja KL, Westerhoff HV, Thomas P, Wilson ID. HPLC-MS/MS methods for the quantitative analysis of 5-oxoproline (pyroglutamate) in rat plasma and hepatic cell line culture medium. Journal of Pharmaceutical and Biomedical Analysis. 56: 655-63. PMID 21752568 DOI: 10.1016/j.jpba.2011.06.001  1
2011 Becla L, Lunshof JE, Gurwitz D, Schulte In den Bäumen T, Westerhoff HV, Lange BM, Brand A. Health technology assessment in the era of personalized health care. International Journal of Technology Assessment in Health Care. 27: 118-26. PMID 21450126 DOI: 10.1017/S026646231100002X  1
2011 Geenen S, Michopoulos F, Kenna JG, Kolaja KL, Westerhoff HV, Wilson I. HPLC-MS/MS methods for the quantitative analysis of ophthalmic acid in rodent plasma and hepatic cell line culture medium. Journal of Pharmaceutical and Biomedical Analysis. 54: 1128-35. PMID 21176868 DOI: 10.1016/j.jpba.2010.11.038  1
2011 Haanstra JR, Kerkhoven EJ, van Tuijl A, Blits M, Wurst M, van Nuland R, Albert MA, Michels PA, Bouwman J, Clayton C, Westerhoff HV, Bakker BM. A domino effect in drug action: from metabolic assault towards parasite differentiation. Molecular Microbiology. 79: 94-108. PMID 21166896 DOI: 10.1111/j.1365-2958.2010.07435.x  1
2011 Boogerd FC, Ma H, Bruggeman FJ, van Heeswijk WC, García-Contreras R, Molenaar D, Krab K, Westerhoff HV. AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3. Febs Letters. 585: 23-8. PMID 21134373 DOI: 10.1016/j.febslet.2010.11.055  1
2011 Murabito E, Smallbone K, Swinton J, Westerhoff HV, Steuer R. A probabilistic approach to identify putative drug targets in biochemical networks. Journal of the Royal Society, Interface / the Royal Society. 8: 880-95. PMID 21123256 DOI: 10.1098/rsif.2010.0540  1
2011 Lehrach H, Subrak R, Boyle P, Pasterk M, Zatloukal K, Müller H, Hubbard T, Brand A, Girolami M, Jameson D, Bruggeman FJ, Westerhoff HV. ITFoM - The IT future of medicine Procedia Computer Science. 7: 26-29. DOI: 10.1016/j.procs.2011.12.012  1
2011 Kolodkin AN, Boogerd FC, Bruggeman FJ, Westerhoff HV. Modeling Approaches in Systems Biology, Including Silicon Cell Models Systems Biology and Livestock Science. 31-51. DOI: 10.1002/9780470963012.ch2  1
2010 Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, ... ... Westerhoff H, et al. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nature Communications. 1: 145. PMID 21266995 DOI: 10.1038/ncomms1150  1
2010 Kolodkin AN, Bruggeman FJ, Plant N, Moné MJ, Bakker BM, Campbell MJ, van Leeuwen JP, Carlberg C, Snoep JL, Westerhoff HV. Design principles of nuclear receptor signaling: how complex networking improves signal transduction. Molecular Systems Biology. 6: 446. PMID 21179018 DOI: 10.1038/msb.2010.102  1
2010 Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, ... ... Westerhoff HV, et al. Systematic integration of experimental data and models in systems biology. Bmc Bioinformatics. 11: 582. PMID 21114840 DOI: 10.1186/1471-2105-11-582  1
2010 Simeonidis E, Murabito E, Smallbone K, Westerhoff HV. Why does yeast ferment? A flux balance analysis study. Biochemical Society Transactions. 38: 1225-9. PMID 20863289 DOI: 10.1042/BST0381225  1
2010 Westerhoff HV, Verma M, Nardelli M, Adamczyk M, van Eunen K, Simeonidis E, Bakker BM. Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control. Biochemical Society Transactions. 38: 1189-96. PMID 20863282 DOI: 10.1042/BST0381189  1
2010 Teusink B, Westerhoff HV, Bruggeman FJ. Comparative systems biology: from bacteria to man. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 518-32. PMID 20836045 DOI: 10.1002/wsbm.74  1
2010 Moreno-Sánchez R, Saavedra E, Rodríguez-Enríquez S, Gallardo-Pérez JC, Quezada H, Westerhoff HV. Metabolic control analysis indicates a change of strategy in the treatment of cancer. Mitochondrion. 10: 626-39. PMID 20599628 DOI: 10.1016/j.mito.2010.06.002  1
2010 Bakker BM, Krauth-Siegel RL, Clayton C, Matthews K, Girolami M, Westerhoff HV, Michels PA, Breitling R, Barrett MP. The silicon trypanosome. Parasitology. 137: 1333-41. PMID 20444304 DOI: 10.1017/S0031182010000466  1
2010 van Eunen K, Dool P, Canelas AB, Kiewiet J, Bouwman J, van Gulik WM, Westerhoff HV, Bakker BM. Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history. Iet Systems Biology. 4: 157-68. PMID 20232995 DOI: 10.1049/iet-syb.2009.0025  1
2010 van Eunen K, Bouwman J, Daran-Lapujade P, Postmus J, Canelas AB, Mensonides FI, Orij R, Tuzun I, van den Brink J, Smits GJ, van Gulik WM, Brul S, Heijnen JJ, de Winde JH, de Mattos MJ, ... ... Westerhoff HV, et al. Measuring enzyme activities under standardized in vivo-like conditions for systems biology. The Febs Journal. 277: 749-60. PMID 20067525 DOI: 10.1111/j.1742-4658.2009.07524.x  1
2010 Conradie R, Bruggeman FJ, Ciliberto A, Csikász-Nagy A, Novák B, Westerhoff HV, Snoep JL. Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex. The Febs Journal. 277: 357-67. PMID 20015233 DOI: 10.1111/j.1742-4658.2009.07473.x  1
