J.J. Heijnen

2018

Comparative performance of different scale-down simulators of substrate gradients in Penicillium chrysogenum cultures: the need of a biological systems response analysis

Wang, G., Zhao, J., Haringa, C., Tang, W., Xia, J., Chu, J., Zhuang, Y., Zhang, S., Deshmukh, A. T., van Gulik, W., Heijnen, J. J. & Noorman, H. J., 1 May 2018, In: Microbial Biotechnology. 11, 3, p. 486-497 12 p.

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29 Citations (Scopus)

116 Downloads (Pure)

Computational fluid dynamics simulation of an industrial P. chrysogenum fermentation with a coupled 9-pool metabolic model: Towards rational scale-down and design optimization

Haringa, C., Tang, W., Wang, G., Deshmukh, A. T., van Winden, W. A., Chu, J., van Gulik, W. M., Heijnen, J. J., Mudde, R. F. & Noorman, H. J., 2018, In: Chemical Engineering Science. 175, p. 12-24 13 p.

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78 Citations (Scopus)

416 Downloads (Pure)

Power input effects on degeneration in prolonged penicillin chemostat cultures: A systems analysis at flux, residual glucose, metabolite, and transcript levels

Wang, G., Wu, B., Zhao, J., Haringa, C., Xia, J., Chu, J., Zhuang, Y., Zhang, S., Heijnen, J. J., van Gulik, W., Deshmukh, A. T. & Noorman, H. J., 1 Jan 2018, In: Biotechnology and Bioengineering. 115, 1, p. 114-125 12 p.

Research output: Contribution to journal › Article › Scientific › peer-review

21 Citations (Scopus)

2017

A 9-pool metabolic structured kinetic model describing days to seconds dynamics of growth and product formation by Penicillium chrysogenum

Tang, W., Deshmukh, A. T., Haringa, C., Wang, G., van Gulik, W., van Winden, W., Reuss, M., Heijnen, J. J., Xia, J., Chu, J. & Noorman, H. J., 1 Aug 2017, In: Biotechnology and Bioengineering. 114, 8, p. 1733-1743 11 p.

Research output: Contribution to journal › Article › Scientific › peer-review

44 Citations (Scopus)

Biochemical engineering's grand adventure

Noorman, H. J. & Heijnen, J. J., 12 Oct 2017, In: Chemical Engineering Science. 170, p. 677-693 17 p.

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53 Citations (Scopus)

128 Downloads (Pure)

Stoichiometry and kinetics of single and mixed substrate uptake in Aspergillus niger

Da Fonte Lameiras, F., Ras, C., Ten Pierick, A., Heijnen, J. J. & van Gulik, W. M., 19 Oct 2017, In: Bioprocess and Biosystems Engineering: bioreactors, upstream and downstream processes, measurement and control. p. 1-14 14 p.

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6 Citations (Scopus)

93 Downloads (Pure)

2016

Accurate Measurement of the in vivo Ammonium Concentration in Saccharomyces cerevisiae

Cueto Rojas, H., Maleki Seifar, R., ten Pierick, A., Heijnen, S. & Wahl, A., 23 Apr 2016, In: Metabolites. 6, 2, p. 1-12 12 p.

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7 Citations (Scopus)

59 Downloads (Pure)

Euler-Lagrange computational fluid dynamics for (bio)reactor scale down: An analysis of organism lifelines

Haringa, C., Tang, W., Deshmukh, A. T., Xia, J., Reuss, M., Heijnen, J. J., Noorman, H. J. & Mudde, R., 2016, In: Engineering in Life Sciences. 16, 7, p. 652-663 12 p.

Research output: Contribution to journal › Article › Scientific › peer-review

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94 Citations (Scopus)

119 Downloads (Pure)

Gas bubble induced oil recovery from emulsions stabilised by yeast components

Heeres, AS., Heijnen, JJ., van der Wielen, LAM. & Cuellar, MC., 2016, In: Chemical Engineering Science. 145, p. 31-44 14 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

18 Citations (Scopus)

Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis

Suarez Mendez, CA., Hanemaaijer, M., ten Pierick, A., Wolters, JC., Heijnen, JJ. & Wahl, SA., 2016, In: Metabolic Engineering Communications. 3, p. 52-63 12 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

16 Citations (Scopus)

In vivo analysis of NH₄ ⁺ transport and central nitrogen metabolism in Saccharomyces cerevisiae during aerobic nitrogen-limited growth

Cueto-Rojas, H. F., Maleki Seifar, R., ten Pierick, A., van Helmond, W., Pieterse, M. M., Heijnen, J. J. & Wahl, S. A., 2016, In: Applied and Environmental Microbiology. 82, 23, p. 6831-6845 15 p.