2010 Jonker CM, Snoep JL, Treur J, Westerhoff HV, Wijngaards WCA. The living cell as a multi-agent organisation: A compositional organisation model of intracellular dynamics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6220: 160-206. DOI: 10.1007/978-3-642-15034-0_10  1
2009 Westerhoff HV, Winder C, Messiha H, Simeonidis E, Adamczyk M, Verma M, Bruggeman FJ, Dunn W. Systems biology: the elements and principles of life. Febs Letters. 583: 3882-90. PMID 19913018 DOI: 10.1016/j.febslet.2009.11.018  1
2009 Bruggeman FJ, Blüthgen N, Westerhoff HV. Noise management by molecular networks. Plos Computational Biology. 5: e1000506. PMID 19763166 DOI: 10.1371/journal.pcbi.1000506  1
2009 Härdin HM, Zagaris A, Krab K, Westerhoff HV. Simplified yet highly accurate enzyme kinetics for cases of low substrate concentrations. The Febs Journal. 276: 5491-506. PMID 19725885 DOI: 10.1111/j.1742-4658.2009.07233.x  1
2009 van Eunen K, Bouwman J, Lindenbergh A, Westerhoff HV, Bakker BM. Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast. The Febs Journal. 276: 5521-36. PMID 19691496 DOI: 10.1111/j.1742-4658.2009.07235.x  1
2009 Degenhardt T, Rybakova KN, Tomaszewska A, Moné MJ, Westerhoff HV, Bruggeman FJ, Carlberg C. Population-level transcription cycles derive from stochastic timing of single-cell transcription. Cell. 138: 489-501. PMID 19665971 DOI: 10.1016/j.cell.2009.05.029  1
2009 Lin B, Westerhoff HV, Röling WF. How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats. Environmental Microbiology. 11: 2425-33. PMID 19638178 DOI: 10.1111/j.1462-2920.2009.01971.x  1
2009 Westerhoff HV, Kelt DB. Matrix method for determining steps most rate-limiting to metabolic fluxes in biotechnological processes. 1987. Biotechnology and Bioengineering. 104: 1-9. PMID 19623536 DOI: 10.1002/bit.22458  1
2009 Monkhorst K, de Hoon B, Jonkers I, Mulugeta Achame E, Monkhorst W, Hoogerbrugge J, Rentmeester E, Westerhoff HV, Grosveld F, Grootegoed JA, Gribnau J. The probability to initiate X chromosome inactivation is determined by the X to autosomal ratio and X chromosome specific allelic properties. Plos One. 4: e5616. PMID 19440388 DOI: 10.1371/journal.pone.0005616  1
2009 van Heeswijk WC, Molenaar D, Hoving S, Westerhoff HV. The pivotal regulator GlnB of Escherichia coli is engaged in subtle and context-dependent control. The Febs Journal. 276: 3324-40. PMID 19438718 DOI: 10.1111/j.1742-4658.2009.07058.x  1
2009 Albers SV, Birkeland NK, Driessen AJ, Gertig S, Haferkamp P, Klenk HP, Kouril T, Manica A, Pham TK, Ruoff P, Schleper C, Schomburg D, Sharkey KJ, Siebers B, Sierocinski P, ... ... Westerhoff HV, et al. SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochemical Society Transactions. 37: 58-64. PMID 19143602 DOI: 10.1042/BST0370058  1
2009 Groeneveld P, Stouthamer AH, Westerhoff HV. Super life--how and why 'cell selection' leads to the fastest-growing eukaryote. The Febs Journal. 276: 254-70. PMID 19087200 DOI: 10.1111/j.1742-4658.2008.06778.x  1
2009 Westerhoff HV, Kolodkin A, Conradie R, Wilkinson SJ, Bruggeman FJ, Krab K, van Schuppen JH, Hardin H, Bakker BM, Moné MJ, Rybakova KN, Eijken M, van Leeuwen HJ, Snoep JL. Systems biology towards life in silico: mathematics of the control of living cells. Journal of Mathematical Biology. 58: 7-34. PMID 18278498 DOI: 10.1007/s00285-008-0160-8  1
2008 Bruggeman FJ, Snoep JL, Westerhoff HV. Control, responses and modularity of cellular regulatory networks: a control analysis perspective. Iet Systems Biology. 2: 397-410. PMID 19045835 DOI: 10.1049/iet-syb:20070065  1
2008 Haanstra JR, van Tuijl A, Kessler P, Reijnders W, Michels PA, Westerhoff HV, Parsons M, Bakker BM. Compartmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes. Proceedings of the National Academy of Sciences of the United States of America. 105: 17718-23. PMID 19008351 DOI: 10.1073/pnas.0806664105  1
2008 HerrgÃ¥rd MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, ... ... Westerhoff HV, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 26: 1155-60. PMID 18846089 DOI: 10.1038/nbt1492  1
2008 Oláh J, Klivényi P, Gardián G, Vécsei L, Orosz F, Kovacs GG, Westerhoff HV, Ovádi J. Increased glucose metabolism and ATP level in brain tissue of Huntington's disease transgenic mice. The Febs Journal. 275: 4740-55. PMID 18721135 DOI: 10.1111/j.1742-4658.2008.06612.x  1
2008 Bevilacqua A, Wilkinson SJ, Dimelow R, Murabito E, Rehman S, Nardelli M, van Eunen K, Rossell S, Bruggeman FJ, Blüthgen N, De Vos D, Bouwman J, Bakker BM, Westerhoff HV. Vertical systems biology: from DNA to flux and back. Seb Experimental Biology Series. 61: 65-91. PMID 18709737  1
2008 Westerhoff HV, Mosekilde E, Noe CR, Clemensen AM. Integrating systems approaches into pharmaceutical sciences. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 35: 1-4. PMID 18602464 DOI: 10.1016/j.ejps.2008.05.011  1
2008 Legewie S, Herzel H, Westerhoff HV, Blüthgen N. Recurrent design patterns in the feedback regulation of the mammalian signalling network. Molecular Systems Biology. 4: 190. PMID 18463614 DOI: 10.1038/msb.2008.29  1
2008 Westerhoff HV. Signalling control strength. Journal of Theoretical Biology. 252: 555-67. PMID 18222488 DOI: 10.1016/j.jtbi.2007.11.035  1
2008 Jonker CM, Snoep JL, Treur J, Westerhoff HV, Wijngaards WC. BDI-modelling of complex intracellular dynamics. Journal of Theoretical Biology. 251: 1-23. PMID 18082772 DOI: 10.1016/j.jtbi.2007.10.017  1
2008 Haanstra JR, Stewart M, Luu VD, van Tuijl A, Westerhoff HV, Clayton C, Bakker BM. Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei. The Journal of Biological Chemistry. 283: 2495-507. PMID 17991737 DOI: 10.1074/jbc.M705782200  1
2008 Rossell S, Lindenbergh A, van der Weijden CC, Kruckeberg AL, van Eunen K, Westerhoff HV, Bakker BM. Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to a HXK2 deletion in Saccharomyces cerevisiae. Fems Yeast Research. 8: 155-64. PMID 17662056 DOI: 10.1111/j.1567-1364.2007.00282.x  1
2008 Bruggeman FJ, Härdin HM, Van Schuppen JH, Westerhoff HV. Silicon Cell Models: Construction, Analysis, and Reduction Biosimulation in Drug Development. 401-423. DOI: 10.1002/9783527622672.ch15  1
2008 Bertau M, Mosekilde E, Westerhoff HV. Preface Biosimulation in Drug Development. xvii-xxii. DOI: 10.1002/9783527622672  1
2007 Bruggeman FJ, Rossell S, Van Eunen K, Bouwman J, Westerhoff HV, Bakker B. Systems biology and the reconstruction of the cell: from molecular components to integral function. Sub-Cellular Biochemistry. 43: 239-62. PMID 17953397  1
2007 Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, Slijper M, Heck AJ, Daran JM, de Winde JH, Westerhoff HV, Pronk JT, Bakker BM. The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proceedings of the National Academy of Sciences of the United States of America. 104: 15753-8. PMID 17898166 DOI: 10.1073/pnas.0707476104  1
2007 Bruggeman FJ, Hornberg JJ, Boogerd FC, Westerhoff HV. Introduction to systems biology. Exs. 97: 1-19. PMID 17432261  1
2007 Westerhoff HV. Systems biology: new paradigms for cell biology and drug design. Ernst Schering Research Foundation Workshop. 45-67. PMID 17249496  1
2007 Ciapaite J, van Bezu J, van Eikenhorst G, Bakker SJ, Teerlink T, Diamant M, Heine RJ, Krab K, Westerhoff HV, Schalkwijk CG. Palmitate and oleate have distinct effects on the inflammatory phenotype of human endothelial cells. Biochimica Et Biophysica Acta. 1771: 147-54. PMID 17240190 DOI: 10.1016/j.bbalip.2006.12.005  1
2007 Ruoff P, Zakhartsev M, Westerhoff HV. Temperature compensation through systems biology. The Febs Journal. 274: 940-50. PMID 17227386 DOI: 10.1111/j.1742-4658.2007.05641.x  1
2007 Röling WF, van Breukelen BM, Bruggeman FJ, Westerhoff HV. Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes. Environmental Microbiology. 9: 500-11. PMID 17222148 DOI: 10.1111/j.1462-2920.2006.01167.x  1
2007 Hornberg JJ, Bruggeman FJ, Bakker BM, Westerhoff HV. Metabolic control analysis to identify optimal drug targets. Progress in Drug Research. Fortschritte Der Arzneimittelforschung. ProgrèS Des Recherches Pharmaceutiques. 64: 171, 173-89. PMID 17195475 DOI: 10.1007/978-3-7643-7567-6_7  1
2007 Ciapaite J, Bakker SJ, Van Eikenhorst G, Wagner MJ, Teerlink T, Schalkwijk CG, Fodor M, Ouwens DM, Diamant M, Heine RJ, Westerhoff HV, Krab K. Functioning of oxidative phosphorylation in liver mitochondria of high-fat diet fed rats. Biochimica Et Biophysica Acta. 1772: 307-16. PMID 17184976 DOI: 10.1016/j.bbadis.2006.10.018  1
2007 Bruggeman FJ, Westerhoff HV. The nature of systems biology. Trends in Microbiology. 15: 45-50. PMID 17113776 DOI: 10.1016/j.tim.2006.11.003  1
2007 Westerhoff HV. Mathematical and theoretical biology for systems biology, and then ... vice versa. Journal of Mathematical Biology. 54: 147-50. PMID 17047955 DOI: 10.1007/s00285-006-0043-9  1
2007 Brul S, Westerhoff HV. Systems biology and food microbiology Modelling Microorganisms in Food. 250-288. DOI: 10.1533/9781845692940.2.250  0.32
2007 Boogerd FC, Bruggeman FJ, Hofmeyr JHS, Westerhoff HV. Afterthoughts as foundations for systems biology Systems Biology. 321-336. DOI: 10.1016/B978-044452085-2/50016-4  1
2007 Westerhoff HV, Kell DB. The methodologies of systems biology Systems Biology. 23-70. DOI: 10.1016/B978-044452085-2/50004-8  1
2007 Boogerd FC, Bruggeman FJ, Hofmeyr JHS, Westerhoff HV. Towards philosophical foundations of Systems Biology: Introduction Systems Biology. 3-19. DOI: 10.1016/B978-044452085-2/50003-6  1
2007 Ciapaite J, Bakker SJL, Heine RJ, Krab K, Westerhoff HV. A Systems Biology Perspective on Obesity and Type 2 Diabetes Molecular System Bioenergetics: Energy For Life. 571-592. DOI: 10.1002/9783527621095.ch18  1
2006 Bruggeman FJ, Westerhoff HV. Approaches to biosimulation of cellular processes. Journal of Biological Physics. 32: 273-88. PMID 19669467 DOI: 10.1007/s10867-006-9016-x  1
2006 Hornberg JJ, Westerhoff HV. Oncogenes are to lose control on signaling following mutation: should we aim off target? Molecular Biotechnology. 34: 109-16. PMID 17172656 DOI: 10.1385/MB:34:2:109  1