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9 Citations (Scopus)

55 Downloads (Pure)

Transport and metabolism of fumaric acid in Saccharomyces cerevisiae in aerobic glucose-limited chemostat culture

Shah, M. V., van Mastrigt, O., Heijnen, J. J. & van Gulik, W. M., 2016, In: Yeast . 33, 4, p. 145-161 17 p.

Research output: Contribution to journal › Article › Scientific › peer-review

4 Citations (Scopus)

2015

A fast sensor for in vivo quantification of cytosolic phosphate in Saccharomyces cerevisiae

Zhang, J., Sassen, T., ten Pierick, A., Ras, C., Heijnen, J. J. & Wahl, S. A., 1 May 2015, In: Biotechnology and Bioengineering. 112, 5, p. 1033-1046 14 p.

Research output: Contribution to journal › Article › Scientific › peer-review

12 Citations (Scopus)

Comparative fluxome and metabolome analysis for overproduction of succinate in Escherichia coli

Taymaz-Nikerel, H., de Mey, M., Baart, GJE., Maertens, J., Foulquie-Moreno, MR., Charlier, D., Heijnen, JJ. & van Gulik, WM., 2015, In: Biotechnology and Bioengineering. 9999, xxx, p. 1-13 13 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Determination of the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae using shikimate dehydrogenase as sensor reaction

Zhang, J., ten Pierick, A., van Rossum, HM., Maleki Seifar, R., Ras, C., Daran, JM., Heijnen, JJ. & Wahl, SA., 2015, In: Scientific Reports. 5, p. 1-12 12 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

43 Citations (Scopus)

Determination of the in vivo NAD:NADH ratio in Saccharomyces cerevisiae under anaerobic conditions, using alcohol dehydrogenase as sensor reaction

Bekers, KM., Heijnen, JJ. & van Gulik, WM., 2015, In: Yeast. 32, 8, p. 541-557 17 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

20 Citations (Scopus)

Development of tools for quantitative intracellular metabolomics of Aspergillus niger chemostat cultures

Da Fonte Lameiras, F., Heijnen, JJ. & van Gulik, WM., 2015, In: Metabolomics. 11, 5, p. 1253-1264 12 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

25 Citations (Scopus)

Fermentation broth components influence droplet coalescence and hinder advanced biofuel recovery during fermentation

Heeres, AS., Schroën, K., Heijnen, JJ., van der Wielen, LAM. & Cuellar Soares, MC., 2015, In: Biotechnology Journal. 10, 8, p. 1206-1215 10 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

21 Citations (Scopus)

In vivo kinetic analysis of the penicillin biosynthesis pathway using PAA stimulus response experiments

Deshmukh, AT., Verheijen, PJT., Maleki Seifar, R. & Heijnen, JJ., 2015, In: Metabolic Engineering. 32, p. 155-173 19 p.

Research output: Contribution to journal › Article › Scientific › peer-review

12 Citations (Scopus)

2014

A fast sensor for in vivo quantification of cytosolic phosphae in Saccharomyces cerevisiae

Zhang, J., Sassen, T., ten Pierick, A., Ras, C., Heijnen, JJ. & Wahl, SA., 2014, In: Biotechnology and Bioengineering. 12, p. 1-37 37 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Fast"Feast/Famine" cycles for studying microbial physiology under dynamic conditions: a case study with Saccharomyces cerevisiae

Suarez-Mendez, C., de Sousa, AC., Heijnen, JJ. & Wahl, SA., 2014, In: Metabolites. 4, 2, p. 347-372 26 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

Fast "Feast/Famine" Cycles for studying microbial physiology under dynamic conditions: a case study woth Saccharomyces cerevisiae

Suarez-Mendez, C., de Sousa, AC., Heijnen, JJ. & Wahl, SA., 2014, In: Metabolites. 4, p. 347-372 26 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Fatal attraction in glycolysis: how Saccharmomyces cerevisiae manages sudden transitions to high glucose

van Heerden, JH., Wortel, MT., Bruggeman, FJ., Heijnen, JJ., Bollen, YJM., Planque, R., Hulshof, J., O'Toole, TG., Wahl, SA. & Teusink, B., 2014, In: Microbial Cell Factories. 1, 3, p. 103-106 4 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Flux response of glycolysis and storage metabolism during rapid feast/famine conditions in Penicillium chrysogenum using dynamic 13C labeling

de Jonge, LP., Buijs, NAA., Heijnen, JJ., van Gulik, WM., Abate, A. & Wahl, SA., 2014, In: Biotechnology Journal. 9, 3, p. 372-385 14 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

31 Citations (Scopus)

Lost in transition: Start-up of glycolysis yields subpopulations of nongrowing cells

van Heerden, JH., Wortel, MT., Bruggeman, FJ., Heijnen, JJ., Bollen, YJM., Planque, R., Hulshof, J., O'Toole, TG., Wahl, SA. & Teusink, B., 2014, In: Science. 343, p. 1-9 9 p.

Research output: Contribution to journal › Article › Scientific › peer-review

216 Citations (Scopus)

Quantitative metabolomics using ID-MS

Wahl, SA., Maleki Seifar, R., ten Pierick, A., van Dam, JC., Ras, C., Heijnen, JJ. & van Gulik, WM., 2014, In: Methods in Molecular Biology. 1191, p. 91-105 15 p.

Research output: Contribution to journal › Article › Scientific › peer-review

11 Citations (Scopus)

Reconstruction of the oxygen uptake and carbon dioxide evolution rates of microbial cultures at near-neutral pH during highly dynamic conditions

de Jonge, LP., Heijnen, JJ. & van Gulik, WM., 2014, In: Biochemical Engineering Journal. 83, p. 42-54 13 p.

Research output: Contribution to journal › Article › Scientific › peer-review

10 Citations (Scopus)

2013

Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses

Taymaz-Nikerel, H., de Mey, M., Baart, G., Maertens, J., Heijnen, JJ. & van Gulik, WM., 2013, In: Metabolic Engineering. p. 1-13 13 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

33 Citations (Scopus)

Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis

Jorda, J., Suarez, C., ten Pierick, A., Heijnen, JJ., van Gulik, WM., Ferrer, P., Albiol, J. & Wahl, SA., 2013, In: BMC Systems Biology. 7, 17, p. 1-16 16 p.

Research output: Contribution to journal › Article › Scientific › peer-review

48 Citations (Scopus)

Large-scale production of diesel-like biofuels - process design as an inherent part of microoorganism development

Cuellar, MC., Heijnen, JJ. & van der Wielen, LAM., 2013, In: Biotechnology Journal. 8, 6, p. 682-689 8 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

13 Citations (Scopus)

Parameter identification of in vivo kinetic models: Limitations and challenges

Heijnen, JJ. & Verheijen, PJT., 2013, In: Biotechnology Journal. 8, p. 768-775 8 p.

Research output: Contribution to journal › Article › Scientific › peer-review

27 Citations (Scopus)

Quantitative analysis of intracellular coenzymes in Saccharomyces cerevisiae using ion pair reversed phase ultra high performance liquid chromatography tandem mass spectrometry

Maleki Seifar, R., Ras, C., Deshmukh, AT., Bekers, KM., Suarez Mendez, CA., da Cruz, ALB., van Gulik, WM. & Heijnen, JJ., 2013, In: Journal of Chromatography A. 1311, p. 115-120 6 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

48 Citations (Scopus)

2012

A generalized reference state extends the applicability of approximative kinetics in metabolic engineering

Nikerel, IE., Verheijen, PJT. & Heijnen, JJ., 2012, In: Journal of Chemical Technology and Biotechnology. 87, 12, p. 1694-1701 8 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

Determination of -aminoadipyl - L valine in cell extracts of Penicillium chrysogenum using ion pair-RP-UPLC-MS/MS

Maleki Seifar, R., Deshmukh, AT., Heijnen, JJ. & van Gulik, WM., 2012, In: Journal of Separation Science. p. 225-230 6 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Determination of δ-[ L -α-aminoadipyl]- L -cysteinyl- D -valine in cell extracts of Penicillium chrysogenum using ion pair-RP-UPLC-MS/MS

Seifar, R. M., Deshmukh, A. T., Heijnen, J. J. & Van Gulik, W. M., Jan 2012, In: Journal of Separation Science. 35, 2, p. 225-230 6 p.

Research output: Contribution to journal › Article › Scientific › peer-review

4 Citations (Scopus)

Development of quantitative metabolomics for Pichia pastoris

Carnicer, M., Canelas, A., ten Pierick, A., Zeng, Z., van Dam, JC., Albiol, J., Ferrer, P., Heijnen, JJ. & van Gulik, WM., 2012, In: Metabolomics. 8, p. 284-298 15 p.

Research output: Contribution to journal › Article › Scientific › peer-review

45 Citations (Scopus)

Fast sampling of the cellular metabolome

van Gulik, WM., Canelas, A., Taymaz-Nikerel, H., Douma, RD., de Jonge, LP. & Heijnen, JJ., 2012, In: Methods in Molecular Biology. 881, p. 279-306 28 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

26 Citations (Scopus)

Identification of informative metabolic responses using a minibioreactor: a small step change in the glucose supply rate creates a large metabolic response in Saccharomyces cerevisiae

Aboka, FO., van Winden, WA., Mashego, MR., van Gulik, WM., van den Berg, M., Oudshoorn, A. & Heijnen, JJ., 2012, In: Yeast. 29, 3-4, p. 95-110 16 p.