2006 Hornberg JJ, Dekker H, Peters PH, Langerak P, Westerhoff HV, Lankelma J, van Zoelen EJ. Epidermal growth factor receptor-induced activator protein 1 activity controls density-dependent growth inhibition in normal rat kidney fibroblasts. Molecular Biotechnology. 34: 101-8. PMID 17172655 DOI: 10.1385/MB:34:2:101  1
2006 Ciapaite J, Bakker SJ, Diamant M, van Eikenhorst G, Heine RJ, Westerhoff HV, Krab K. Metabolic control of mitochondrial properties by adenine nucleotide translocator determines palmitoyl-CoA effects. Implications for a mechanism linking obesity and type 2 diabetes. The Febs Journal. 273: 5288-302. PMID 17059463 DOI: 10.1111/j.1742-4658.2006.05523.x  1
2006 Brady NR, Hamacher-Brady A, Westerhoff HV, Gottlieb RA. A wave of reactive oxygen species (ROS)-induced ROS release in a sea of excitable mitochondria. Antioxidants & Redox Signaling. 8: 1651-65. PMID 16987019 DOI: 10.1089/ars.2006.8.1651  1
2006 Snoep JL, Westerhoff HV, Rohwer JM, Hofmeyr JH. Is there an optimal ribosome concentration for maximal protein production? Systems Biology. 153: 398-400. PMID 16986326 DOI: 10.1049/ip-syb:20060023  1
2006 Bruggeman FJ, de Haan J, Hardin H, Bouwman J, Rossell S, van Eunen K, Bakker BM, Westerhoff HV. Time-dependent hierarchical regulation analysis: Deciphering cellular adaptation Iee Proceedings: Systems Biology. 153: 318-322. PMID 16986307 DOI: 10.1049/ip-syb:20060027  1
2006 Conradie R, Westerhoff HV, Rohwer JM, Hofmeyr JHS, Snoep JL. Summation theorems for flux and concentration control coefficients of dynamic systems Iee Proceedings: Systems Biology. 153: 314-317. PMID 16986306 DOI: 10.1049/ip-syb:20060024  1
2006 Blüthgen N, Bruggeman FJ, Legewie S, Herzel H, Westerhoff HV, Kholodenko BN. Effects of sequestration on signal transduction cascades. The Febs Journal. 273: 895-906. PMID 16478465 DOI: 10.1111/j.1742-4658.2006.05105.x  1
2006 Rossell S, Van Der Weijden CC, Lindenbergh A, Van Tuijl A, Francke C, Bakker BM, Westerhoff HV. Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae Proceedings of the National Academy of Sciences of the United States of America. 103: 2166-2171. PMID 16467155 DOI: 10.1073/pnas.0509831103  1
2006 Rautenbach M, Gerstner GD, Vlok NM, Kulenkampff J, Westerhoff HV. Analyses of dose-response curves to compare the antimicrobial activity of model cationic α-helical peptides highlights the necessity for a minimum of two activity parameters Analytical Biochemistry. 350: 81-90. PMID 16434018 DOI: 10.1016/j.ab.2005.11.027  1
2006 Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J. Cancer: A Systems Biology disease Biosystems. 83: 81-90. PMID 16426740 DOI: 10.1016/j.biosystems.2005.05.014  1
2006 Snoep JL, Bruggeman F, Olivier BG, Westerhoff HV. Towards building the silicon cell: a modular approach. Bio Systems. 83: 207-16. PMID 16242236 DOI: 10.1016/j.biosystems.2005.07.006  1
2006 Westerhoff HV. Systems biology and the silicon cell: Order out of chaos Computer Aided Chemical Engineering. 21: 81-93. DOI: 10.1016/S1570-7946(06)80029-5  1
2006 Bruggeman FJ, Bakker BM, Hornberg JJ, Westerhoff HV. Introduction to computational models of biochemical reaction networks Computational Systems Biology. 127-148. DOI: 10.1016/B978-012088786-6/50026-5  1
2005 Sakaki Y, Kholodenko BN, Hatakeyama M, Kitano H, Kolch W, De Meyts P, Yarden Y, Westerhoff HV, Wiley HS. The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks. Systems Biology. 152: 53-4. PMID 17044231 DOI: 10.1049/ip-syb:20059002  1
2005 Lin B, Braster M, Van Breukelen BM, Van Verseveld HW, Westerhoff HV, Röling WFM. Geobacteraceae community composition is related to hydrochemistry and biodegradation in an iron-reducing aquifer polluted by a neighboring landfill Applied and Environmental Microbiology. 71: 5983-5991. PMID 16204512 DOI: 10.1128/AEM.71.10.5983-5991.2005  1
2005 Beaumont HJE, Lens SI, Westerhoff HV, Van Spanning RJM. Novel nirK cluster genes in Nitrosomonas europaea are required for NirK-dependent tolerance to nitrite Journal of Bacteriology. 187: 6849-6851. PMID 16166549 DOI: 10.1128/JB.187.19.6849-6851.2005  1
2005 Hornberg JJ, Binder B, Bruggeman FJ, Schoeberl B, Heinrich R, Westerhoff HV. Control of MAPK signalling: from complexity to what really matters. Oncogene. 24: 5533-42. PMID 16007170 DOI: 10.1038/sj.onc.1208817  1
2005 Bruggeman FJ, Boogerd FC, Westerhoff HV. The multifarious short-term regulation of ammonium assimilation of Escherichia coli: Dissection using an in silico replica Febs Journal. 272: 1965-1985. PMID 15819889 DOI: 10.1111/j.1742-4658.2005.04626.x  1
2005 Reijenga KA, Bakker BM, Van Der Weijden CC, Westerhoff HV. Training of yeast cell dynamics Febs Journal. 272: 1616-1624. PMID 15794749 DOI: 10.1111/j.1742-4658.2005.04582.x  1
2005 Ciapaite J, Van Eikenhorst G, Bakker SJL, Diamant M, Heine RJ, Wagner MJ, Westerhoff HV, Krab K. Modular kinetic analysis of the adenine nucleotide translocator-mediated effects of palmitoyl-CoA on the oxidative phosphorylation in isolated rat liver mitochondria Diabetes. 54: 944-951. PMID 15793231 DOI: 10.2337/diabetes.54.4.944  1