Research output: Contribution to journal › Article › Scientific › peer-review

7 Citations (Scopus)

Novel insight in transport mechanisms and kinetics of phenylacetic acid and penicillin-G in Penicillium chrysogenum

Douma, RD., Deshmukh, AT., de Jonge, LP., de Jong, BW., Maleki Seifar, R., Heijnen, JJ. & van Gulik, WM., 2012, In: Biotechnology Progress. 28, 2, p. 337-348 12 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

18 Citations (Scopus)

Optimization of cold methanol quenching for quantitative metabolomics of Peniccillium chrysogenum

de Jonge, LP., Douma, RD., Heijnen, JJ. & van Gulik, WM., 2012, In: Metabolomics. 8, p. 727-735 9 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

57 Citations (Scopus)

pH-Dependent uptake of fumaric acid in Saccharomyces cerevisiae under anaerobic conditions

Jamalzadeh, E., Verheijen, PJT., Heijnen, JJ. & van Gulik, WM., 2012, In: Applied and Environmental Microbiology. 78, 3, p. 705-716 12 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

20 Citations (Scopus)

Process intensification in the future production of base chemicals from biomass

Sanders, JPM., Clark, JH., Harmsen, GJ., Heeres, HJ., Heijnen, JJ., Kersten, SRA., van Swaaij, WPM. & Moulijn, JA., 2012, In: Chemical Engineering and Processing: process intensification. 51, SI, p. 117-136 20 p.

Research output: Contribution to journal › Article › Scientific › peer-review

115 Citations (Scopus)

Quantitative metabolomics analysis of amino acid metabolism in recombinant Pichia pastoris under different oxygen availability conditions

Carnicer, M., ten Pierick, A., van Dam, JC., Heijnen, JJ., Albiol, J., van Gulik, WM. & Ferrer, P., 2012, In: Microbial Cell Factories. 11, 83, p. 1-10 10 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

39 Citations (Scopus)

Similar temperature-dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics?

da Cruz, ALB., Hebly, M., Duong, GH., Wahl, SA., Pronk, JT., Heijnen, JJ., Daran-Lapujade, PAS. & van Gulik, WM., 2012, In: BMC Systems Biology. 6, 151, p. 1-16 16 p.

Research output: Contribution to journal › Article › Scientific › peer-review

26 Citations (Scopus)

Substrate cycles in Penicillium chrysogenum quantified by isotopic non-stationary flux analysis

Zhao, Z., ten Pierick, A., de Jonge, LP., Heijnen, JJ. & Wahl, SA., 2012, In: Microbial Cell Factories. 11, 140, p. 1-14 14 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

18 Citations (Scopus)

Use of sequential batch fermentations to characterize the impact of mild hypothermic temperatures on the anaerobic stoichiometry and kinetics of Saccharomyces cerevisiae

da Cruz, ALB., Verbon, AJ., Geurink, LJ., Verheijen, PJT., Heijnen, JJ. & van Gulik, WM., 2012, In: Biotechnology and Bioengineering. 109, 7, p. 1735-1744 10 p.

Research output: Contribution to journal › Article › Scientific › peer-review

10 Citations (Scopus)

2011

An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data

Canelas, A., Ras, C., ten Pierick, A., van Gulik, WM. & Heijnen, JJ., 2011, In: Metabolic Engineering. 13, p. 294-306 13 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

76 Citations (Scopus)

Construction of kinetic models for metabolic reaction networks: Lessons learned in analysing short-term stimulus response data

Nikerel, IE., Canelas, A., Jol, SJ., Verheijen, PJT. & Heijnen, JJ., 2011, In: Mathematical and Computer Modelling of Dynamical Systems: methods, tools and applications in engineering and related sciences. 17, 3, p. 243-260 18 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

10 Citations (Scopus)

Cytosolic NADPH balancing in Penicillium chrysogenum cultivated on mixtures of glucose and ethanol

Zhao, Z., Kuijvenhoven, K., van Gulik, WM., Heijnen, JJ., van Winden, WA. & Verheijen, PJT., 2011, In: Applied Microbiology and Biotechnology. 89, p. 63-72 10 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Open Access

8 Citations (Scopus)

Degeneration of penicillin production in ethanol-limited chemostat cultivations of Penicillium chrysogenum: A system biology approach

Douma, RD., Batista, JIM., Touw, KM., Kiel, JA., Krikken, AM., Zhao, Z., Veiga, T., Klaassen, P., Bovenberg, RA., Daran, JM., Heijnen, JJ. & van Gulik, WM., 2011, In: BMC Systems Biology. 132, 5

Research output: Contribution to journal › Article › Scientific › peer-review

J.J. Heijnen

Research output

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