2005 Rossell S, Van Der Weijden CC, Kruckeberg AL, Bakker BM, Westerhoff HV. Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae Fems Yeast Research. 5: 611-619. PMID 15780660 DOI: 10.1016/j.femsyr.2004.11.003  1
2005 Hornberg JJ, Bruggeman FJ, Binder B, Geest CR, de Vaate AJ, Lankelma J, Heinrich R, Westerhoff HV. Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control. The Febs Journal. 272: 244-58. PMID 15634347 DOI: 10.1111/j.1432-1033.2004.04404.x  1
2005 Reijenga KA, Van Megen YMGA, Kooi BW, Bakker BM, Snoep JL, Van Verseveld HW, Westerhoff HV. Yeast glycolytic oscillations that are not controlled by a single oscillophore: A new definition of oscillophore strength Journal of Theoretical Biology. 232: 385-398. PMID 15572063 DOI: 10.1016/j.jtbi.2004.08.019  1
2005 Westerhoff HV. Systems biology...in action Current Opinion in Biotechnology. 16: 326-328. DOI: 10.1016/j.copbio.2005.05.002  1
2005 Boogerd FC, Bruggeman FJ, Richardson RC, Stephan A, Westerhoff HV. Emergence and its place in nature: A case study of biochemical networks Synthese. 145: 131-164. DOI: 10.1007/s11229-004-4421-9  1
2004 Westerhoff HV, Palsson BO. The evolution of molecular biology into systems biology. Nature Biotechnology. 22: 1249-52. PMID 15470464 DOI: 10.1038/nbt1020  1
2004 Beaumont HJE, Lens SI, Reijnders WNM, Westerhoff HV, Van Spanning RJM. Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor Molecular Microbiology. 54: 148-158. PMID 15458412 DOI: 10.1111/j.1365-2958.2004.04248.x  1
2004 Goldstein BN, Ermakov G, Centelles JJ, Westerhoff HV, Cascante M. What makes biochemical networks tick? A graphical tool for the identification of oscillophores European Journal of Biochemistry. 271: 3877-3887. PMID 15373833 DOI: 10.1111/j.1432-1033.2004.04324.x  1
2004 Brady NR, Elmore SP, van Beek JJ, Krab K, Courtoy PJ, Hue L, Westerhoff HV. Coordinated behavior of mitochondria in both space and time: a reactive oxygen species-activated wave of mitochondrial depolarization. Biophysical Journal. 87: 2022-34. PMID 15345578 DOI: 10.1529/biophysj.103.035097  1
2004 Beaumont HJE, Van Schooten B, Lens SI, Westerhoff HV, Van Spanning RJM. Nitrosomonas europaea expresses a nitric oxide reductase during nitrification Journal of Bacteriology. 186: 4417-4421. PMID 15205449 DOI: 10.1128/JB.186.13.4417-4421.2004  1
2004 Lloyd-Smith JO, Getz WM, Westerhoff HV. Frequency-dependent incidence in models of sexually transmitted diseases: portrayal of pair-based transmission and effects of illness on contact behaviour. Proceedings. Biological Sciences / the Royal Society. 271: 625-34. PMID 15156921 DOI: 10.1098/rspb.2003.2632  1
2004 Snoep JL, Westerhoff HV. The silicon cell initiative Current Genomics. 5: 687-697. DOI: 10.2174/1389202043348553  1
2003 Westerhoff HV, Bruggeman F, Hofmeyr JH, Snoep JL. Attractive models: how to make the silicon cell relevant and dynamic. Comparative and Functional Genomics. 4: 155-8. PMID 18629108 DOI: 10.1002/cfg.205  1
2003 Peletier MA, Westerhoff HV, Kholodenko BN. Control of spatially heterogeneous and time-varying cellular reaction networks: A new summation law Journal of Theoretical Biology. 225: 477-487. PMID 14615206 DOI: 10.1016/S0022-5193(03)00289-3  1
2003 Francke C, Postma PW, Westerhoff HV, Blom JG, Peletier MA. Why the phosphotransferase system of Escherichia coli escapes diffusion limitation Biophysical Journal. 85: 612-622. PMID 12829515  1
2003 Getz WM, Westerhoff HV, Hofmeyr JHS, Snoep JL. Control analysis of trophic chains Ecological Modelling. 168: 153-171. DOI: 10.1016/S0304-3800(03)00208-4  1
2002 Bruggeman FJ, Westerhoff HV, Hoek JB, Kholodenko BN. Modular response analysis of cellular regulatory networks Journal of Theoretical Biology. 218: 507-520. PMID 12384053 DOI: 10.1016/S0022-5193(02)93096-1  1
2002 Somsen OJG, Siderius M, Bauer FF, Snoep JL, Westerhoff HV. Selectivity in overlapping MAP kinase cascades Journal of Theoretical Biology. 218: 343-354. PMID 12381435 DOI: 10.1006/jtbi.2002.3082  1
2002 Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, Hoek JB. Untangling the wires: A strategy to trace functional interactions in signaling and gene networks Proceedings of the National Academy of Sciences of the United States of America. 99: 12841-12846. PMID 12242336 DOI: 10.1073/pnas.192442699  1
2002 Koebmann BJ, Westerhoff HV, Snoep JL, Solem C, Pedersen MB, Nilsson D, Michelsen O, Jensen PR. The extent to which ATP demand controls the glycolytic flux depends strongly on the organism and conditions for growth Molecular Biology Reports. 29: 41-45. PMID 12241072 DOI: 10.1023/A:1020398117281  1
2002 Rossell S, Van Der Weijden CC, Kruckeberg A, Bakker BM, Westerhoff HV. Loss of fermentative capacity in baker's yeast can partly be explained by reduced glucose uptake capacity Molecular Biology Reports. 29: 255-257. PMID 12241067 DOI: 10.1023/A:1020398401293  1
2002 Ortega F, Ehrenberg M, Acerenza L, Westerhoff HV, Mas F, Cascante M. Sensitivity analysis of metabolic cascades catalyzed by bifunctional enzymes. Molecular Biology Reports. 29: 211-5. PMID 12241060 DOI: 10.1023/A:1020334014497  1
2002 Francke C, Westerhoff HV, Blom JG, Peletier MA. Flux control of the bacterial phosphoenolpyruvate:glucose phosphotransferase system and the effect of diffusion Molecular Biology Reports. 29: 21-26. PMID 12241059 DOI: 10.1023/A:1020389915464  1
2002 Westerhoff HV, Getz WM, Bruggeman F, Hofmeyr JH, Rohwer JM, Snoep JL. ECA: control in ecosystems. Molecular Biology Reports. 29: 113-7. PMID 12241039 DOI: 10.1023/A:1020396906319  1
2002 Hofmeyr JH, Rohwer JM, Snoep JL, Westerhoff HV, Konings WN. How to distinguish between the vacuum cleaner and flippase mechanisms of the lmrA multi-drug transporter in Lactococcus lactis. Molecular Biology Reports. 29: 107-12. PMID 12241038 DOI: 10.1023/A:1020344922249  1
2002 De La Fuente A, Snoep JL, Westerhoff HV, Mendes P. Metabolic control in integrated biochemical systems European Journal of Biochemistry. 269: 4399-4408. PMID 12230551 DOI: 10.1046/j.1432-1033.2002.03088.x  1
2002 Koefoed S, Otten MF, Koebmann BJ, Bruggeman FJ, Bakker BM, Snoep JL, Krab K, Van Spanning RJM, Van Verseveld HW, Jensen PR, Koster JG, Westerhoff HV. A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life Biochimica Et Biophysica Acta - Bioenergetics. 1555: 75-82. PMID 12206895 DOI: 10.1016/S0005-2728(02)00258-X  1
2002 Koebmann BJ, Westerhoff HV, Snoep JL, Nilsson D, Jensen PR. The glycolytic flux in Escherichia coli is controlled by the demand for ATP Journal of Bacteriology. 184: 3909-3916. PMID 12081962 DOI: 10.1128/JB.184.14.3909-3916.2002  1
2002 Westerhoff HV, Getz WM, van Verseveld HW, Hofmeyr JH, Snoep JL. Bioinformatics, cellular flows, and calculation. Ernst Schering Research Foundation Workshop. 221-43. PMID 12061004  1
2002 Beaumont HJ, Hommes NG, Sayavedra-Soto LA, Arp DJ, Arciero DM, Hooper AB, Westerhoff HV, van Spanning RJ. Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite. Journal of Bacteriology. 184: 2557-60. PMID 11948173 DOI: 10.1128/JB.184.9.2557-2560.2002  1
2002 Hoefnagel MHN, Starrenburg MJC, Martens DE, Hugenholtz J, Kleerebezem M, Van Swam II, Bongers R, Westerhoff HV, Snoep JL. Metabolic engineering of lactic acid bacteria, the combined approach: Kinetic modelling, metabolic control and experimental analysis Microbiology. 148: 1003-1013. PMID 11932446  1
2002 Snoep JL, Van Der Weijden CC, Andersen HW, Westerhoff HV, Jensen PR. DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase European Journal of Biochemistry. 269: 1662-1669. PMID 11895436 DOI: 10.1046/j.1432-1327.2002.02803.x  1
2002 Ortega F, Acerenza L, Westerhoff HV, Mas F, Cascante M. Product dependence and bifunctionality compromise the ultrasensitivity of signal transduction cascades. Proceedings of the National Academy of Sciences of the United States of America. 99: 1170-5. PMID 11830657 DOI: 10.1073/pnas.022267399  1
2002 Jonker CM, Snoep JL, Treur J, Westerhoff HV, Wijngaards WC. Putting intentions into cell biochemistry: an artificial intelligence perspective. Journal of Theoretical Biology. 214: 105-34. PMID 11786036 DOI: 10.1006/jtbi.2001.2444  1
2002 Van Rotterdam BJ, Crielaard W, Van Stokkum IHM, Hellingwerf KJ, Westerhoff HV. Simplicity in complexity: The photosynthetic reaction center performs as a simple 0.2 V battery Febs Letters. 510: 105-107. PMID 11755540 DOI: 10.1016/S0014-5793(01)03210-0  1
2002 Reijenga KA, Westerhoff HV, Kholodenko BN, Snoep JL. Control analysis for autonomously oscillating biochemical networks Biophysical Journal. 82: 99-108. PMID 11751299  1
2002 Bruggeman FJ, Westerhoff HV, Boogerd FC. BioComplexity: A pluralist research strategy is necessary for a mechanistic explanation of the "live" state Philosophical Psychology. 15: 411-440. DOI: 10.1080/0951508021000041996  1
2002 Jonker CM, Snoep JL, Treur J, Westerhoff HV, Wijngaards WCA. Embodied intentional dynamics of bacterial behaviour (extended abstract) Proceedings of the International Conference On Autonomous Agents. 465-466.  1
2001 Demin OV, Kholodenko BN, Westerhoff HV. Kinetic modeling of energy metabolism and superoxide generation in hepatocyte mitochondria Molekulyarnaya Biologiya. 35: 1095-1104. PMID 11771135 DOI: 10.1023/A:1013211007465  1
2001 Otten MF, Van der Oost J, Reijnders WNM, Westerhoff HV, Ludwig B, Van Spanning RJM. Cytochromes c550, c552, and c1in the electron transport network of Paracoccus denitrificans: Redundant or subtly different in function? Journal of Bacteriology. 183: 7017-7026. PMID 11717258 DOI: 10.1128/JB.183.24.7017-7026.2001  1
2001 Hoffer SM, Westerhoff HV, Hellingwerf KJ, Postma PW, Tommassen J. Autoamplification of a two-component regulatory system results in "learning" behavior. Journal of Bacteriology. 183: 4914-7. PMID 11466297 DOI: 10.1128/JB.183.16.4914-4917.2001  1
2001 Westerhoff HV. The silicon cell, not dead but live! Metabolic Engineering. 3: 207-210. PMID 11461142 DOI: 10.1006/mben.2001.0192  1
2001 Kuile BH, Westerhoff HV. Transcriptome meets metabolome: Hierarchical and metabolic regulation of the glycolytic pathway Febs Letters. 500: 169-171. PMID 11445079 DOI: 10.1016/S0014-5793(01)02613-8  1
2001 Otten MF, Stork DM, Reijnders WNM, Westerhoff HV, Van Spanning RJM. Regulation of expression of terminal oxidases in Paracoccus denitrificans European Journal of Biochemistry. 268: 2486-2497. PMID 11298768 DOI: 10.1046/j.1432-1327.2001.02131.x  1
2001 Bakker SJL, Gans ROB, Ter Maaten JC, Teerlink T, Westerhoff HV, Heine RJ. The potential role of adenosine in the pathophysiology of the insulin resistance syndrome Atherosclerosis. 155: 283-290. PMID 11254897 DOI: 10.1016/S0021-9150(00)00745-0  1
2001 Hofmeyr JHS, Westerhoff HV. Building the cellular puzzle: Control in multi-level reaction networks Journal of Theoretical Biology. 208: 261-285. PMID 11207090 DOI: 10.1006/jtbi.2000.2216  1
2001 van Rotterdam BJ, Westerhoff HV, Visschers RW, Bloch DA, Hellingwerf KJ, Jones MR, Crielaard W. Pumping capacity of bacterial reaction centers and backpressure regulation of energy transduction. European Journal of Biochemistry / Febs. 268: 958-70. PMID 11179962 DOI: 10.1046/j.1432-1327.2001.01951.x  1
2001 Reijenga KA, Snoep JL, Diderich JA, Van Verseveld HW, Westerhoff HV, Teusink B. Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae Biophysical Journal. 80: 626-634. PMID 11159431  1
2001 Raamsdonk LM, Teusink B, Broadhurst D, Zhang N, Hayes A, Walsh MC, Berden JA, Brindle KM, Kell DB, Rowland JJ, Westerhoff HV, van Dam K, Oliver SG. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnology. 19: 45-50. PMID 11135551 DOI: 10.1038/83496  1
2000 van Rotterdam BJ, Westerhoff HV, Visschers RW, Jones MR, Hellingwerf KJ, Crielaard W. Steady-state cyclic electron transfer through solubilized Rhodobacter sphaeroides reaction centres. Biophysical Chemistry. 88: 137-52. PMID 11152271 DOI: 10.1016/S0301-4622(00)00206-4  1
2000 Somsen OJG, Hoeben MA, Esgalhado E, Snoep JL, Visser D, Van der Heijden RTJM, Heijnen JJ, Westerhoff HV. Glucose and the ATP paradox in yeast Biochemical Journal. 352: 593-599. PMID 11085955 DOI: 10.1042/0264-6021:3520593  1
2000 Saunders NF, Hornberg JJ, Reijnders WN, Westerhoff HV, de Vries S, van Spanning RJ. The NosX and NirX proteins of Paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase. Journal of Bacteriology. 182: 5211-7. PMID 10960107 DOI: 10.1128/JB.182.18.5211-5217.2000  1
2000 Jongsma APM, Riethorst A, Lankelma J, Dekker H, Westerhoff HV. Evaluating limited specificity of drug pumps reduced relative resistance in human MDR phenotypes European Journal of Biochemistry. 267: 5369-5377. PMID 10951194 DOI: 10.1046/j.1432-1327.2000.01560.x  1
2000 Westerhoff HV, Riethorst A, Jongsma APM. Relating multidrug resistance phenotypes to the kinetic properties of their drug-efflux pumps European Journal of Biochemistry. 267: 5355-5368. PMID 10951193 DOI: 10.1046/j.1432-1327.2000.01559.x  1
2000 Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, Snoep JL. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. European Journal of Biochemistry / Febs. 267: 5313-29. PMID 10951190 DOI: 10.1046/j.1432-1327.2000.01527.x  1
2000 Jeneson JA, Westerhoff HV, Kushmerick MJ. A metabolic control analysis of kinetic controls in ATP free energy metabolism in contracting skeletal muscle. American Journal of Physiology. Cell Physiology. 279: C813-32. PMID 10942732  1
2000 Rohwer JM, Meadow ND, Roseman S, Westerhoff HV, Postma PW. Understanding glucose transport by the bacterial phosphoenolpyruvate:glycose phosphotransferase system on the basis of kinetic measurements in vitro. The Journal of Biological Chemistry. 275: 34909-21. PMID 10889194 DOI: 10.1074/jbc.M002461200  1
2000 Ward DE, van Der Weijden CC, van Der Merwe MJ, Westerhoff HV, Claiborne A, Snoep JL. Branched-chain alpha-keto acid catabolism via the gene products of the bkd operon in Enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink. Journal of Bacteriology. 182: 3239-46. PMID 10809705 DOI: 10.1128/JB.182.11.3239-3246.2000  1
2000 van Heeswijk WC, Wen D, Clancy P, Jaggi R, Ollis DL, Westerhoff HV, Vasudevan SG. The Escherichia coli signal transducers PII (GlnB) and GlnK form heterotrimers in vivo: fine tuning the nitrogen signal cascade. Proceedings of the National Academy of Sciences of the United States of America. 97: 3942-7. PMID 10760266 DOI: 10.1073/pnas.97.8.3942  1
2000 Kholodenko BN, Hoek JB, Westerhoff HV. Why cytoplasmic signalling proteins should be recruited to cell membranes Trends in Cell Biology. 10: 173-178. PMID 10754559 DOI: 10.1016/S0962-8924(00)01741-4  1
2000 Teusink B, Westerhoff HV. 'Slave' metabolites and enzymes. A rapid way of delineating metabolic control European Journal of Biochemistry. 267: 1889-1893. PMID 10727927 DOI: 10.1046/j.1432-1327.2000.01220.x  1
2000 Bier M, Bakker BM, Westerhoff HV. How yeast cells synchronize their glycolytic oscillations: A perturbation analytic treatment Biophysical Journal. 78: 1087-1093. PMID 10692299  1
1998 Teusink B, Walsh MC, van Dam K, Westerhoff HV. The danger of metabolic pathways with turbo design. Trends in Biochemical Sciences. 23: 162-9. PMID 9612078 DOI: 10.1016/S0968-0004(98)01205-5  1
1998 Teusink B, Diderich JA, Westerhoff HV, van Dam K, Walsh MC. Intracellular glucose concentration in derepressed yeast cells consuming glucose is high enough to reduce the glucose transport rate by 50%. Journal of Bacteriology. 180: 556-62. PMID 9457857  1
1996 Richard P, Teusink B, Hemker MB, Van Dam K, Westerhoff HV. Sustained oscillations in free-energy state and hexose phosphates in yeast. Yeast (Chichester, England). 12: 731-40. PMID 8813760 DOI: 10.1002/(SICI)1097-0061(19960630)12:8<731::AID-YEA961>3.0.CO;2-Z  1
1996 Teusink B, Larsson C, Diderich J, Richard P, van Dam K, Gustafsson L, Westerhoff HV. Synchronized heat flux oscillations in yeast cell populations. The Journal of Biological Chemistry. 271: 24442-8. PMID 8798702 DOI: 10.1074/jbc.271.40.24442  1
1996 Richard P, Bakker BM, Teusink B, Van Dam K, Westerhoff HV. Acetaldehyde mediates the synchronization of sustained glycolytic oscillations in populations of yeast cells. European Journal of Biochemistry / Febs. 235: 238-41. PMID 8631335  1
1995 Westerhoff HV, Kholodenko BN, Cascante M, Van Dam K. Elusive control. Journal of Bioenergetics and Biomembranes. 27: 491-7. PMID 8718454 DOI: 10.1007/BF02110189  1
1994 Richard P, Diderich JA, Bakker BM, Teusink B, van Dam K, Westerhoff HV. Yeast cells with a specific cellular make-up and an environment that removes acetaldehyde are prone to sustained glycolytic oscillations. Febs Letters. 341: 223-6. PMID 8137943 DOI: 10.1016/0014-5793(94)80461-3  0.32
1993 van Dam K, van der Vlag J, Kholodenko BN, Westerhoff HV. The sum of the control coefficients of all enzymes on the flux through a group-transfer pathway can be as high as two. European Journal of Biochemistry / Febs. 212: 791-9. PMID 8462550  1
1993 Richard P, Teusink B, Westerhoff HV, van Dam K. Around the growth phase transition S. cerevisiae's make-up favours sustained oscillations of intracellular metabolites. Febs Letters. 318: 80-2. PMID 8436231 DOI: 10.1016/0014-5793(93)81332-T  1
1991 Aon MA, Cortassa S, Westerhoff HV, Berden JA, Van Spronsen E, Van Dam K. Dynamic regulation of yeast glycolytic oscillations by mitochondrial functions. Journal of Cell Science. 99: 325-34. PMID 1885673  1
1989 Westerhoff HV, Wiechmann AH, van Dam K, Hellingwerf KJ. On the evaluation of data from flow-dialysis experiments. Journal of Biochemical and Biophysical Methods. 18: 53-64. PMID 2723331 DOI: 10.1016/0165-022X(89)90013-4  1
1987 Westerhoff HV, Plomp PJ, Groen AK, Wanders RJ, Bode JA, van Dam K. On the origin of the limited control of mitochondrial respiration by the adenine nucleotide translocator. Archives of Biochemistry and Biophysics. 257: 154-69. PMID 2888431 DOI: 10.1016/0003-9861(87)90554-6  1
1986 Westerhoff HV, Van der Bend RL, Van Dam K, Berden J, Peterson J. A model system for delocalized chemiosmotic coupling exhibited the features thought diagnostic of localized coupling. The Biochemical Journal. 236: 932-3. PMID 2947574  1
1985 Van der Bend RL, Petersen J, Berden JA, Van Dam K, Westerhoff HV. A critical appraisal of evidence for localized energy coupling. Kinetic studies on liposomes containing bacteriorhodopsin and ATP synthase. The Biochemical Journal. 230: 543-9. PMID 2996506  1
1984 Van Dam K, Woelders H, Colen A, Westerhoff HV. A structural basis for mosaic protonic energy coupling. Biochemical Society Transactions. 12: 401-2. PMID 6329842  1
1983 Westerhoff HV, Hellingwerf KJ, Van Dam K. Thermodynamic efficiency of microbial growth is low but optimal for maximal growth rate. Proceedings of the National Academy of Sciences of the United States of America. 80: 305-9. PMID 6572006  1
1983 Westerhoff HV, Colen AM, van Dam K. Metabolic control by pump slippage and proton leakage in 'delocalized' and more localized chemiosmotic energy-coupling schemes. Biochemical Society Transactions. 11: 81-5. PMID 6298029  1
1981 Westerhoff HV, Simonetti AL, Van Dam K. The hypothesis of localized chemiosmosis is unsatisfactory. The Biochemical Journal. 200: 193-202. PMID 6280679  1
1981 Westerhoff HV, Hellingwerf KJ, Arents JC, Scholte BJ, Van Dam K. Mosaic nonequilibrium thermodynamics describes biological energy transduction. Proceedings of the National Academy of Sciences of the United States of America. 78: 3554-8. PMID 6267598 DOI: 10.1073/pnas.78.6.3554  1
1981 Heinz E, Westerhoff HV, van Dam K. The residual protonmotive force in mitochondria after an oxygen pulse. European Journal of Biochemistry / Febs. 115: 107-13. PMID 6262076  1
1980 Van Dam K, Westerhoff HV, Krab K, van der Meer R, Arents JC. Relationship between chemiosomotic flows and thermodynamic forces in oxidative phosphorylation. Biochimica Et Biophysica Acta. 591: 240-50. PMID 7397123  1
1977 Van Dam K, Wiechmann AH, Westerhoff HV, Hellingwerf KJ. Proton gradients across energy-transducing membranes. Biochemical Society Transactions. 5: 28-9. PMID 19321  1
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